Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP0ABS5
DateThu Jan 5 11:16:14 GMT 2012
Unique Job ID8fee6cce2e146eef

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c2au3A_
Top template information
PDB header:transferase
Chain: A: PDB Molecule:dna primase;
PDBTitle: crystal structure of the aquifex aeolicus primase (zinc binding and2 rna polymerase domains)
Confidence and coverage
Confidence:100.0% Coverage: 69%
402 residues ( 69% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.
533 residues ( 92%) could be modelled at >90% confidence using multiple-templates.
You may wish to try resubmitting your sequence in "intensive" mode to model more of your sequence.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MAGRIPRVFINDLLARTDIVDLIDARVKLKKQGKNFHACCPFHNEKTPSFTVNGEKQFYH
Secondary structure 
SS confidence 
Disorder  ??????
?
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  CFGCGAHGNAIDFLMNYDKLEFVETVEELAAMHNLEVPFEAGSGPSQIERHQRQTLYQLM
Secondary structure 
SS confidence 
Disorder 
?????????????
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  DGLNTFYQQSLQQPVATSARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGNPENRQ
Secondary structure 
SS confidence 
Disorder 
???
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  SLIDAGMLVTNDQGRSYDRFRERVMFPIRDKRGRVIGFGGRVLGNDTPKYLNSPETDIFH
Secondary structure 
SS confidence 
Disorder 
??
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  KGRQLYGLYEAQQDNAEPNRLLVVEGYMDVVALAQYGINYAVASLGTSTTADHIQLLFRA
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  TNNVICCYDGDRAGRDAAWRALETALPYMTDGRQLRFMFLPDGEDPDTLVRKEGKEAFEA
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  RMEQAMPLSAFLFNSLMPQVDLSTPDGRARLSTLALPLISQVPGETLRIYLRQELGNKLG
Secondary structure 
SS confidence 
Disorder 
?
????
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  ILDDSQLERLMPKAAESGVSRPVPQLKRTTMRILIGLLVQNPELATLVPPLENLDENKLP
Secondary structure 
SS confidence 
Disorder 
?
???????????????????
Disorder confidence 
 
   .........490.........500.........510.........520.........530.........540
Sequence  GLGLFRELVNTCLSQPGLTTGQLLEHYRGTNNAATLEKLSMWDDIADKNIAEQTFTDSLN
Secondary structure 
SS confidence 
Disorder 
???
??
??
Disorder confidence 
 
   .........550.........560.........570.........580.
Sequence  HMFDSLLELRQEELIARERTHGLSNEERLELWTLNQELAKK
Secondary structure 
SS confidence 
Disorder 
????
???
Disorder confidence 
 

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 2au3 chain A

3D model

Region: 1 - 430
Aligned: 402
Modelled: 430
Confidence: 100.0%
Identity: 34%
PDB header:transferase
Chain: A: PDB Molecule:dna primase;
PDBTitle: crystal structure of the aquifex aeolicus primase (zinc binding and2 rna polymerase domains)

Phyre2

PDB 1dd9 chain A

3D model

Region: 116 - 428
Aligned: 309
Modelled: 313
Confidence: 100.0%
Identity: 99%
Fold: DNA primase core
Superfamily: DNA primase core
Family: DNA primase DnaG catalytic core

Phyre2

PDB 1dd9 chain A

3D model

Region: 116 - 428
Aligned: 309
Modelled: 313
Confidence: 100.0%
Identity: 99%
PDB header:transferase
Chain: A: PDB Molecule:dna primase;
PDBTitle: structure of the dnag catalytic core

Phyre2

PDB 1nui chain A

3D model

Region: 36 - 362
Aligned: 232
Modelled: 242
Confidence: 100.0%
Identity: 20%
PDB header:replication
Chain: A: PDB Molecule:dna primase/helicase;
PDBTitle: crystal structure of the primase fragment of bacteriophage t7 primase-2 helicase protein

Phyre2

PDB 1d0q chain A

3D model

Region: 3 - 103
Aligned: 101
Modelled: 101
Confidence: 100.0%
Identity: 48%
Fold: Rubredoxin-like
Superfamily: Zinc beta-ribbon
Family: DNA primase zinc finger

Phyre2

PDB 1q57 chain G

3D model

Region: 132 - 367
Aligned: 184
Modelled: 201
Confidence: 99.9%
Identity: 23%
PDB header:transferase
Chain: G: PDB Molecule:dna primase/helicase;
PDBTitle: the crystal structure of the bifunctional primase-helicase of2 bacteriophage t7

