Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP11880
DateThu Jan 5 11:33:00 GMT 2012
Unique Job ID90e9311716693d6a

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c1gg4A_
Top template information
PDB header:ligase
Chain: A: PDB Molecule:udp-n-acetylmuramoylalanyl-d-glutamyl-2,6-
PDBTitle: crystal structure of escherichia coli udpmurnac-tripeptide2 d-alanyl-d-alanine-adding enzyme (murf) at 2.3 angstrom3 resolution
Confidence and coverage
Confidence:100.0% Coverage: 97%
439 residues ( 97% 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  MISVTLSQLTDILNGELQGADITLDAVTTDTRKLTPGCLFVALKGERFDAHDFADQAKAG
Secondary structure 
SS confidence 
Disorder  ?????
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  GAGALLVSRPLDIDLPQLIVKDTRLAFGELAAWVRQQVPARVVALTGSSGKTSVKEMTAA
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  ILSQCGNTLYTAGNLNNDIGVPMTLLRLTPEYDYAVIELGANHQGEIAWTVSLTRPEAAL
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  VNNLAAAHLEGFGSLAGVAKAKGEIFSGLPENGIAIMNADNNDWLNWQSVIGSRKVWRFS
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  PNAANSDFTATNIHVTSHGTEFTLQTPTGSVDVLLPLPGRHNIANALAAAALSMSVGATL
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  DAIKAGLANLKAVPGRLFPIQLAENQLLLDDSYNANVGSMTAAVQVLAEMPGYRVLVVGD
Secondary structure 
SS confidence 
Disorder 
???????
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  MAELGAESEACHVQVGEAAKAAGIDRVLSVGKQSHAISTASGVGEHFADKTALITRLKLL
Secondary structure 
SS confidence 
Disorder 
???
Disorder confidence 
 
   .........430.........440.........450..
Sequence  IAEQQVITILVKGSRSAAMEEVVRALQENGTC
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 1gg4 chain A

3D model

Region: 1 - 447
Aligned: 439
Modelled: 445
Confidence: 100.0%
Identity: 98%
PDB header:ligase
Chain: A: PDB Molecule:udp-n-acetylmuramoylalanyl-d-glutamyl-2,6-
PDBTitle: crystal structure of escherichia coli udpmurnac-tripeptide2 d-alanyl-d-alanine-adding enzyme (murf) at 2.3 angstrom3 resolution

Phyre2

PDB 2am1 chain A

3D model

Region: 3 - 447
Aligned: 433
Modelled: 440
Confidence: 100.0%
Identity: 28%
PDB header:ligase
Chain: A: PDB Molecule:udp-n-acetylmuramoylalanine-d-glutamyl-lysine-d-alanyl-d-
PDBTitle: sp protein ligand 1

Phyre2

PDB 2wtz chain C

3D model

Region: 2 - 433
Aligned: 399
Modelled: 413
Confidence: 100.0%
Identity: 26%
PDB header:ligase
Chain: C: PDB Molecule:udp-n-acetylmuramoyl-l-alanyl-d-glutamate-
PDBTitle: mure ligase of mycobacterium tuberculosis

Phyre2

PDB 1e8c chain B

3D model

Region: 3 - 435
Aligned: 422
Modelled: 431
Confidence: 100.0%
Identity: 21%
PDB header:ligase
Chain: B: PDB Molecule:udp-n-acetylmuramoylalanyl-d-glutamate--2,6-
PDBTitle: structure of mure the udp-n-acetylmuramyl tripeptide2 synthetase from e. coli

Phyre2

PDB 3lk7 chain A

3D model

Region: 25 - 449
Aligned: 398
Modelled: 417
Confidence: 100.0%
Identity: 21%
PDB header:ligase
Chain: A: PDB Molecule:udp-n-acetylmuramoylalanine--d-glutamate ligase;
PDBTitle: the crystal structure of udp-n-acetylmuramoylalanine-d-2 glutamate (murd) ligase from streptococcus agalactiae to3 1.5a

Phyre2

PDB 2f00 chain A

3D model

Region: 6 - 448
Aligned: 403
Modelled: 421
Confidence: 100.0%
Identity: 18%
PDB header:ligase
Chain: A: PDB Molecule:udp-n-acetylmuramate--l-alanine ligase;
PDBTitle: escherichia coli murc

