Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP07118
DateThu Jan 5 11:00:14 GMT 2012
Unique Job ID787975fc6fffba03

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c1gaxB_
Top template information
PDB header:ligase/rna
Chain: B: PDB Molecule:valyl-trna synthetase;
PDBTitle: crystal structure of thermus thermophilus valyl-trna2 synthetase complexed with trna(val) and valyl-adenylate3 analogue
Confidence and coverage
Confidence:100.0% Coverage: 90%
857 residues ( 90% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MEKTYNPQDIEQPLYEHWEKQGYFKPNGDESQESFCIMIPPPNVTGSLHMGHAFQQTIMD
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Disorder  ??????














??
?????






























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   .........70.........80.........90.........100.........110.........120
Sequence  TMIRYQRMQGKNTLWQVGTDHAGIATQMVVERKIAAEEGKTRHDYGREAFIDKIWEWKAE
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????????

??














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   .........130.........140.........150.........160.........170.........180
Sequence  SGGTITRQMRRLGNSVDWERERFTMDEGLSNAVKEVFVRLYKEDLIYRGKRLVNWDPKLR
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   .........190.........200.........210.........220.........230.........240
Sequence  TAISDLEVENRESKGSMWHIRYPLADGAKTADGKDYLVVATTRPETLLGDTGVAVNPEDP
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?

??














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   .........250.........260.........270.........280.........290.........300
Sequence  RYKDLIGKYVILPLVNRRIPIVGDEHADMEKGTGCVKITPAHDFNDYEVGKRHALPMINI
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   .........310.........320.........330.........340.........350.........360
Sequence  LTFDGDIRESAQVFDTKGNESDVYSSEIPAEFQKLERFAARKAVVAAVDALGLLEEIKPH
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   .........370.........380.........390.........400.........410.........420
Sequence  DLTVPYGDRGGVVIEPMLTDQWYVRADVLAKPAVEAVENGDIQFVPKQYENMYFSWMRDI
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   .........430.........440.........450.........460.........470.........480
Sequence  QDWCISRQLWWGHRIPAWYDEAGNVYVGRNEDEVRKENNLGADVVLRQDEDVLDTWFSSA
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?

















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   .........490.........500.........510.........520.........530.........540
Sequence  LWTFSTLGWPENTDALRQFHPTSVMVSGFDIIFFWIARMIMMTMHFIKDENGKPQVPFHT
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?









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   .........550.........560.........570.........580.........590.........600
Sequence  VYMTGLIRDDEGQKMSKSKGNVIDPLDMVDGISLPELLEKRTGNMMQPQLADKIRKRTEK
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??????????????





???????
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   .........610.........620.........630.........640.........650.........660
Sequence  QFPNGIEPHGTDALRFTLAALASTGRDINWDMKRLEGYRNFCNKLWNASRFVLMNTEGQD
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   .........670.........680.........690.........700.........710.........720
Sequence  CGFNGGEMTLSLADRWILAEFNQTIKAYREALDSFRFDIAAGILYEFTWNQFCDWYLELT
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   .........730.........740.........750.........760.........770.........780
Sequence  KPVMNGGTEAELRGTRHTLVTVLEGLLRLAHPIIPFITETIWQRVKVLCGITADTIMLQP
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   .........790.........800.........810.........820.........830.........840
Sequence  FPQYDASQVDEAALADTEWLKQAIVAVRNIRAEMNIAPGKPLELLLRGCSADAERRVNEN
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   .........850.........860.........870.........880.........890.........900
Sequence  RGFLQTLARLESITVLPADDKGPVSVTKIIDGAELLIPMAGLINKEDELARLAKEVAKIE
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??

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   .........910.........920.........930.........940.........950.
Sequence  GEISRIENKLANEGFVARAPEAVIAKEREKLEGYAEAKAKLIEQQAVIAAL
Secondary structure 





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?????

































???
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Confidence Key
High(9)                    Low (0)
?Disordered
Alpha helix
Beta strand

Domain analysis 

Hover over an aligned region to see model and summary info

Please note, only up to the top 20 hits are modelled to reduce computer load

RankAligned region

PDB 1gax chain B

3D model

Region: 1 - 949
Aligned: 857
Modelled: 887
Confidence: 100.0%
Identity: 43%
PDB header:ligase/rna
Chain: B: PDB Molecule:valyl-trna synthetase;
PDBTitle: crystal structure of thermus thermophilus valyl-trna2 synthetase complexed with trna(val) and valyl-adenylate3 analogue

Phyre2

PDB 1qu2 chain A

3D model

Region: 2 - 866
Aligned: 788
Modelled: 805
Confidence: 100.0%
Identity: 22%
PDB header:ligase/rna
Chain: A: PDB Molecule:isoleucyl-trna synthetase;
PDBTitle: insights into editing from an ile-trna synthetase structure2 with trna(ile) and mupirocin

Phyre2

PDB 1ile chain A

3D model

Region: 3 - 816
Aligned: 749
Modelled: 751
Confidence: 100.0%
Identity: 26%
PDB header:aminoacyl-trna synthetase
Chain: A: PDB Molecule:isoleucyl-trna synthetase;
PDBTitle: isoleucyl-trna synthetase