Phyre2

PDB 1nui chain A domain 1

3D model

Region: 134 - 362
Aligned: 177
Modelled: 190
Confidence: 99.9%
Identity: 20%
Fold: DNA primase core
Superfamily: DNA primase core
Family: Primase fragment of primase-helicase protein

Phyre2

PDB 1t6t chain 1

3D model

Region: 245 - 361
Aligned: 106
Modelled: 117
Confidence: 99.7%
Identity: 23%
Fold: Toprim domain
Superfamily: Toprim domain
Family: Toprim domain

Phyre2

PDB 1t3w chain A

3D model

Region: 447 - 580
Aligned: 134
Modelled: 134
Confidence: 99.2%
Identity: 98%
Fold: DNA primase DnaG, C-terminal domain
Superfamily: DNA primase DnaG, C-terminal domain
Family: DNA primase DnaG, C-terminal domain

Phyre2

PDB 2fcj chain A domain 1

3D model

Region: 255 - 324
Aligned: 69
Modelled: 70
Confidence: 98.8%
Identity: 20%
Fold: Toprim domain
Superfamily: Toprim domain
Family: Toprim domain

Phyre2

PDB 2r6c chain G

3D model

Region: 443 - 580
Aligned: 135
Modelled: 138
Confidence: 98.2%
Identity: 14%
PDB header:replication
Chain: G: PDB Molecule:dnag primase, helicase binding domain;
PDBTitle: crystal form bh2

Phyre2

PDB 2r5u chain D

3D model

Region: 443 - 578
Aligned: 134
Modelled: 136
Confidence: 96.4%
Identity: 8%
PDB header:hydrolase
Chain: D: PDB Molecule:replicative dna helicase;
PDBTitle: crystal structure of the n-terminal domain of dnab helicase from2 mycobacterium tuberculosis

Phyre2

PDB 2q6t chain B

3D model

Region: 442 - 560
Aligned: 119
Modelled: 119
Confidence: 96.2%
Identity: 7%
PDB header:hydrolase
Chain: B: PDB Molecule:dnab replication fork helicase;
PDBTitle: crystal structure of the thermus aquaticus dnab monomer

Phyre2

PDB 1jwe chain A

3D model

Region: 443 - 550
Aligned: 108
Modelled: 108
Confidence: 95.3%
Identity: 11%
Fold: N-terminal domain of DnaB helicase
Superfamily: N-terminal domain of DnaB helicase
Family: N-terminal domain of DnaB helicase

Phyre2

PDB 1vdd chain C

3D model

Region: 256 - 347
Aligned: 89
Modelled: 92
Confidence: 93.8%
Identity: 19%
PDB header:recombination
Chain: C: PDB Molecule:recombination protein recr;
PDBTitle: crystal structure of recombinational repair protein recr

Phyre2

PDB 1vdd chain A

3D model

Region: 256 - 347
Aligned: 89
Modelled: 92
Confidence: 93.4%
Identity: 19%
Fold: Recombination protein RecR
Superfamily: Recombination protein RecR
Family: Recombination protein RecR

Phyre2

PDB 3gxv chain A

3D model

Region: 450 - 562
Aligned: 108
Modelled: 113
Confidence: 92.8%
Identity: 8%
PDB header:hydrolase/replication
Chain: A: PDB Molecule:replicative dna helicase;
PDBTitle: three-dimensional structure of n-terminal domain of dnab2 helicase from helicobacter pylori and its interactions with3 primase

Phyre2

PDB 1b79 chain A

3D model

Region: 444 - 543
Aligned: 100
Modelled: 100
Confidence: 92.6%
Identity: 11%
Fold: N-terminal domain of DnaB helicase
Superfamily: N-terminal domain of DnaB helicase
Family: N-terminal domain of DnaB helicase

Phyre2

PDB 2e9h chain A

3D model

Region: 3 - 70
Aligned: 52
Modelled: 68
Confidence: 91.7%
Identity: 29%
PDB header:translation
Chain: A: PDB Molecule:eukaryotic translation initiation factor 5;
PDBTitle: solution structure of the eif-5_eif-2b domain from human2 eukaryotic translation initiation factor 5