Phyre2

PDB 3hn7 chain A

3D model

Region: 6 - 448
Aligned: 417
Modelled: 442
Confidence: 100.0%
Identity: 18%
PDB header:ligase
Chain: A: PDB Molecule:udp-n-acetylmuramate-l-alanine ligase;
PDBTitle: crystal structure of a murein peptide ligase mpl (psyc_0032) from2 psychrobacter arcticus 273-4 at 1.65 a resolution

Phyre2

PDB 3uag chain A

3D model

Region: 1 - 446
Aligned: 394
Modelled: 435
Confidence: 100.0%
Identity: 21%
PDB header:ligase
Chain: A: PDB Molecule:protein (udp-n-acetylmuramoyl-l-alanine:d-
PDBTitle: udp-n-acetylmuramoyl-l-alanine:d-glutamate ligase

Phyre2

PDB 1j6u chain A

3D model

Region: 6 - 449
Aligned: 390
Modelled: 410
Confidence: 100.0%
Identity: 17%
PDB header:ligase
Chain: A: PDB Molecule:udp-n-acetylmuramate-alanine ligase murc;
PDBTitle: crystal structure of udp-n-acetylmuramate-alanine ligase2 murc (tm0231) from thermotoga maritima at 2.3 a resolution

Phyre2

PDB 2vos chain A

3D model

Region: 90 - 450
Aligned: 345
Modelled: 353
Confidence: 100.0%
Identity: 21%
PDB header:ligase
Chain: A: PDB Molecule:folylpolyglutamate synthase protein folc;
PDBTitle: mycobacterium tuberculosis folylpolyglutamate synthase2 complexed with adp

Phyre2

PDB 1gqq chain A

3D model

Region: 6 - 447
Aligned: 375
Modelled: 391
Confidence: 100.0%
Identity: 19%
PDB header:cell wall biosynthesis
Chain: A: PDB Molecule:udp-n-acetylmuramate-l-alanine ligase;
PDBTitle: murc - crystal structure of the apo-enzyme from haemophilus2 influenzae

Phyre2

PDB 1w78 chain A

3D model

Region: 80 - 449
Aligned: 338
Modelled: 365
Confidence: 100.0%
Identity: 18%
PDB header:synthase
Chain: A: PDB Molecule:folc bifunctional protein;
PDBTitle: e.coli folc in complex with dhpp and adp

Phyre2

PDB 2gc6 chain A

3D model

Region: 80 - 447
Aligned: 337
Modelled: 368
Confidence: 100.0%
Identity: 21%
PDB header:ligase
Chain: A: PDB Molecule:folylpolyglutamate synthase;
PDBTitle: s73a mutant of l. casei fpgs

Phyre2

PDB 1o5z chain A

3D model

Region: 81 - 448
Aligned: 335
Modelled: 364
Confidence: 100.0%
Identity: 21%
PDB header:ligase
Chain: A: PDB Molecule:folylpolyglutamate synthase/dihydrofolate synthase;
PDBTitle: crystal structure of folylpolyglutamate synthase (tm0166) from2 thermotoga maritima at 2.10 a resolution

Phyre2

PDB 3n2a chain A

3D model

Region: 88 - 446
Aligned: 327
Modelled: 345
Confidence: 100.0%
Identity: 17%
PDB header:ligase
Chain: A: PDB Molecule:bifunctional folylpolyglutamate synthase/dihydrofolate
PDBTitle: crystal structure of bifunctional folylpolyglutamate2 synthase/dihydrofolate synthase from yersinia pestis co92

Phyre2

PDB 3eag chain A

3D model

Region: 6 - 315
Aligned: 290
Modelled: 305
Confidence: 100.0%
Identity: 20%
PDB header:ligase
Chain: A: PDB Molecule:udp-n-acetylmuramate:l-alanyl-gamma-d-glutamyl-meso-
PDBTitle: the crystal structure of udp-n-acetylmuramate:l-alanyl-gamma-d-2 glutamyl-meso-diaminopimelate ligase (mpl) from neisseria3 meningitides

Phyre2

PDB 1gg4 chain A domain 4

3D model

Region: 99 - 312
Aligned: 206
Modelled: 206
Confidence: 100.0%
Identity: 90%
Fold: Ribokinase-like
Superfamily: MurD-like peptide ligases, catalytic domain
Family: MurCDEF