Phyre2

PDB 1wz2 chain B

3D model

Region: 6 - 920
Aligned: 836
Modelled: 868
Confidence: 100.0%
Identity: 23%
PDB header:ligase/rna
Chain: B: PDB Molecule:leucyl-trna synthetase;
PDBTitle: the crystal structure of leucyl-trna synthetase and trna(leucine)2 complex

Phyre2

PDB 1wkb chain A

3D model

Region: 5 - 766
Aligned: 696
Modelled: 719
Confidence: 100.0%
Identity: 24%
PDB header:ligase
Chain: A: PDB Molecule:leucyl-trna synthetase;
PDBTitle: crystal structure of leucyl-trna synthetase from the2 archaeon pyrococcus horikoshii reveals a novel editing3 domain orientation

Phyre2

PDB 1obh chain A

3D model

Region: 3 - 791
Aligned: 644
Modelled: 668
Confidence: 100.0%
Identity: 25%
PDB header:synthetase
Chain: A: PDB Molecule:leucyl-trna synthetase;
PDBTitle: leucyl-trna synthetase from thermus thermophilus complexed2 with a pre-transfer editing substrate analogue in both3 synthetic active site and editing site

Phyre2

PDB 1rqg chain A

3D model

Region: 33 - 783
Aligned: 515
Modelled: 531
Confidence: 100.0%
Identity: 22%
PDB header:ligase
Chain: A: PDB Molecule:methionyl-trna synthetase;
PDBTitle: methionyl-trna synthetase from pyrococcus abyssi

Phyre2

PDB 1ffy chain A domain 3

3D model

Region: 1 - 640
Aligned: 410
Modelled: 424
Confidence: 100.0%
Identity: 28%
Fold: Adenine nucleotide alpha hydrolase-like
Superfamily: Nucleotidylyl transferase
Family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain

Phyre2

PDB 1h3n chain A domain 3

3D model

Region: 1 - 640
Aligned: 409
Modelled: 425
Confidence: 100.0%
Identity: 30%
Fold: Adenine nucleotide alpha hydrolase-like
Superfamily: Nucleotidylyl transferase
Family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain

Phyre2

PDB 1pfu chain A

3D model

Region: 32 - 802
Aligned: 524
Modelled: 555
Confidence: 100.0%
Identity: 20%
PDB header:ligase
Chain: A: PDB Molecule:methionyl-trna synthetase;
PDBTitle: methionyl-trna synthetase from escherichia coli complexed2 with methionine phosphinate

Phyre2

PDB 1ile chain A domain 3

3D model

Region: 4 - 640
Aligned: 420
Modelled: 428
Confidence: 100.0%
Identity: 29%
Fold: Adenine nucleotide alpha hydrolase-like
Superfamily: Nucleotidylyl transferase
Family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain

Phyre2

PDB 3kfl chain A

3D model

Region: 31 - 782
Aligned: 487
Modelled: 520
Confidence: 100.0%
Identity: 21%
PDB header:ligase
Chain: A: PDB Molecule:methionyl-trna synthetase;
PDBTitle: leishmania major methionyl-trna synthetase in complex with2 methionyladenylate and pyrophosphate

Phyre2

PDB 1ivs chain A domain 4

3D model

Region: 1 - 641
Aligned: 420
Modelled: 428
Confidence: 100.0%
Identity: 55%
Fold: Adenine nucleotide alpha hydrolase-like
Superfamily: Nucleotidylyl transferase
Family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain

Phyre2

PDB 1woy chain A

3D model

Region: 32 - 791
Aligned: 483
Modelled: 502
Confidence: 100.0%
Identity: 26%
PDB header:ligase
Chain: A: PDB Molecule:methionyl-trna synthetase;
PDBTitle: crystal structure of methionyl trna synthetase y225f mutant2 from thermus thermophilus

Phyre2

PDB 2x1l chain C

3D model

Region: 32 - 782
Aligned: 450
Modelled: 479
Confidence: 100.0%
Identity: 25%
PDB header:ligase
Chain: C: PDB Molecule:methionyl-trna synthetase;
PDBTitle: crystal structure of mycobacterium smegmatis methionyl-trna2 synthetase in complex with methionine and adenosine

Phyre2

PDB 2ct8 chain A

3D model

Region: 33 - 791
Aligned: 443
Modelled: 482
Confidence: 100.0%
Identity: 26%
PDB header:ligase/rna
Chain: A: PDB Molecule:methionyl-trna synthetase;
PDBTitle: crystal structure of aquifex aeolicus methionyl-trna2 synthetase complexed with trna(met) and methionyl-adenylate3 anologue

Phyre2

PDB 1rqg chain A domain 2

3D model

Region: 33 - 640
Aligned: 342
Modelled: 353
Confidence: 100.0%
Identity: 25%
Fold: Adenine nucleotide alpha hydrolase-like
Superfamily: Nucleotidylyl transferase
Family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain

Phyre2

PDB 2d5b chain A domain 2

3D model

Region: 32 - 640
Aligned: 341
Modelled: 351
Confidence: 100.0%
Identity: 30%
Fold: Adenine nucleotide alpha hydrolase-like
Superfamily: Nucleotidylyl transferase
Family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain

Phyre2

PDB 1pfv chain A domain 2

3D model

Region: 32 - 644
Aligned: 337
Modelled: 366
Confidence: 100.0%
Identity: 24%
Fold: Adenine nucleotide alpha hydrolase-like
Superfamily: Nucleotidylyl transferase
Family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain

Phyre2

PDB 1ivs chain A domain 2

3D model

Region: 643 - 883
Aligned: 217
Modelled: 241
Confidence: 100.0%
Identity: 35%
Fold: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
Superfamily: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
Family: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases

Phyre2
1

c1gaxB_
2

c1qu2A_
3

c1ileA_
4

c1wz2B_
5

c1wkbA_
6

c1obhA_
7

c1rqgA_
8

d1ffya3
9

d1h3na3
10

c1pfuA_
11

d1ilea3
12

c3kflA_
13

d1ivsa4
14

c1woyA_
15

c2x1lC_
16

c2ct8A_
17

d1rqga2
18

d2d5ba2
19

d1pfva2
20

d1ivsa2
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c1gaxB_



100.0 43 PDB header:ligase/rna
Chain: B: PDB Molecule:valyl-trna synthetase;
PDBTitle: crystal structure of thermus thermophilus valyl-trna2 synthetase complexed with trna(val) and valyl-adenylate3 analogue
2c1qu2A_



100.0 22 PDB header:ligase/rna
Chain: A: PDB Molecule:isoleucyl-trna synthetase;
PDBTitle: insights into editing from an ile-trna synthetase structure2 with trna(ile) and mupirocin
3c1ileA_



100.0 26 PDB header:aminoacyl-trna synthetase
Chain: A: PDB Molecule:isoleucyl-trna synthetase;
PDBTitle: isoleucyl-trna synthetase
4c1wz2B_



100.0 23 PDB header:ligase/rna
Chain: B: PDB Molecule:leucyl-trna synthetase;
PDBTitle: the crystal structure of leucyl-trna synthetase and trna(leucine)2 complex
5c1wkbA_



100.0 24 PDB header:ligase
Chain: A: PDB Molecule:leucyl-trna synthetase;
PDBTitle: crystal structure of leucyl-trna synthetase from the2 archaeon pyrococcus horikoshii reveals a novel editing3 domain orientation
6c1obhA_



100.0 25 PDB header:synthetase
Chain: A: PDB Molecule:leucyl-trna synthetase;
PDBTitle: leucyl-trna synthetase from thermus thermophilus complexed2 with a pre-transfer editing substrate analogue in both3 synthetic active site and editing site
7c1rqgA_



100.0 22 PDB header:ligase
Chain: A: PDB Molecule:methionyl-trna synthetase;
PDBTitle: methionyl-trna synthetase from pyrococcus abyssi
8d1ffya3



100.0 28 Fold:Adenine nucleotide alpha hydrolase-like
Superfamily:Nucleotidylyl transferase
Family:Class I aminoacyl-tRNA synthetases (RS), catalytic domain
9d1h3na3



100.0 30 Fold:Adenine nucleotide alpha hydrolase-like
Superfamily:Nucleotidylyl transferase
Family:Class I aminoacyl-tRNA synthetases (RS), catalytic domain
10c1pfuA_



100.0 20 PDB header:ligase
Chain: A: PDB Molecule:methionyl-trna synthetase;
PDBTitle: methionyl-trna synthetase from escherichia coli complexed2 with methionine phosphinate
11d1ilea3



100.0 29 Fold:Adenine nucleotide alpha hydrolase-like
Superfamily:Nucleotidylyl transferase
Family:Class I aminoacyl-tRNA synthetases (RS), catalytic domain
12c3kflA_



100.0 21 PDB header:ligase
Chain: A: PDB Molecule:methionyl-trna synthetase;
PDBTitle: leishmania major methionyl-trna synthetase in complex with2 methionyladenylate and pyrophosphate
13d1ivsa4



100.0 55 Fold:Adenine nucleotide alpha hydrolase-like
Superfamily:Nucleotidylyl transferase
Family:Class I aminoacyl-tRNA synthetases (RS), catalytic domain
14c1woyA_



100.0 26 PDB header:ligase
Chain: A: PDB Molecule:methionyl-trna synthetase;
PDBTitle: crystal structure of methionyl trna synthetase y225f mutant2 from thermus thermophilus
15c2x1lC_



100.0 25 PDB header:ligase
Chain: C: PDB Molecule:methionyl-trna synthetase;
PDBTitle: crystal structure of mycobacterium smegmatis methionyl-trna2 synthetase in complex with methionine and adenosine
16c2ct8A_



100.0 26 PDB header:ligase/rna
Chain: A: PDB Molecule:methionyl-trna synthetase;
PDBTitle: crystal structure of aquifex aeolicus methionyl-trna2 synthetase complexed with trna(met) and methionyl-adenylate3 anologue
17d1rqga2