Phyre2

PDB 3bgw chain D

3D model

Region: 448 - 576
Aligned: 126
Modelled: 129
Confidence: 90.5%
Identity: 8%
PDB header:replication
Chain: D: PDB Molecule:dnab-like replicative helicase;
PDBTitle: the structure of a dnab-like replicative helicase and its interactions2 with primase

Phyre2
1
c2au3A_
2
d1dd9a_
3
c1dd9A_
4
c1nuiA_
5
d1d0qa_
6
c1q57G_
7
d1nuia1
8
d1t6t1_
9
d1t3wa_
10
d2fcja1
11
c2r6cG_
12
c2r5uD_
13
c2q6tB_
14
d1jwea_
15
c1vddC_
16
d1vdda_
17
c3gxvA_
18
d1b79a_
19
c2e9hA_
20
c3bgwD_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c2au3A_
100.0 34 PDB header:transferase
Chain: A: PDB Molecule:dna primase;
PDBTitle: crystal structure of the aquifex aeolicus primase (zinc binding and2 rna polymerase domains)
2d1dd9a_
100.0 99 Fold:DNA primase core
Superfamily:DNA primase core
Family:DNA primase DnaG catalytic core
3c1dd9A_
100.0 99 PDB header:transferase
Chain: A: PDB Molecule:dna primase;
PDBTitle: structure of the dnag catalytic core
4c1nuiA_
100.0 20 PDB header:replication
Chain: A: PDB Molecule:dna primase/helicase;
PDBTitle: crystal structure of the primase fragment of bacteriophage t7 primase-2 helicase protein
5d1d0qa_
100.0 48 Fold:Rubredoxin-like
Superfamily:Zinc beta-ribbon
Family:DNA primase zinc finger
6c1q57G_
99.9 23 PDB header:transferase
Chain: G: PDB Molecule:dna primase/helicase;
PDBTitle: the crystal structure of the bifunctional primase-helicase of2 bacteriophage t7
7d1nuia1
99.9 20 Fold:DNA primase core
Superfamily:DNA primase core
Family:Primase fragment of primase-helicase protein
8d1t6t1_
99.7 23 Fold:Toprim domain
Superfamily:Toprim domain
Family:Toprim domain
9d1t3wa_
99.2 98 Fold:DNA primase DnaG, C-terminal domain
Superfamily:DNA primase DnaG, C-terminal domain
Family:DNA primase DnaG, C-terminal domain
10d2fcja1
98.8 20 Fold:Toprim domain
Superfamily:Toprim domain
Family:Toprim domain
11c2r6cG_
98.2 14 PDB header:replication
Chain: G: PDB Molecule:dnag primase, helicase binding domain;
PDBTitle: crystal form bh2
12c2r5uD_
96.4 8 PDB header:hydrolase
Chain: D: PDB Molecule:replicative dna helicase;
PDBTitle: crystal structure of the n-terminal domain of dnab helicase from2 mycobacterium tuberculosis
13c2q6tB_
96.2 7 PDB header:hydrolase
Chain: B: PDB Molecule:dnab replication fork helicase;
PDBTitle: crystal structure of the thermus aquaticus dnab monomer
14d1jwea_
95.3 11 Fold:N-terminal domain of DnaB helicase
Superfamily:N-terminal domain of DnaB helicase
Family:N-terminal domain of DnaB helicase
15c1vddC_
93.8 19 PDB header:recombination
Chain: C: PDB Molecule:recombination protein recr;
PDBTitle: crystal structure of recombinational repair protein recr
16d1vdda_
93.4 19 Fold:Recombination protein RecR
Superfamily:Recombination protein RecR
Family:Recombination protein RecR
17c3gxvA_
92.8 8 PDB header:hydrolase/replication
Chain: A: PDB Molecule:replicative dna helicase;
PDBTitle: three-dimensional structure of n-terminal domain of dnab2 helicase from helicobacter pylori and its interactions with3 primase
18d1b79a_
92.6 11 Fold:N-terminal domain of DnaB helicase
Superfamily:N-terminal domain of DnaB helicase
Family:N-terminal domain of DnaB helicase
19c2e9hA_
91.7 29 PDB header:translation
Chain: A: PDB Molecule:eukaryotic translation initiation factor 5;
PDBTitle: solution structure of the eif-5_eif-2b domain from human2 eukaryotic translation initiation factor 5
20c3bgwD_
90.5 8 PDB header:replication
Chain: D: PDB Molecule:dnab-like replicative helicase;