Phyre2

PDB 1e8c chain A domain 3

3D model

Region: 96 - 312
Aligned: 213
Modelled: 217
Confidence: 100.0%
Identity: 21%
Fold: Ribokinase-like
Superfamily: MurD-like peptide ligases, catalytic domain
Family: MurCDEF

Phyre2

PDB 1p3d chain A domain 3

3D model

Region: 88 - 311
Aligned: 211
Modelled: 217
Confidence: 100.0%
Identity: 23%
Fold: Ribokinase-like
Superfamily: MurD-like peptide ligases, catalytic domain
Family: MurCDEF

Phyre2

PDB 2jfg chain A domain 3

3D model

Region: 92 - 311
Aligned: 201
Modelled: 215
Confidence: 100.0%
Identity: 23%
Fold: Ribokinase-like
Superfamily: MurD-like peptide ligases, catalytic domain
Family: MurCDEF

Phyre2
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c1gg4A_
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c2am1A_
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c2wtzC_
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c1e8cB_
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c3lk7A_
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c2f00A_
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c3hn7A_
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c3uagA_
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c1j6uA_
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c2vosA_
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c1gqqA_
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c1w78A_
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c2gc6A_
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c1o5zA_
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c3n2aA_
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c3eagA_
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d1gg4a4
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d1e8ca3
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d1p3da3
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d2jfga3
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c1gg4A_
100.0 98 PDB header:ligase
Chain: A: PDB Molecule:udp-n-acetylmuramoylalanyl-d-glutamyl-2,6-
PDBTitle: crystal structure of escherichia coli udpmurnac-tripeptide2 d-alanyl-d-alanine-adding enzyme (murf) at 2.3 angstrom3 resolution
2c2am1A_
100.0 28 PDB header:ligase
Chain: A: PDB Molecule:udp-n-acetylmuramoylalanine-d-glutamyl-lysine-d-alanyl-d-
PDBTitle: sp protein ligand 1
3c2wtzC_
100.0 26 PDB header:ligase
Chain: C: PDB Molecule:udp-n-acetylmuramoyl-l-alanyl-d-glutamate-
PDBTitle: mure ligase of mycobacterium tuberculosis
4c1e8cB_
100.0 21 PDB header:ligase
Chain: B: PDB Molecule:udp-n-acetylmuramoylalanyl-d-glutamate--2,6-
PDBTitle: structure of mure the udp-n-acetylmuramyl tripeptide2 synthetase from e. coli
5c3lk7A_
100.0 21 PDB header:ligase
Chain: A: PDB Molecule:udp-n-acetylmuramoylalanine--d-glutamate ligase;
PDBTitle: the crystal structure of udp-n-acetylmuramoylalanine-d-2 glutamate (murd) ligase from streptococcus agalactiae to3 1.5a
6c2f00A_
100.0 18 PDB header:ligase
Chain: A: PDB Molecule:udp-n-acetylmuramate--l-alanine ligase;
PDBTitle: escherichia coli murc
7c3hn7A_
100.0 18 PDB header:ligase
Chain: A: PDB Molecule:udp-n-acetylmuramate-l-alanine ligase;
PDBTitle: crystal structure of a murein peptide ligase mpl (psyc_0032) from2 psychrobacter arcticus 273-4 at 1.65 a resolution
8c3uagA_
100.0 21 PDB header:ligase
Chain: A: PDB Molecule:protein (udp-n-acetylmuramoyl-l-alanine:d-
PDBTitle: udp-n-acetylmuramoyl-l-alanine:d-glutamate ligase
9c1j6uA_
100.0 17 PDB header:ligase
Chain: A: PDB Molecule:udp-n-acetylmuramate-alanine ligase murc;
PDBTitle: crystal structure of udp-n-acetylmuramate-alanine ligase2 murc (tm0231) from thermotoga maritima at 2.3 a resolution
10c2vosA_
100.0 21 PDB header:ligase
Chain: A: PDB Molecule:folylpolyglutamate synthase protein folc;
PDBTitle: mycobacterium tuberculosis folylpolyglutamate synthase2 complexed with adp