100.0 25 Fold:Adenine nucleotide alpha hydrolase-like
Superfamily:Nucleotidylyl transferase
Family:Class I aminoacyl-tRNA synthetases (RS), catalytic domain
18d2d5ba2



100.0 30 Fold:Adenine nucleotide alpha hydrolase-like
Superfamily:Nucleotidylyl transferase
Family:Class I aminoacyl-tRNA synthetases (RS), catalytic domain
19d1pfva2



100.0 24 Fold:Adenine nucleotide alpha hydrolase-like
Superfamily:Nucleotidylyl transferase
Family:Class I aminoacyl-tRNA synthetases (RS), catalytic domain
20d1ivsa2



100.0 35 Fold:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
Superfamily:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
Family:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
21c1u0bB_



not modelled 100.0 19 PDB header:ligase/rna
Chain: B: PDB Molecule:cysteinyl trna;
PDBTitle: crystal structure of cysteinyl-trna synthetase binary2 complex with trnacys
22d1qu3a1



not modelled 100.0 15 Fold:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
Superfamily:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
Family:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
23d1wkaa1



not modelled 100.0 38 Fold:ValRS/IleRS/LeuRS editing domain
Superfamily:ValRS/IleRS/LeuRS editing domain
Family:ValRS/IleRS/LeuRS editing domain
24c3tqoA_



not modelled 100.0 22 PDB header:ligase
Chain: A: PDB Molecule:cysteinyl-trna synthetase;
PDBTitle: structure of the cysteinyl-trna synthetase (cyss) from coxiella2 burnetii.
25c3sp1B_



not modelled 100.0 19 PDB header:ligase
Chain: B: PDB Molecule:cysteinyl-trna synthetase;
PDBTitle: crystal structure of cysteinyl-trna synthetase (cyss) from borrelia2 burgdorferi
26c3c8zB_



not modelled 100.0 21 PDB header:ligase
Chain: B: PDB Molecule:cysteinyl-trna synthetase;
PDBTitle: the 1.6 a crystal structure of mshc: the rate limiting2 enzyme in the mycothiol biosynthetic pathway
27d1ilea1



not modelled 100.0 24 Fold:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
Superfamily:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
Family:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
28c3fnrA_



not modelled 100.0 17 PDB header:transferase
Chain: A: PDB Molecule:arginyl-trna synthetase;
PDBTitle: crystal structure of putative arginyl t-rna synthetase from2 campylobacter jejuni;
29d1ffya1



not modelled 100.0 18 Fold:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
Superfamily:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
Family:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
30d1udza_



not modelled 100.0 29 Fold:ValRS/IleRS/LeuRS editing domain
Superfamily:ValRS/IleRS/LeuRS editing domain
Family:ValRS/IleRS/LeuRS editing domain
31c1iq0A_



not modelled 100.0 13 PDB header:ligase
Chain: A: PDB Molecule:arginyl-trna synthetase;
PDBTitle: thermus thermophilus arginyl-trna synthetase
32d1h3na2



not modelled 100.0 29 Fold:ValRS/IleRS/LeuRS editing domain
Superfamily:ValRS/IleRS/LeuRS editing domain
Family:ValRS/IleRS/LeuRS editing domain
33c3o0aB_



not modelled 100.0 26 PDB header:ligase
Chain: B: PDB Molecule:leucyl-trna synthetase subunit alpha;
PDBTitle: crystal structure of the wild type cp1 hydrolitic domain from aquifex2 aeolicus leucyl-trna
34c2ajhA_



not modelled 100.0 28 PDB header:ligase
Chain: A: PDB Molecule:leucyl-trna synthetase;
PDBTitle: crystal structure of the editing domain of e. coli leucyl-2 trna synthetase complexes with methionine
35d1ffya2



not modelled 100.0 24 Fold:ValRS/IleRS/LeuRS editing domain
Superfamily:ValRS/IleRS/LeuRS editing domain
Family:ValRS/IleRS/LeuRS editing domain
36c2wfdB_



not modelled 100.0 19 PDB header:ligase
Chain: B: PDB Molecule:leucyl-trna synthetase, cytoplasmic;
PDBTitle: structure of the human cytosolic leucyl-trna synthetase2 editing domain
37d1li5a2



not modelled 100.0 21 Fold:Adenine nucleotide alpha hydrolase-like
Superfamily:Nucleotidylyl transferase
Family:Class I aminoacyl-tRNA synthetases (RS), catalytic domain
38c2wfgA_



not modelled 100.0 25 PDB header:ligase
Chain: A: PDB Molecule:cytosolic leucyl-trna synthetase;
PDBTitle: structure of the candida albicans cytosolic leucyl-trna2 synthetase editing domain bound to a benzoxaborole-amp3 adduct
39c3pz6F_



not modelled 100.0 24 PDB header:ligase
Chain: F: PDB Molecule:leucyl-trna synthetase;
PDBTitle: the crystal structure of glleurs-cp1
40c2zufA_



not modelled 99.9 19 PDB header:ligase/rna
Chain: A: PDB Molecule:arginyl-trna synthetase;
PDBTitle: crystal structure of pyrococcus horikoshii arginyl-trna2 synthetase complexed with trna(arg)
41d1iq0a2



