Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP76577
DateThu Jan 5 12:24:46 GMT 2012
Unique Job IDb636f3932749a5f4

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c3dwkC_
Top template information
PDB header:transferase
Chain: C: PDB Molecule:penicillin-binding protein 2;
PDBTitle: identification of dynamic structural motifs involved in2 peptidoglycan glycosyltransfer
Confidence and coverage
Confidence:100.0% Coverage: 72%
558 residues ( 72% 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.
651 residues ( 85%) 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  MPRLLTKRGCWITLAAAPFLLFLAAWGADKLWPLPLHEVNPARVVVAQDGTPLWRFADAD
Secondary structure 
SS confidence 
Disorder  ???
????????
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  GIWRYPVTIEDVSPRYLEALINYEDRWFWKHPGVNPFSVARAAWQDLTSGRVISGGSTLT
Secondary structure 
SS confidence 
Disorder 
????????
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  MQVARLLDPHPKTFGGKIRQLWRALQLEWHLSKREILTLYLNRAPFGGTLQGIGAASWAY
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  LGKSPANLSYSEAAMLAVLPQAPSRLRPDRWPERAEAARNKVLERMAVQGVWSREQVKES
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  REEPIWLAPRQMPQLAPLFSRMMLGKSKSDKITTTLDAGLQRRLEELAQNWKGRLPPRSS
Secondary structure 
SS confidence 
Disorder 
??
?????????
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  LAMIVVDHTDMRVRGWVGSVDLNDDSRFGHVDMVNSIRSPGSVLKPFVYGLALDEGLIHP
Secondary structure 
SS confidence 
Disorder 
????
?
?
?
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  ASLLQDVPRRTGDYRPGNFDSGFHGPISMSEALVRSLNLPAVQVLEAYGPKRFAAKLRNV
Secondary structure 
SS confidence 
Disorder  ?
?
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  GLPLYLPNGAAPNLSLILGGAGAKLEDMAAAYTAFARHGKAGKLRLQPDDPLLERPLMSS
Secondary structure 
SS confidence 
Disorder 
?
???????
?
Disorder confidence 
 
   .........490.........500.........510.........520.........530.........540
Sequence  GAAWIIRRIMADEAQPLPDSALPRVAPLAWKTGTSYGYRDAWAIGVNARYVIGIWTGRPD
Secondary structure 
SS confidence 
Disorder 
?
??
Disorder confidence 
 
   .........550.........560.........570.........580.........590.........600
Sequence  GTPVVGQFGFASAVPLLNQVNNILLSRSANLPEDPRPNSVTRGVICWPGGQSLPEGDGNC
Secondary structure 
SS confidence 
Disorder 
?
????
?
??????????
?
???????
Disorder confidence 
 
   .........610.........620.........630.........640.........650.........660
Sequence  RRRLATWLLDGSQPPTLLLPEQEGINGIRFPIWLDENGKRVAADCPQARQEMINVWPLPL
Secondary structure 
SS confidence 
Disorder  ?
?
????
?
????
?
?
Disorder confidence 
 
   .........670.........680.........690.........700.........710.........720
Sequence  EPWLPASERRAVRLPPASTSCPPYGHDAQLPLQLTGVRDGAIIKRLPGAAEATLPLQSSG
Secondary structure 
SS confidence 
Disorder  ???
??????????
?
??????????????
?
???
Disorder confidence 
 
   .........730.........740.........750.........760.........770
Sequence  GAGERWWFLNGEPLTERGRNVTLHLTDKGDYQLLVMDDVGQIATVKFVMQ
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 3dwk chain C

3D model

Region: 38 - 605
Aligned: 558
Modelled: 568
Confidence: 100.0%
Identity: 23%
PDB header:transferase
Chain: C: PDB Molecule:penicillin-binding protein 2;
PDBTitle: identification of dynamic structural motifs involved in2 peptidoglycan glycosyltransfer

Phyre2

PDB 3fwl chain A

3D model

Region: 49 - 619
Aligned: 528
Modelled: 550
Confidence: 100.0%
Identity: 25%
PDB header:transferase, hydrolase
Chain: A: PDB Molecule:penicillin-binding protein 1b;
PDBTitle: crystal structure of the full-length transglycosylase pbp1b2 from escherichia coli