11c1gqqA_
100.0 19 PDB header:cell wall biosynthesis
Chain: A: PDB Molecule:udp-n-acetylmuramate-l-alanine ligase;
PDBTitle: murc - crystal structure of the apo-enzyme from haemophilus2 influenzae
12c1w78A_
100.0 18 PDB header:synthase
Chain: A: PDB Molecule:folc bifunctional protein;
PDBTitle: e.coli folc in complex with dhpp and adp
13c2gc6A_
100.0 21 PDB header:ligase
Chain: A: PDB Molecule:folylpolyglutamate synthase;
PDBTitle: s73a mutant of l. casei fpgs
14c1o5zA_
100.0 21 PDB header:ligase
Chain: A: PDB Molecule:folylpolyglutamate synthase/dihydrofolate synthase;
PDBTitle: crystal structure of folylpolyglutamate synthase (tm0166) from2 thermotoga maritima at 2.10 a resolution
15c3n2aA_
100.0 17 PDB header:ligase
Chain: A: PDB Molecule:bifunctional folylpolyglutamate synthase/dihydrofolate
PDBTitle: crystal structure of bifunctional folylpolyglutamate2 synthase/dihydrofolate synthase from yersinia pestis co92
16c3eagA_
100.0 20 PDB header:ligase
Chain: A: PDB Molecule:udp-n-acetylmuramate:l-alanyl-gamma-d-glutamyl-meso-
PDBTitle: the crystal structure of udp-n-acetylmuramate:l-alanyl-gamma-d-2 glutamyl-meso-diaminopimelate ligase (mpl) from neisseria3 meningitides
17d1gg4a4
100.0 90 Fold:Ribokinase-like
Superfamily:MurD-like peptide ligases, catalytic domain
Family:MurCDEF
18d1e8ca3
100.0 21 Fold:Ribokinase-like
Superfamily:MurD-like peptide ligases, catalytic domain
Family:MurCDEF
19d1p3da3
100.0 23 Fold:Ribokinase-like
Superfamily:MurD-like peptide ligases, catalytic domain
Family:MurCDEF
20d2jfga3
100.0 23 Fold:Ribokinase-like
Superfamily:MurD-like peptide ligases, catalytic domain
Family:MurCDEF
21d2gc6a2
not modelled 100.0 21 Fold:Ribokinase-like
Superfamily:MurD-like peptide ligases, catalytic domain
Family:Folylpolyglutamate synthetase
22d1j6ua3
not modelled 100.0 20 Fold:Ribokinase-like
Superfamily:MurD-like peptide ligases, catalytic domain
Family:MurCDEF
23d1o5za2
not modelled 100.0 22 Fold:Ribokinase-like
Superfamily:MurD-like peptide ligases, catalytic domain
Family:Folylpolyglutamate synthetase
24d1gg4a1
not modelled 100.0 97 Fold:MurD-like peptide ligases, peptide-binding domain
Superfamily:MurD-like peptide ligases, peptide-binding domain
Family:MurCDEF C-terminal domain
25d1gg4a3
not modelled 99.9 99 Fold:MurF and HprK N-domain-like
Superfamily:MurE/MurF N-terminal domain
Family:MurE/MurF N-terminal domain
26d2jfga2
not modelled 99.9 19 Fold:MurD-like peptide ligases, peptide-binding domain
Superfamily:MurD-like peptide ligases, peptide-binding domain
Family:MurCDEF C-terminal domain
27d1e8ca1
not modelled 99.8 24 Fold:MurF and HprK N-domain-like
Superfamily:MurE/MurF N-terminal domain
Family:MurE/MurF N-terminal domain
28d1e8ca2
not modelled 99.7 15 Fold:MurD-like peptide ligases, peptide-binding domain
Superfamily:MurD-like peptide ligases, peptide-binding domain
Family:MurCDEF C-terminal domain
29d1p3da2
not modelled 99.7 15 Fold:MurD-like peptide ligases, peptide-binding domain
Superfamily:MurD-like peptide ligases, peptide-binding domain
Family:MurCDEF C-terminal domain
30c3mvnA_
not modelled 99.7 17 PDB header:ligase
Chain: A: PDB Molecule:udp-n-acetylmuramate:l-alanyl-gamma-d-glutamayl-medo-
PDBTitle: crystal structure of a domain from a putative udp-n-acetylmuramate:l-2 alanyl-gamma-d-glutamayl-medo-diaminopimelate ligase from haemophilus3 ducreyi 35000hp
31d1j6ua2
not modelled 99.6 15 Fold:MurD-like peptide ligases, peptide-binding domain
Superfamily:MurD-like peptide ligases, peptide-binding domain
Family:MurCDEF C-terminal domain
32d1o5za1
not modelled 99.4 16 Fold:MurD-like peptide ligases, peptide-binding domain
Superfamily:MurD-like peptide ligases, peptide-binding domain
Family:Folylpolyglutamate synthetase, C-terminal domain
33d2gc6a1
not modelled 99.3 21 Fold:MurD-like peptide ligases, peptide-binding domain