PDBTitle: the structure of a dnab-like replicative helicase and its interactions2 with primase
21c1neeA_
not modelled 86.8 25 PDB header:translation
Chain: A: PDB Molecule:probable translation initiation factor 2 beta
PDBTitle: structure of archaeal translation factor aif2beta from2 methanobacterium thermoautrophicum
22c2vyeA_
not modelled 86.7 10 PDB header:hydrolase
Chain: A: PDB Molecule:replicative dna helicase;
PDBTitle: crystal structure of the dnac-ssdna complex
23c2dcuB_
not modelled 75.6 25 PDB header:translation
Chain: B: PDB Molecule:translation initiation factor 2 beta subunit;
PDBTitle: crystal structure of translation initiation factor aif2betagamma2 heterodimer with gdp
24c4a17Y_
not modelled 73.4 32 PDB header:ribosome
Chain: Y: PDB Molecule:rpl37a;
PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 5s rrna,3 5.8s rrna and proteins of molecule 2.
25c2pfsA_
not modelled 71.4 6 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:universal stress protein;
PDBTitle: crystal structure of universal stress protein from nitrosomonas2 europaea
26c3nmeA_
not modelled 71.3 17 PDB header:hydrolase
Chain: A: PDB Molecule:sex4 glucan phosphatase;
PDBTitle: structure of a plant phosphatase
27c2imgA_
not modelled 68.4 23 PDB header:hydrolase
Chain: A: PDB Molecule:dual specificity protein phosphatase 23;
PDBTitle: crystal structure of dual specificity protein phosphatase2 23 from homo sapiens in complex with ligand malate ion
28c3cc4Z_
not modelled 67.6 22 PDB header:ribosome
Chain: Z: PDB Molecule:50s ribosomal protein l37ae;
PDBTitle: co-crystal structure of anisomycin bound to the 50s ribosomal subunit
29d1v3aa_
not modelled 67.5 13 Fold:(Phosphotyrosine protein) phosphatases II
Superfamily:(Phosphotyrosine protein) phosphatases II
Family:Dual specificity phosphatase-like
30c2oudA_
not modelled 67.3 17 PDB header:hydrolase
Chain: A: PDB Molecule:dual specificity protein phosphatase 10;
PDBTitle: crystal structure of the catalytic domain of human mkp5
31c3emuA_
not modelled 66.6 23 PDB header:hydrolase
Chain: A: PDB Molecule:leucine rich repeat and phosphatase domain
PDBTitle: crystal structure of a leucine rich repeat and phosphatase2 domain containing protein from entamoeba histolytica
32c3k7aM_
not modelled 63.8 23 PDB header:transcription
Chain: M: PDB Molecule:transcription initiation factor iib;
PDBTitle: crystal structure of an rna polymerase ii-tfiib complex
33c2qa4Z_
not modelled 63.6 21 PDB header:ribosome
Chain: Z: PDB Molecule:50s ribosomal protein l37ae;
PDBTitle: a more complete structure of the the l7/l12 stalk of the2 haloarcula marismortui 50s large ribosomal subunit
34c1yshD_
not modelled 63.6 36 PDB header:structural protein/rna
Chain: D: PDB Molecule:ribosomal protein l37a;
PDBTitle: localization and dynamic behavior of ribosomal protein l30e
35d1nuia2
not modelled 61.4 14 Fold:Rubredoxin-like
Superfamily:Zinc beta-ribbon
Family:DNA primase zinc finger
36c2esbA_
not modelled 61.4 17 PDB header:hydrolase
Chain: A: PDB Molecule:dual specificity protein phosphatase 18;
PDBTitle: crystal structure of human dusp18
37c1oheA_
not modelled 61.3 29 PDB header:hydrolase
Chain: A: PDB Molecule:cdc14b2 phosphatase;
PDBTitle: structure of cdc14b phosphatase with a peptide ligand
38d1ffkw_
not modelled 60.9 25 Fold:Rubredoxin-like
Superfamily:Zn-binding ribosomal proteins
Family:Ribosomal protein L37ae
39c3rgqA_
not modelled 59.5 17 PDB header:hydrolase
Chain: A: PDB Molecule:protein-tyrosine phosphatase mitochondrial 1;
PDBTitle: crystal structure of ptpmt1 in complex with pi(5)p