not modelled 99.9 15 Fold:Adenine nucleotide alpha hydrolase-like
Superfamily:Nucleotidylyl transferase
Family:Class I aminoacyl-tRNA synthetases (RS), catalytic domain
42d1h3na1



not modelled 99.9 20 Fold:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
Superfamily:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
Family:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
43d1f7ua2



not modelled 99.9 15 Fold:Adenine nucleotide alpha hydrolase-like
Superfamily:Nucleotidylyl transferase
Family:Class I aminoacyl-tRNA synthetases (RS), catalytic domain
44d1rqga1



not modelled 99.8 18 Fold:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
Superfamily:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
Family:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
45d1irxa2



not modelled 99.8 19 Fold:Adenine nucleotide alpha hydrolase-like
Superfamily:Nucleotidylyl transferase
Family:Class I aminoacyl-tRNA synthetases (RS), catalytic domain
46c1f7uA_



not modelled 99.8 18 PDB header:ligase/rna
Chain: A: PDB Molecule:arginyl-trna synthetase;
PDBTitle: crystal structure of the arginyl-trna synthetase complexed with the2 trna(arg) and l-arg
47d1pfva1



not modelled 99.7 20 Fold:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
Superfamily:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
Family:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
48d2d5ba1



not modelled 99.7 15 Fold:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
Superfamily:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
Family:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
49c1g59A_



not modelled 99.5 23 PDB header:ligase/rna
Chain: A: PDB Molecule:glutamyl-trna synthetase;
PDBTitle: glutamyl-trna synthetase complexed with trna(glu).
50c2ja2A_



not modelled 99.5 22 PDB header:ligase
Chain: A: PDB Molecule:glutamyl-trna synthetase;
PDBTitle: mycobacterium tuberculosis glutamyl-trna synthetase
51c3afhA_



not modelled 99.4 29 PDB header:ligase
Chain: A: PDB Molecule:glutamyl-trna synthetase 2;
PDBTitle: crystal structure of thermotoga maritima nondiscriminating glutamyl-2 trna synthetase in complex with a glutamyl-amp analog
52c2cfoA_



not modelled 99.3 18 PDB header:ligase
Chain: A: PDB Molecule:glutamyl-trna synthetase;
PDBTitle: non-discriminating glutamyl-trna synthetase from2 thermosynechococcus elongatus in complex with glu
53c2o5rA_



not modelled 99.3 24 PDB header:ligase
Chain: A: PDB Molecule:glutamyl-trna synthetase 1;
PDBTitle: crystal structure of glutamyl-trna synthetase 1 (ec 6.1.1.17)2 (glutamate-trna ligase 1) (glurs 1) (tm1351) from thermotoga maritima3 at 2.5 a resolution
54d1gtra2



not modelled 99.2 22 Fold:Adenine nucleotide alpha hydrolase-like
Superfamily:Nucleotidylyl transferase
Family:Class I aminoacyl-tRNA synthetases (RS), catalytic domain
55d1ivsa1



not modelled 99.1 26 Fold:Long alpha-hairpin
Superfamily:tRNA-binding arm
Family:Valyl-tRNA synthetase (ValRS) C-terminal domain
56c1irxA_



not modelled 98.3 10 PDB header:ligase
Chain: A: PDB Molecule:lysyl-trna synthetase;
PDBTitle: crystal structure of class i lysyl-trna synthetase
57c3aiiA_



not modelled 98.3 29 PDB header:ligase
Chain: A: PDB Molecule:glutamyl-trna synthetase;
PDBTitle: archaeal non-discriminating glutamyl-trna synthetase from2 methanothermobacter thermautotrophicus
58c1exdA_



not modelled 98.2 24 PDB header:ligase/rna
Chain: A: PDB Molecule:glutaminyl-trna synthetase;
PDBTitle: crystal structure of a tight-binding glutamine trna bound2 to glutamine aminoacyl trna synthetase
59c2hz7A_



not modelled 98.2 26 PDB header:ligase
Chain: A: PDB Molecule:glutaminyl-trna synthetase;
PDBTitle: crystal structure of the glutaminyl-trna synthetase from2 deinococcus radiodurans
60d1nzja_



not modelled 98.1 22 Fold:Adenine nucleotide alpha hydrolase-like
Superfamily:Nucleotidylyl transferase
Family:Class I aminoacyl-tRNA synthetases (RS), catalytic domain
61d1j09a2



not modelled 98.1 27 Fold:Adenine nucleotide alpha hydrolase-like
Superfamily:Nucleotidylyl transferase
Family:Class I aminoacyl-tRNA synthetases (RS), catalytic domain
62c3al0C_



not modelled 97.8 30 PDB header:ligase/rna
Chain: C: PDB Molecule:glutamyl-trna(gln) amidotransferase subunit c, glutamyl-
PDBTitle: crystal structure of the glutamine transamidosome from thermotoga2 maritima in the glutamylation state.
63c1h3eA_