Superfamily:MurD-like peptide ligases, peptide-binding domain
Family:Folylpolyglutamate synthetase, C-terminal domain
34c3pmoA_
not modelled 98.3 24 PDB header:transferase
Chain: A: PDB Molecule:udp-3-o-[3-hydroxymyristoyl] glucosamine n-acyltransferase;
PDBTitle: the structure of lpxd from pseudomonas aeruginosa at 1.3 a resolution
35c3eh0C_
not modelled 98.3 20 PDB header:transferase
Chain: C: PDB Molecule:udp-3-o-[3-hydroxymyristoyl] glucosamine n-
PDBTitle: crystal structure of lpxd from escherichia coli
36c2iu9C_
not modelled 96.9 24 PDB header:transferase
Chain: C: PDB Molecule:udp-3-o-[3-hydroxymyristoyl] glucosamine
PDBTitle: chlamydia trachomatis lpxd with 100mm udpglcnac (complex ii)
37d1a7ja_
not modelled 96.6 24 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Phosphoribulokinase/pantothenate kinase
38c3fmfA_
not modelled 96.1 28 PDB header:ligase
Chain: A: PDB Molecule:dethiobiotin synthetase;
PDBTitle: crystal structure of mycobacterium tuberculosis dethiobiotin2 synthetase complexed with 7,8 diaminopelargonic acid carbamate
39c3tqcB_
not modelled 95.6 18 PDB header:transferase
Chain: B: PDB Molecule:pantothenate kinase;
PDBTitle: structure of the pantothenate kinase (coaa) from coxiella burnetii
40c2og2A_
not modelled 95.5 17 PDB header:protein transport
Chain: A: PDB Molecule:putative signal recognition particle receptor;
PDBTitle: crystal structure of chloroplast ftsy from arabidopsis2 thaliana
41c3of5A_
not modelled 95.5 11 PDB header:ligase
Chain: A: PDB Molecule:dethiobiotin synthetase;
PDBTitle: crystal structure of a dethiobiotin synthetase from francisella2 tularensis subsp. tularensis schu s4
42c3b9qA_
not modelled 95.2 17 PDB header:protein transport
Chain: A: PDB Molecule:chloroplast srp receptor homolog, alpha subunit
PDBTitle: the crystal structure of cpftsy from arabidopsis thaliana
43d1sq5a_
not modelled 95.1 18 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Phosphoribulokinase/pantothenate kinase
44c2cnwF_
not modelled 95.1 16 PDB header:signal recognition
Chain: F: PDB Molecule:cell division protein ftsy;
PDBTitle: gdpalf4 complex of the srp gtpases ffh and ftsy
45c2qy9A_
not modelled 95.0 13 PDB header:protein transport
Chain: A: PDB Molecule:cell division protein ftsy;
PDBTitle: structure of the ng+1 construct of the e. coli srp receptor2 ftsy
46c2yhsA_
not modelled 95.0 13 PDB header:cell cycle
Chain: A: PDB Molecule:cell division protein ftsy;
PDBTitle: structure of the e. coli srp receptor ftsy
47d2g0ta1
not modelled 95.0 17 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Nitrogenase iron protein-like
48c2ozeA_
not modelled 94.9 18 PDB header:dna binding protein
Chain: A: PDB Molecule:orf delta';
PDBTitle: the crystal structure of delta protein of psm19035 from2 streptoccocus pyogenes
49d1byia_
not modelled 94.9 19 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Nitrogenase iron protein-like
50c3c8uA_
not modelled 94.9 35 PDB header:transferase
Chain: A: PDB Molecule:fructokinase;
PDBTitle: crystal structure of putative fructose transport system kinase2 (yp_612366.1) from silicibacter sp. tm1040 at 1.95 a resolution
51c3cioA_
not modelled 94.8 22 PDB header:signaling protein, transferase
Chain: A: PDB Molecule:tyrosine-protein kinase etk;
PDBTitle: the kinase domain of escherichia coli tyrosine kinase etk
52d1vmaa2
not modelled 94.7 19 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Nitrogenase iron protein-like
53c1zu4A_
not modelled 94.7 11 PDB header:protein transport
Chain: A: PDB Molecule:ftsy;
PDBTitle: crystal structure of ftsy from mycoplasma mycoides- space2 group p21212
54d2qy9a2
not modelled 94.4 20 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Nitrogenase iron protein-like
55d1okkd2