40d1ohea2
not modelled 59.2 15 Fold:(Phosphotyrosine protein) phosphatases II
Superfamily:(Phosphotyrosine protein) phosphatases II
Family:Dual specificity phosphatase-like
41d1vqoz1
not modelled 59.0 21 Fold:Rubredoxin-like
Superfamily:Zn-binding ribosomal proteins
Family:Ribosomal protein L37ae
42d1wiia_
not modelled 58.5 29 Fold:Rubredoxin-like
Superfamily:Zinc beta-ribbon
Family:Putative zinc binding domain
43c2zkrz_
not modelled 57.8 21 PDB header:ribosomal protein/rna
Chain: Z: PDB Molecule:e site t-rna;
PDBTitle: structure of a mammalian ribosomal 60s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map
44d1jj2y_
not modelled 56.5 25 Fold:Rubredoxin-like
Superfamily:Zn-binding ribosomal proteins
Family:Ribosomal protein L37ae
45c2r0bA_
not modelled 56.1 11 PDB header:hydrolase
Chain: A: PDB Molecule:serine/threonine/tyrosine-interacting protein;
PDBTitle: crystal structure of human tyrosine phosphatase-like2 serine/threonine/tyrosine-interacting protein
46c1yn9B_
not modelled 55.3 20 PDB header:hydrolase
Chain: B: PDB Molecule:polynucleotide 5'-phosphatase;
PDBTitle: crystal structure of baculovirus rna 5'-phosphatase2 complexed with phosphate
47c2y96A_
not modelled 54.6 20 PDB header:hydrolase
Chain: A: PDB Molecule:dual specificity phosphatase dupd1;
PDBTitle: structure of human dual-specificity phosphatase 27
48c2gwoC_
not modelled 54.0 26 PDB header:hydrolase
Chain: C: PDB Molecule:dual specificity protein phosphatase 13;
PDBTitle: crystal structure of tmdp
49c3jyw9_
not modelled 53.4 36 PDB header:ribosome
Chain: 9: PDB Molecule:60s ribosomal protein l43;
PDBTitle: structure of the 60s proteins for eukaryotic ribosome based on cryo-em2 map of thermomyces lanuginosus ribosome at 8.9a resolution
50c3rz2B_
not modelled 51.7 16 PDB header:hydrolase
Chain: B: PDB Molecule:protein tyrosine phosphatase type iva 1;
PDBTitle: crystal of prl-1 complexed with peptide
51d1vhra_
not modelled 50.6 20 Fold:(Phosphotyrosine protein) phosphatases II
Superfamily:(Phosphotyrosine protein) phosphatases II
Family:Dual specificity phosphatase-like
52c2g6zB_
not modelled 50.2 14 PDB header:hydrolase
Chain: B: PDB Molecule:dual specificity protein phosphatase 5;
PDBTitle: crystal structure of human dusp5
53c2i50A_
not modelled 49.7 14 PDB header:hydrolase
Chain: A: PDB Molecule:ubiquitin carboxyl-terminal hydrolase 16;
PDBTitle: solution structure of ubp-m znf-ubp domain
54d1i9sa_
not modelled 49.7 22 Fold:(Phosphotyrosine protein) phosphatases II
Superfamily:(Phosphotyrosine protein) phosphatases II
Family:Dual specificity phosphatase-like
55c2c46B_
not modelled 49.5 22 PDB header:transferase
Chain: B: PDB Molecule:mrna capping enzyme;
PDBTitle: crystal structure of the human rna guanylyltransferase and2 5'-phosphatase
56c3cw2M_
not modelled 49.5 22 PDB header:translation
Chain: M: PDB Molecule:translation initiation factor 2 subunit beta;
PDBTitle: crystal structure of the intact archaeal translation2 initiation factor 2 from sulfolobus solfataricus .
57d1mkpa_
not modelled 49.0 14 Fold:(Phosphotyrosine protein) phosphatases II
Superfamily:(Phosphotyrosine protein) phosphatases II
Family:Dual specificity phosphatase-like
58c1s1i9_
not modelled 48.5 29 PDB header:ribosome
Chain: 9: PDB Molecule:60s ribosomal protein l43;
PDBTitle: structure of the ribosomal 80s-eef2-sordarin complex from2 yeast obtained by docking atomic models for rna and protein3 components into a 11.7 a cryo-em map. this file, 1s1i,4 contains 60s subunit. the 40s ribosomal subunit is in file5 1s1h.