not modelled 96.9 23 PDB header:ligase
Chain: A: PDB Molecule:tyrosyl-trna synthetase;
PDBTitle: tyrosyl-trna synthetase from thermus thermophilus complexed2 with wild-type trnatyr(gua) and with atp and tyrosinol
64c2cybA_



not modelled 96.8 25 PDB header:ligase
Chain: A: PDB Molecule:tyrosyl-trna synthetase;
PDBTitle: crystal structure of tyrosyl-trna synthetase complexed with2 l-tyrosine from archaeoglobus fulgidus
65c1jiiA_



not modelled 96.7 18 PDB header:ligase
Chain: A: PDB Molecule:tyrosyl-trna synthetase;
PDBTitle: crystal structure of s. aureus tyrrs in complex with sb-219383
66c2janD_



not modelled 96.5 20 PDB header:ligase
Chain: D: PDB Molecule:tyrosyl-trna synthetase;
PDBTitle: tyrosyl-trna synthetase from mycobacterium tuberculosis in2 unliganded state
67d1h3fa1



not modelled 96.5 22 Fold:Adenine nucleotide alpha hydrolase-like
Superfamily:Nucleotidylyl transferase
Family:Class I aminoacyl-tRNA synthetases (RS), catalytic domain
68d1jila_



not modelled 96.3 18 Fold:Adenine nucleotide alpha hydrolase-like
Superfamily:Nucleotidylyl transferase
Family:Class I aminoacyl-tRNA synthetases (RS), catalytic domain
69c2j5bA_



not modelled 96.1 15 PDB header:ligase
Chain: A: PDB Molecule:tyrosyl-trna synthetase;
PDBTitle: structure of the tyrosyl trna synthetase from acanthamoeba2 polyphaga mimivirus complexed with tyrosynol
70c1x8xA_



not modelled 95.9 14 PDB header:ligase
Chain: A: PDB Molecule:tyrosyl-trna synthetase;
PDBTitle: tyrosyl t-rna synthetase from e.coli complexed with tyrosine
71c2rkjM_



not modelled 95.9 20 PDB header:ligase/rna
Chain: M: PDB Molecule:tyrosyl-trna synthetase;
PDBTitle: cocrystal structure of a tyrosyl-trna synthetase splicing2 factor with a group i intron rna
72c3focB_



not modelled 95.8 18 PDB header:ligase
Chain: B: PDB Molecule:tryptophanyl-trna synthetase;
PDBTitle: tryptophanyl-trna synthetase from giardia lamblia
73c3prhB_



not modelled 95.8 22 PDB header:ligase
Chain: B: PDB Molecule:tryptophanyl-trna synthetase;
PDBTitle: tryptophanyl-trna synthetase val144pro mutant from b. subtilis
74c3hv0A_



not modelled 95.8 18 PDB header:ligase
Chain: A: PDB Molecule:tryptophanyl-trna synthetase;
PDBTitle: tryptophanyl-trna synthetase from cryptosporidium parvum
75c3hzrD_



not modelled 95.7 12 PDB header:ligase
Chain: D: PDB Molecule:tryptophanyl-trna synthetase;
PDBTitle: tryptophanyl-trna synthetase homolog from entamoeba histolytica
76c2dlcX_



not modelled 95.5 15 PDB header:ligase/trna
Chain: X: PDB Molecule:tyrosyl-trna synthetase, cytoplasmic;
PDBTitle: crystal structure of the ternary complex of yeast tyrosyl-trna2 synthetase
77c2g36A_



not modelled 95.4 21 PDB header:ligase
Chain: A: PDB Molecule:tryptophanyl-trna synthetase;
PDBTitle: crystal structure of tryptophanyl-trna synthetase (ec 6.1.1.2)2 (tryptophan-trna ligase)(trprs) (tm0492) from thermotoga maritima at3 2.50 a resolution
78d1i6la_



not modelled 95.3 15 Fold:Adenine nucleotide alpha hydrolase-like
Superfamily:Nucleotidylyl transferase
Family:Class I aminoacyl-tRNA synthetases (RS), catalytic domain
79d1n3la_



not modelled 95.0 16 Fold:Adenine nucleotide alpha hydrolase-like
Superfamily:Nucleotidylyl transferase
Family:Class I aminoacyl-tRNA synthetases (RS), catalytic domain
80c3jxeB_



not modelled 95.0 17 PDB header:ligase
Chain: B: PDB Molecule:tryptophanyl-trna synthetase;
PDBTitle: crystal structure of pyrococcus horikoshii tryptophanyl-trna2 synthetase in complex with trpamp
81c2el7A_



not modelled 95.0 19 PDB header:ligase
Chain: A: PDB Molecule:tryptophanyl-trna synthetase;
PDBTitle: crystal structure of tryptophanyl-trna synthetase from thermus2 thermophilus
82c2cyaA_



not modelled 95.0 20 PDB header:ligase
Chain: A: PDB Molecule:tyrosyl-trna synthetase;
PDBTitle: crystal structure of tyrosyl-trna synthetase from aeropyrum pernix
83c2ts1A_



not modelled 94.9 13 PDB header:ligase (synthetase)
Chain: A: PDB Molecule:tyrosyl-trna synthetase;
PDBTitle: structure of tyrosyl-t/rna synthetase refined at 2.3 angstroms2 resolution. interaction of the enzyme with the tyrosyl adenylate3 intermediate
84d2ts1a_