not modelled 94.3 21 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Nitrogenase iron protein-like
56c2bekB_
not modelled 94.2 29 PDB header:chromosome segregation
Chain: B: PDB Molecule:segregation protein;
PDBTitle: structure of the bacterial chromosome segregation protein2 soj
57c2qmoA_
not modelled 94.1 18 PDB header:ligase
Chain: A: PDB Molecule:dethiobiotin synthetase;
PDBTitle: crystal structure of dethiobiotin synthetase (biod) from helicobacter2 pylori
58c1hyqA_
not modelled 93.8 21 PDB header:cell cycle
Chain: A: PDB Molecule:cell division inhibitor (mind-1);
PDBTitle: mind bacterial cell division regulator from a. fulgidus
59d1hyqa_
not modelled 93.8 21 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Nitrogenase iron protein-like
60c2f1rA_
not modelled 93.8 27 PDB header:biosynthetic protein
Chain: A: PDB Molecule:molybdopterin-guanine dinucleotide biosynthesis
PDBTitle: crystal structure of molybdopterin-guanine biosynthesis2 protein b (mobb)
61d1rz3a_
not modelled 93.8 26 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Phosphoribulokinase/pantothenate kinase
62d2afhe1
not modelled 93.6 24 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Nitrogenase iron protein-like
63c2j37W_
not modelled 93.4 13 PDB header:ribosome
Chain: W: PDB Molecule:signal recognition particle 54 kda protein
PDBTitle: model of mammalian srp bound to 80s rncs
64c2vedA_
not modelled 93.3 12 PDB header:transferase
Chain: A: PDB Molecule:membrane protein capa1, protein tyrosine kinase;
PDBTitle: crystal structure of the chimerical mutant capabk55m2 protein
65c2gesA_
not modelled 93.1 19 PDB header:transferase
Chain: A: PDB Molecule:pantothenate kinase;
PDBTitle: pantothenate kinase from mycobacterium tuberculosis (mtpank) in2 complex with a coenzyme a derivative, form-i (rt)
66c2iy3A_
not modelled 93.1 14 PDB header:rna-binding
Chain: A: PDB Molecule:signal recognition particle protein ffh;
PDBTitle: structure of the e. coli signal recognition particle2 bound to a translating ribosome
67c3la6P_
not modelled 92.9 26 PDB header:transferase
Chain: P: PDB Molecule:tyrosine-protein kinase wzc;
PDBTitle: octameric kinase domain of the e. coli tyrosine kinase wzc with bound2 adp
68c1qzwC_
not modelled 92.8 13 PDB header:signaling protein/rna
Chain: C: PDB Molecule:signal recognition 54 kda protein;
PDBTitle: crystal structure of the complete core of archaeal srp and2 implications for inter-domain communication
69c2ph1A_
not modelled 92.8 19 PDB header:ligand binding protein
Chain: A: PDB Molecule:nucleotide-binding protein;
PDBTitle: crystal structure of nucleotide-binding protein af2382 from2 archaeoglobus fulgidus, northeast structural genomics target gr165
70d1nksa_
not modelled 92.8 27 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Nucleotide and nucleoside kinases
71c3endA_
not modelled 92.8 26 PDB header:oxidoreductase
Chain: A: PDB Molecule:light-independent protochlorophyllide reductase
PDBTitle: crystal structure of the l protein of rhodobacter2 sphaeroides light-independent protochlorophyllide3 reductase (bchl) with mgadp bound: a homologue of the4 nitrogenase fe protein
72c2xj9B_
not modelled 92.7 21 PDB header:replication
Chain: B: PDB Molecule:mipz;
PDBTitle: dimer structure of the bacterial cell division regulator mipz
73c1vmaA_
not modelled 92.6 15 PDB header:protein transport
Chain: A: PDB Molecule:cell division protein ftsy;
PDBTitle: crystal structure of cell division protein ftsy (tm0570) from2 thermotoga maritima at 1.60 a resolution
74c3dmdA_
not modelled 92.4 18 PDB header:transport protein
Chain: A: PDB Molecule:signal recognition particle receptor;
PDBTitle: structures and conformations in solution of the signal recognition2 particle receptor from the archaeon pyrococcus furiosus
75d1cp2a_
not modelled 92.4 27 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Nitrogenase iron protein-like