59c3fldA_
not modelled 47.7 23 PDB header:hydrolase
Chain: A: PDB Molecule:protein trai;
PDBTitle: crystal structure of the trai c-terminal domain
60c3s4oB_
not modelled 46.2 17 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:protein tyrosine phosphatase-like protein;
PDBTitle: protein tyrosine phosphatase (putative) from leishmania major
61d2z3va1
not modelled 46.2 14 Fold:Adenine nucleotide alpha hydrolase-like
Superfamily:Adenine nucleotide alpha hydrolases-like
Family:Universal stress protein-like
62c2k8dA_
not modelled 45.6 24 PDB header:oxidoreductase
Chain: A: PDB Molecule:peptide methionine sulfoxide reductase msrb;
PDBTitle: solution structure of a zinc-binding methionine sulfoxide reductase
63d1rxda_
not modelled 45.3 15 Fold:(Phosphotyrosine protein) phosphatases II
Superfamily:(Phosphotyrosine protein) phosphatases II
Family:Dual specificity phosphatase-like
64c3e90B_
not modelled 45.2 40 PDB header:hydrolase
Chain: B: PDB Molecule:ns3 protease;
PDBTitle: west nile vi rus ns2b-ns3protease in complexed with2 inhibitor naph-kkr-h
65c2e0tA_
not modelled 44.9 26 PDB header:hydrolase
Chain: A: PDB Molecule:dual specificity phosphatase 26;
PDBTitle: crystal structure of catalytic domain of dual specificity phosphatase2 26, ms0830 from homo sapiens
66d2ijob1
not modelled 44.9 40 Fold:Trypsin-like serine proteases
Superfamily:Trypsin-like serine proteases
Family:Viral proteases
67d1xria_
not modelled 44.9 23 Fold:(Phosphotyrosine protein) phosphatases II
Superfamily:(Phosphotyrosine protein) phosphatases II
Family:Dual specificity phosphatase-like
68c1yz4A_
not modelled 44.8 20 PDB header:hydrolase
Chain: A: PDB Molecule:dual specificity phosphatase-like 15 isoform a;
PDBTitle: crystal structure of dusp15
69d1muma_
not modelled 44.8 17 Fold:TIM beta/alpha-barrel
Superfamily:Phosphoenolpyruvate/pyruvate domain
Family:Phosphoenolpyruvate mutase/Isocitrate lyase-like
70d1befa_
not modelled 44.3 36 Fold:Trypsin-like serine proteases
Superfamily:Trypsin-like serine proteases
Family:Viral proteases
71c2i6oA_
not modelled 44.3 24 PDB header:hydrolase
Chain: A: PDB Molecule:sulfolobus solfataricus protein tyrosine
PDBTitle: crystal structure of the complex of the archaeal sulfolobus2 ptp-fold phosphatase with phosphopeptides n-g-(p)y-k-n
72c2nt2C_
not modelled 42.6 11 PDB header:hydrolase
Chain: C: PDB Molecule:protein phosphatase slingshot homolog 2;
PDBTitle: crystal structure of slingshot phosphatase 2
73c3hcjB_
not modelled 41.9 22 PDB header:oxidoreductase
Chain: B: PDB Molecule:peptide methionine sulfoxide reductase;
PDBTitle: structure of msrb from xanthomonas campestris (oxidized2 form)
74d1w0ba_
not modelled 41.9 20 Fold:Spectrin repeat-like
Superfamily:Alpha-hemoglobin stabilizing protein AHSP
Family:Alpha-hemoglobin stabilizing protein AHSP
75d2fp7b1
not modelled 41.9 40 Fold:Trypsin-like serine proteases
Superfamily:Trypsin-like serine proteases
Family:Viral proteases
76d1z8ua1
not modelled 40.5 20 Fold:Spectrin repeat-like
Superfamily:Alpha-hemoglobin stabilizing protein AHSP
Family:Alpha-hemoglobin stabilizing protein AHSP
77d1jeya2
not modelled 40.2 22 Fold:vWA-like
Superfamily:vWA-like
Family:Ku70 subunit N-terminal domain
78d1pnoa_
not modelled 39.5 16 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Transhydrogenase domain III (dIII)
79c2vdwA_
not modelled 39.0 9 PDB header:transferase
Chain: A: PDB Molecule:vaccinia virus capping enzyme d1 subunit;