not modelled 94.9 13 Fold:Adenine nucleotide alpha hydrolase-like
Superfamily:Nucleotidylyl transferase
Family:Class I aminoacyl-tRNA synthetases (RS), catalytic domain
85c1q11A_



not modelled 94.7 16 PDB header:ligase
Chain: A: PDB Molecule:tyrosyl-trna synthetase;
PDBTitle: crystal structure of an active fragment of human tyrosyl-trna2 synthetase with tyrosinol
86c3i05B_



not modelled 94.3 17 PDB header:ligase
Chain: B: PDB Molecule:tryptophanyl-trna synthetase;
PDBTitle: tryptophanyl-trna synthetase from trypanosoma brucei
87c3a05A_



not modelled 94.3 19 PDB header:ligase
Chain: A: PDB Molecule:tryptophanyl-trna synthetase;
PDBTitle: crystal structure of tryptophanyl-trna synthetase from2 hyperthermophilic archaeon, aeropyrum pernix k1 complex3 with tryptophan
88c3m5wB_



not modelled 94.2 17 PDB header:ligase
Chain: B: PDB Molecule:tryptophanyl-trna synthetase;
PDBTitle: crystal structure of tryptophanyl-trna synthetase from2 campylobacter jejuni
89c3p0jD_



not modelled 94.1 16 PDB header:ligase
Chain: D: PDB Molecule:tyrosyl-trna synthetase;
PDBTitle: leishmania major tyrosyl-trna synthetase in complex with tyrosinol,2 triclinic crystal form 1
90d1j1ua_



not modelled 93.8 17 Fold:Adenine nucleotide alpha hydrolase-like
Superfamily:Nucleotidylyl transferase
Family:Class I aminoacyl-tRNA synthetases (RS), catalytic domain
91c1yi8C_



not modelled 93.8 20 PDB header:ligase
Chain: C: PDB Molecule:tryptophanyl-trna synthetase;
PDBTitle: crystal structure of tryptophanyl trrna synthetase ii from deinococcus2 radiodurans in complex with l-trp
92c2quiB_



not modelled 93.6 14 PDB header:ligase
Chain: B: PDB Molecule:tryptophanyl-trna synthetase;
PDBTitle: crystal structures of human tryptophanyl-trna synthetase in2 complex with tryptophanamide and atp
93c2ip1A_



not modelled 93.5 15 PDB header:ligase
Chain: A: PDB Molecule:tryptophanyl-trna synthetase;
PDBTitle: crystal structure analysis of s. cerevisiae tryptophanyl trna2 synthetase
94c2cycB_



not modelled 92.8 16 PDB header:ligase
Chain: B: PDB Molecule:tyrosyl-trna synthetase;
PDBTitle: crystal structure of tyrosyl-trna synthetase complexed with l-tyrosine2 from pyrococcus horikoshii
95c3n9iA_



not modelled 92.8 8 PDB header:ligase
Chain: A: PDB Molecule:tryptophanyl-trna synthetase;
PDBTitle: crystal structure of tryptophanyl-trna synthetase from yersinia pestis2 co92
96c2pidB_



not modelled 92.4 15 PDB header:ligase
Chain: B: PDB Molecule:tyrosyl-trna synthetase;
PDBTitle: crystal structure of human mitochondrial tyrosyl-trna synthetase in2 complex with an adenylate analog
97d1r6ta2



not modelled 89.2 13 Fold:Adenine nucleotide alpha hydrolase-like
Superfamily:Nucleotidylyl transferase
Family:Class I aminoacyl-tRNA synthetases (RS), catalytic domain
98c1r6uB_



not modelled 87.4 13 PDB header:ligase
Chain: B: PDB Molecule:tryptophanyl-trna synthetase;
PDBTitle: crystal structure of an active fragment of human tryptophanyl-trna2 synthetase with cytokine activity
99c3sz3A_



not modelled 83.3 20 PDB header:ligase
Chain: A: PDB Molecule:tryptophanyl-trna synthetase;
PDBTitle: crystal structure of tryptophanyl-trna synthetase from vibrio cholerae2 with an endogenous tryptophan
100c2yy5C_



not modelled 81.3 16 PDB header:ligase
Chain: C: PDB Molecule:tryptophanyl-trna synthetase;
PDBTitle: crystal structure of tryptophanyl-trna synthetase from mycoplasma2 pneumoniae
101c3lssA_



not modelled 70.9 13 PDB header:ligase
Chain: A: PDB Molecule:seryl-trna synthetase;
PDBTitle: trypanosoma brucei seryl-trna synthetase in complex with atp
102d1iq0a1



not modelled 64.0 14 Fold:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
Superfamily:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
Family:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
103c3hnwB_



not modelled 60.4 9 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of a basic coiled-coil protein of unknown function2 from eubacterium eligens atcc 27750
104d1f7ua1



not modelled 54.7 21 Fold:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
Superfamily:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
Family:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
105c3ojaB_