76d1iona_
not modelled 92.3 24 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Nitrogenase iron protein-like
77c2j7pA_
not modelled 92.2 14 PDB header:signal recognition
Chain: A: PDB Molecule:signal recognition particle protein;
PDBTitle: gmppnp-stabilized ng domain complex of the srp gtpases ffh2 and ftsy
78c2v3cC_
not modelled 91.9 14 PDB header:signaling protein
Chain: C: PDB Molecule:signal recognition 54 kda protein;
PDBTitle: crystal structure of the srp54-srp19-7s.s srp rna complex2 of m. jannaschii
79d1np6a_
not modelled 91.8 21 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Nitrogenase iron protein-like
80d1deka_
not modelled 91.7 24 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Nucleotide and nucleoside kinases
81d2ioja1
not modelled 91.7 18 Fold:MurF and HprK N-domain-like
Superfamily:HprK N-terminal domain-like
Family:DRTGG domain
82d1g3qa_
not modelled 91.7 27 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Nitrogenase iron protein-like
83c2wwiC_
not modelled 91.5 14 PDB header:transferase
Chain: C: PDB Molecule:thymidilate kinase, putative;
PDBTitle: plasmodium falciparum thymidylate kinase in complex with2 aztmp and adp
84c3k9gA_
not modelled 91.3 21 PDB header:biosynthetic protein
Chain: A: PDB Molecule:pf-32 protein;
PDBTitle: crystal structure of a plasmid partition protein from borrelia2 burgdorferi at 2.25a resolution, iodide soak
85c3lv8A_
not modelled 91.3 24 PDB header:transferase
Chain: A: PDB Molecule:thymidylate kinase;
PDBTitle: 1.8 angstrom resolution crystal structure of a thymidylate kinase2 (tmk) from vibrio cholerae o1 biovar eltor str. n16961 in complex3 with tmp, thymidine-5'-diphosphate and adp
86c3dm5A_
not modelled 91.3 13 PDB header:rna binding protein, transport protein
Chain: A: PDB Molecule:signal recognition 54 kda protein;
PDBTitle: structures of srp54 and srp19, the two proteins assembling2 the ribonucleic core of the signal recognition particle3 from the archaeon pyrococcus furiosus.
87c3zq6D_
not modelled 91.1 21 PDB header:hydrolase
Chain: D: PDB Molecule:putative arsenical pump-driving atpase;
PDBTitle: adp-alf4 complex of m. therm. trc40
88d1uj2a_
not modelled 91.1 28 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Phosphoribulokinase/pantothenate kinase
89d1qzxa3
not modelled 90.9 21 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Nitrogenase iron protein-like
90c3ibgF_
not modelled 90.5 20 PDB header:hydrolase
Chain: F: PDB Molecule:atpase, subunit of the get complex;
PDBTitle: crystal structure of aspergillus fumigatus get3 with bound2 adp
91c2w0sB_
not modelled 90.5 14 PDB header:transferase
Chain: B: PDB Molecule:thymidylate kinase;
PDBTitle: crystal structure of vaccinia virus thymidylate kinase2 bound to brivudin-5'-monophosphate
92c3q9lB_
not modelled 90.3 33 PDB header:cell cycle, hydrolase
Chain: B: PDB Molecule:septum site-determining protein mind;
PDBTitle: the structure of the dimeric e.coli mind-atp complex
93c2plrB_
not modelled 90.2 20 PDB header:transferase
Chain: B: PDB Molecule:probable thymidylate kinase;
PDBTitle: crystal structure of dtmp kinase (st1543) from sulfolobus tokodaii2 strain7
94c2z0hA_
not modelled 90.1 21 PDB header:transferase
Chain: A: PDB Molecule:thymidylate kinase;
PDBTitle: crystal structure of thymidylate kinase in complex with dtdp2 and adp from thermotoga maritima
95c2gksB_
not modelled 89.7 25 PDB header:transferase
Chain: B: PDB Molecule:bifunctional sat/aps kinase;
PDBTitle: crystal structure of the bi-functional atp sulfurylase-aps kinase from2 aquifex aeolicus, a chemolithotrophic thermophile
96c3asyB_
not modelled 89.7 33 PDB header:transferase
Chain: B: PDB Molecule:uridine kinase;
PDBTitle: ligand-free structure of uridine kinase from thermus thermophilus hb8
97d1khta_