PDBTitle: guanosine n7 methyl-transferase sub-complex (d1-d12) of the2 vaccinia virus mrna capping enzyme
80d1d4oa_
not modelled 38.5 18 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Transhydrogenase domain III (dIII)
81c2kxoA_
not modelled 37.4 7 PDB header:cell cycle
Chain: A: PDB Molecule:cell division topological specificity factor;
PDBTitle: solution nmr structure of the cell division regulator mine protein2 from neisseria gonorrhoeae
82c2pdtD_
not modelled 37.3 25 PDB header:circadian clock protein
Chain: D: PDB Molecule:vivid pas protein vvd;
PDBTitle: 2.3 angstrom structure of phosphodiesterase treated vivid
83c3lyeA_
not modelled 36.0 19 PDB header:hydrolase
Chain: A: PDB Molecule:oxaloacetate acetyl hydrolase;
PDBTitle: crystal structure of oxaloacetate acetylhydrolase
84d1twfj_
not modelled 36.0 27 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:RNA polymerase subunit RPB10
Family:RNA polymerase subunit RPB10
85d1dl6a_
not modelled 36.0 25 Fold:Rubredoxin-like
Superfamily:Zinc beta-ribbon
Family:Transcriptional factor domain
86c1pt9B_
not modelled 35.7 18 PDB header:oxidoreductase
Chain: B: PDB Molecule:nad(p) transhydrogenase, mitochondrial;
PDBTitle: crystal structure analysis of the diii component of transhydrogenase2 with a thio-nicotinamide nucleotide analogue
87c1zzwA_
not modelled 35.4 17 PDB header:hydrolase
Chain: A: PDB Molecule:dual specificity protein phosphatase 10;
PDBTitle: crystal structure of catalytic domain of human map kinase2 phosphatase 5
88d2fomb1
not modelled 35.4 33 Fold:Trypsin-like serine proteases
Superfamily:Trypsin-like serine proteases
Family:Viral proteases
89c2p3qA_
not modelled 35.3 17 PDB header:viral protein,transferase
Chain: A: PDB Molecule:type ii methyltransferase;
PDBTitle: crystal structure of dengue methyltransferase in complex with gpppg2 and s-adenosyl-l-homocysteine
90d1ywfa1
not modelled 34.5 22 Fold:(Phosphotyrosine protein) phosphatases II
Superfamily:(Phosphotyrosine protein) phosphatases II
Family:Mycobacterial PtpB-like
91d1g26a_
not modelled 34.3 50 Fold:Knottins (small inhibitors, toxins, lectins)
Superfamily:Granulin repeat
Family:Granulin repeat
92d1jmva_
not modelled 34.0 7 Fold:Adenine nucleotide alpha hydrolase-like
Superfamily:Adenine nucleotide alpha hydrolases-like
Family:Universal stress protein-like
93d1xmxa_
not modelled 33.8 12 Fold:Restriction endonuclease-like
Superfamily:Restriction endonuclease-like
Family:Hypothetical protein VC1899
94d1ef4a_
not modelled 33.7 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:RNA polymerase subunit RPB10
Family:RNA polymerase subunit RPB10
95c2l1uA_
not modelled 33.3 24 PDB header:oxidoreductase
Chain: A: PDB Molecule:methionine-r-sulfoxide reductase b2, mitochondrial;
PDBTitle: structure-functional analysis of mammalian msrb2 protein
96c2j17A_
not modelled 32.4 23 PDB header:hydrolase
Chain: A: PDB Molecule:tyrosine-protein phosphatase yil113w;
PDBTitle: ptyr bound form of sdp-1
97c3e0mB_
not modelled 32.3 14 PDB header:oxidoreductase
Chain: B: PDB Molecule:peptide methionine sulfoxide reductase msra/msrb
PDBTitle: crystal structure of fusion protein of msra and msrb
98c1ee8A_
not modelled 32.2 21 PDB header:dna binding protein
Chain: A: PDB Molecule:mutm (fpg) protein;
PDBTitle: crystal structure of mutm (fpg) protein from thermus thermophilus hb8
99d1pfta_
not modelled 32.1 25 Fold:Rubredoxin-like
Superfamily:Zinc beta-ribbon
Family:Transcriptional factor domain
100d1l1da_
not modelled 31.5 9 Fold:Mss4-like
Superfamily:Mss4-like