not modelled 54.6 12 PDB header:protein binding
Chain: B: PDB Molecule:anopheles plasmodium-responsive leucine-rich repeat protein
PDBTitle: crystal structure of lrim1/apl1c complex
106c2opfA_



not modelled 48.3 13 PDB header:hydrolase/dna
Chain: A: PDB Molecule:endonuclease viii;
PDBTitle: crystal structure of the dna repair enzyme endonuclease-viii (nei)2 from e. coli (r252a) in complex with ap-site containing dna substrate
107c2dq0A_



not modelled 47.5 16 PDB header:ligase
Chain: A: PDB Molecule:seryl-trna synthetase;
PDBTitle: crystal structure of seryl-trna synthetase from pyrococcus2 horikoshii complexed with a seryl-adenylate analog
108c1nnjA_



not modelled 46.7 20 PDB header:hydrolase
Chain: A: PDB Molecule:formamidopyrimidine-dna glycosylase;
PDBTitle: crystal structure complex between the lactococcus lactis fpg and an2 abasic site containing dna
109c3d5cX_



not modelled 46.4 7 PDB header:ribosome
Chain: X: PDB Molecule:peptide chain release factor 1;
PDBTitle: structural basis for translation termination on the 70s ribosome. this2 file contains the 30s subunit, release factor 1 (rf1), two trna, and3 mrna molecules of the second 70s ribosome. the entire crystal4 structure contains two 70s ribosomes as described in remark 400.
110d1seta1



not modelled 46.1 17 Fold:Long alpha-hairpin
Superfamily:tRNA-binding arm
Family:Seryl-tRNA synthetase (SerRS)
111c1k82D_



not modelled 45.0 7 PDB header:hydrolase/dna
Chain: D: PDB Molecule:formamidopyrimidine-dna glycosylase;
PDBTitle: crystal structure of e.coli formamidopyrimidine-dna2 glycosylase (fpg) covalently trapped with dna
112c2f5qA_



not modelled 44.9 13 PDB header:hydrolase/dna
Chain: A: PDB Molecule:formamidopyrimidine-dna glycosidase;
PDBTitle: catalytically inactive (e3q) mutm crosslinked to oxog:c2 containing dna cc2
113c1ee8A_



not modelled 42.3 13 PDB header:dna binding protein
Chain: A: PDB Molecule:mutm (fpg) protein;
PDBTitle: crystal structure of mutm (fpg) protein from thermus thermophilus hb8
114c3bmaC_



not modelled 41.0 13 PDB header:ligase
Chain: C: PDB Molecule:d-alanyl-lipoteichoic acid synthetase;
PDBTitle: crystal structure of d-alanyl-lipoteichoic acid synthetase from2 streptococcus pneumoniae r6
115c3chfA_



not modelled 39.9 24 PDB header:hydrolase/hydrolase inhibitor
Chain: A: PDB Molecule:chitinase;
PDBTitle: crystal structure of aspergillus fumigatus chitinase b1 in complex2 with tetrapeptide
116c2dq3A_



not modelled 39.6 13 PDB header:ligase
Chain: A: PDB Molecule:seryl-trna synthetase;
PDBTitle: crystal structure of aq_298
117c3cz8A_



not modelled 38.8 15 PDB header:hydrolase
Chain: A: PDB Molecule:putative sporulation-specific glycosylase ydhd;
PDBTitle: crystal structure of putative sporulation-specific glycosylase ydhd2 from bacillus subtilis
118c1u0iA_



not modelled 38.7 48 PDB header:de novo protein
Chain: A: PDB Molecule:iaal-e3;
PDBTitle: iaal-e3/k3 heterodimer
119c2v2gC_



not modelled 38.1 19 PDB header:oxidoreductase
Chain: C: PDB Molecule:peroxiredoxin 6;
PDBTitle: crystal structure of the c45s mutant of the peroxiredoxin 62 of arenicola marina. monoclinic form
120d1k3xa3



not modelled 36.5 20 Fold:Glucocorticoid receptor-like (DNA-binding domain)
Superfamily:Glucocorticoid receptor-like (DNA-binding domain)
Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins

Binding site prediction 

Due to computational demand, binding site predictions are not run for batch jobs

If you want to predict binding sites, please manually submit your model of choice to 3DLigandSite



Phyre is for academic use only

Please cite: Protein structure prediction on the web: a case study using the Phyre server
Kelley LA and Sternberg MJE. Nature Protocols 4, 363 - 371 (2009) [pdf] [Import into BibTeX]
 
If you use the binding site predictions from 3DLigandSite, please also cite:
3DLigandSite: predicting ligand-binding sites using similar structures.
Wass MN, Kelley LA and Sternberg MJ Nucleic Acids Research 38, W469-73 (2010) [PubMed]
 
© Structural Bioinformatics Group
Imperial College London
Lawrence Kelley, Benjamin Jefferys
Disclaimer
Terms and Conditions
Component software
Template detection: HHpred 1.51
Secondary structure prediction: Psi-pred 2.5
Disorder prediction: Disopred 2.4
Transmembrane prediction: Memsat_SVM
Multi-template modelling and ab initio: Poing 1.0