not modelled 89.4 28 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Nucleotide and nucleoside kinases
98c3fkqA_
not modelled 89.3 19 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:ntrc-like two-domain protein;
PDBTitle: crystal structure of ntrc-like two-domain protein (rer070207001320)2 from eubacterium rectale at 2.10 a resolution
99c2grjH_
not modelled 89.1 28 PDB header:transferase
Chain: H: PDB Molecule:dephospho-coa kinase;
PDBTitle: crystal structure of dephospho-coa kinase (ec 2.7.1.24)2 (dephosphocoenzyme a kinase) (tm1387) from thermotoga maritima at3 2.60 a resolution
100d1nn5a_
not modelled 89.1 19 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Nucleotide and nucleoside kinases
101d1odfa_
not modelled 89.0 14 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Phosphoribulokinase/pantothenate kinase
102d1ckea_
not modelled 88.9 35 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Nucleotide and nucleoside kinases
103d1ki9a_
not modelled 88.5 26 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Nucleotide and nucleoside kinases
104c1ueiB_
not modelled 88.5 29 PDB header:transferase
Chain: B: PDB Molecule:uridine-cytidine kinase 2;
PDBTitle: crystal structure of human uridine-cytidine kinase 22 complexed with a feedback-inhibitor, utp
105c3ch4B_
not modelled 88.5 25 PDB header:transferase
Chain: B: PDB Molecule:phosphomevalonate kinase;
PDBTitle: the crystal structure of human phosphomavelonate kinase at2 1.8 a resolution
106c2wooC_
not modelled 88.5 19 PDB header:hydrolase
Chain: C: PDB Molecule:atpase get3;
PDBTitle: nucleotide-free form of s. pombe get3
107d1ls1a2
not modelled 88.4 18 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Nitrogenase iron protein-like
108c1m8pB_
not modelled 88.2 21 PDB header:transferase
Chain: B: PDB Molecule:sulfate adenylyltransferase;
PDBTitle: crystal structure of p. chrysogenum atp sulfurylase in the t-state
109c3akcA_
not modelled 88.2 50 PDB header:transferase
Chain: A: PDB Molecule:cytidylate kinase;
PDBTitle: crystal structure of cmp kinase in complex with cdp and adp from2 thermus thermophilus hb8
110c2f6rA_
not modelled 87.9 40 PDB header:transferase
Chain: A: PDB Molecule:bifunctional coenzyme a synthase;
PDBTitle: crystal structure of bifunctional coenzyme a synthase (coa synthase):2 (18044849) from mus musculus at 1.70 a resolution
111c3ug7D_
not modelled 87.7 21 PDB header:hydrolase
Chain: D: PDB Molecule:arsenical pump-driving atpase;
PDBTitle: crystal structure of get3 from methanocaldococcus jannaschii
112d1tmka_
not modelled 87.4 19 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Nucleotide and nucleoside kinases
113d1m8pa3
not modelled 87.4 29 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:ATP sulfurylase C-terminal domain
114d4tmka_
not modelled 87.3 22 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Nucleotide and nucleoside kinases
115d1xjca_
not modelled 87.1 32 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Nitrogenase iron protein-like
116c3ea0B_
not modelled 86.9 19 PDB header:hydrolase
Chain: B: PDB Molecule:atpase, para family;
PDBTitle: crystal structure of para family atpase from chlorobium tepidum tls
117d1x6va3
not modelled 86.8 34 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Adenosine-5'phosphosulfate kinase (APS kinase)
118c3hdtB_
not modelled 86.6 24 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:putative kinase;
PDBTitle: crystal structure of putative kinase from clostridium symbiosum atcc2 14940
119d1qf9a_
not modelled 86.4 22 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Nucleotide and nucleoside kinases
120c3io3A_
not modelled 86.1 20 PDB header:chaperone
Chain: A: PDB Molecule:deha2d07832p;
PDBTitle: get3 with adp from d. hansenii in closed form

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