Family:SelR domain
101c3gn5B_
not modelled 31.2 16 PDB header:dna binding protein
Chain: B: PDB Molecule:hth-type transcriptional regulator mqsa (ygit/b3021);
PDBTitle: structure of the e. coli protein mqsa (ygit/b3021)
102d2dkta2
not modelled 31.2 38 Fold:Zinc hairpin stack
Superfamily:Zinc hairpin stack
Family:Zinc hairpin stack
103c3cezA_
not modelled 30.8 16 PDB header:oxidoreductase
Chain: A: PDB Molecule:methionine-r-sulfoxide reductase;
PDBTitle: crystal structure of methionine-r-sulfoxide reductase from2 burkholderia pseudomallei
104c2vbcA_
not modelled 30.6 33 PDB header:hydrolase
Chain: A: PDB Molecule:dengue 4 ns3 full-length protein;
PDBTitle: crystal structure of the ns3 protease-helicase from dengue2 virus
105d1vd4a_
not modelled 28.9 14 Fold:Rubredoxin-like
Superfamily:Zinc beta-ribbon
Family:Transcriptional factor domain
106c3r9jD_
not modelled 28.8 17 PDB header:cell cycle,hydrolase/cell cycle
Chain: D: PDB Molecule:cell division topological specificity factor;
PDBTitle: 4.3a resolution structure of a mind-mine(i24n) protein complex
107d2fiya1
not modelled 28.7 19 Fold:FdhE-like
Superfamily:FdhE-like
Family:FdhE-like
108c1wrmA_
not modelled 28.7 17 PDB header:hydrolase
Chain: A: PDB Molecule:dual specificity phosphatase 22;
PDBTitle: crystal structure of jsp-1
109c3idfA_
not modelled 28.1 13 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:usp-like protein;
PDBTitle: the crystal structure of a usp-like protein from wolinella2 succinogenes to 2.0a
110c1drwA_
not modelled 27.9 16 PDB header:oxidoreductase
Chain: A: PDB Molecule:dihydrodipicolinate reductase;
PDBTitle: escherichia coli dhpr/nhdh complex
111d1di1a_
not modelled 27.7 28 Fold:Terpenoid synthases
Superfamily:Terpenoid synthases
Family:Aristolochene/pentalenene synthase
112d1xm0a1
not modelled 27.1 11 Fold:Mss4-like
Superfamily:Mss4-like
Family:SelR domain
113d1p32a_
not modelled 27.1 17 Fold:Mitochondrial glycoprotein MAM33-like
Superfamily:Mitochondrial glycoprotein MAM33-like
Family:Mitochondrial glycoprotein MAM33-like
114c3lkwA_
not modelled 26.9 24 PDB header:viral protein,hydrolase
Chain: A: PDB Molecule:fusion protein of nonstructural protein 2b and
PDBTitle: crystal structure of dengue virus 1 ns2b/ns3 protease active2 site mutant
115c2ysaA_
not modelled 26.9 50 PDB header:metal binding protein
Chain: A: PDB Molecule:retinoblastoma-binding protein 6;
PDBTitle: solution structure of the zinc finger cchc domain from the2 human retinoblastoma-binding protein 6 (retinoblastoma-3 binding q protein 1, rbq-1)
116d1yqfa1
not modelled 26.0 33 Fold:Mitochondrial glycoprotein MAM33-like
Superfamily:Mitochondrial glycoprotein MAM33-like
Family:Mitochondrial glycoprotein MAM33-like
117c2pmzN_
not modelled 25.8 17 PDB header:translation, transferase
Chain: N: PDB Molecule:dna-directed rna polymerase subunit n;
PDBTitle: archaeal rna polymerase from sulfolobus solfataricus
118d1vh4a_
not modelled 25.7 18 Fold:Single-stranded right-handed beta-helix
Superfamily:Stabilizer of iron transporter SufD
Family:Stabilizer of iron transporter SufD
119c3qv0A_
not modelled 25.4 39 PDB header:protein binding
Chain: A: PDB Molecule:mitochondrial acidic protein mam33;
PDBTitle: crystal structure of saccharomyces cerevisiae mam33
120c3f62A_
not modelled 25.1 29 PDB header:cytokine
Chain: A: PDB Molecule:interleukin 18 binding protein;
PDBTitle: crystal structure of human il-18 in complex with ectromelia virus il-2 18 binding protein

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