Phyre2

PDB 2olv chain A

3D model

Region: 38 - 605
Aligned: 549
Modelled: 562
Confidence: 100.0%
Identity: 22%
PDB header:transferase
Chain: A: PDB Molecule:penicillin-binding protein 2;
PDBTitle: structural insight into the transglycosylation step of bacterial cell2 wall biosynthesis : donor ligand complex

Phyre2

PDB 3udi chain A

3D model

Region: 41 - 578
Aligned: 465
Modelled: 479
Confidence: 100.0%
Identity: 30%
PDB header:penicillin-binding protein/antibiotic
Chain: A: PDB Molecule:penicillin-binding protein 1a;
PDBTitle: crystal structure of acinetobacter baumannii pbp1a in complex with2 penicillin g

Phyre2

PDB 2jci chain A

3D model

Region: 185 - 619
Aligned: 404
Modelled: 422
Confidence: 100.0%
Identity: 19%
PDB header:drug-binding protein
Chain: A: PDB Molecule:penicillin-binding protein 1b;
PDBTitle: structural insights into the catalytic mechanism and the2 role of streptococcus pneumoniae pbp1b

Phyre2

PDB 2bg1 chain A

3D model

Region: 206 - 619
Aligned: 396
Modelled: 414
Confidence: 100.0%
Identity: 19%
PDB header:peptidoglycan
Chain: A: PDB Molecule:penicillin-binding protein 1b;
PDBTitle: active site restructuring regulates ligand recognition in2 classa penicillin-binding proteins (pbps)

Phyre2

PDB 2bg1 chain A domain 1

3D model

Region: 213 - 621
Aligned: 385
Modelled: 409
Confidence: 100.0%
Identity: 19%
Fold: beta-lactamase/transpeptidase-like
Superfamily: beta-lactamase/transpeptidase-like
Family: beta-Lactamase/D-ala carboxypeptidase

Phyre2

PDB 2wad chain B

3D model

Region: 35 - 569
Aligned: 510
Modelled: 533
Confidence: 100.0%
Identity: 14%
PDB header:peptide binding protein
Chain: B: PDB Molecule:penicillin-binding protein 2b;
PDBTitle: penicillin-binding protein 2b (pbp-2b) from streptococcus2 pneumoniae (strain 5204)

Phyre2

PDB 2c5w chain B domain 1

3D model

Region: 251 - 582
Aligned: 331
Modelled: 332
Confidence: 100.0%
Identity: 24%
Fold: beta-lactamase/transpeptidase-like
Superfamily: beta-lactamase/transpeptidase-like
Family: beta-Lactamase/D-ala carboxypeptidase

Phyre2

PDB 2olu chain A domain 2

3D model

Region: 255 - 605
Aligned: 343
Modelled: 351
Confidence: 100.0%
Identity: 21%
Fold: beta-lactamase/transpeptidase-like
Superfamily: beta-lactamase/transpeptidase-like
Family: beta-Lactamase/D-ala carboxypeptidase

Phyre2

PDB 1pmd chain A

3D model

Region: 45 - 579
Aligned: 463
Modelled: 463
Confidence: 100.0%
Identity: 15%
PDB header:peptidoglycan synthesis
Chain: A: PDB Molecule:peptidoglycan synthesis multifunctional enzyme;
PDBTitle: penicillin-binding protein 2x (pbp-2x)

Phyre2

PDB 3pbq chain A

3D model

Region: 39 - 576
Aligned: 436
Modelled: 462
Confidence: 100.0%
Identity: 18%
PDB header:hydrolase/antibiotic
Chain: A: PDB Molecule:penicillin-binding protein 3;
PDBTitle: crystal structure of pbp3 complexed with imipenem

Phyre2

PDB 3lo7 chain A

3D model

Region: 268 - 566
Aligned: 289
Modelled: 299
Confidence: 100.0%
Identity: 20%
PDB header:transferase
Chain: A: PDB Molecule:penicillin-binding protein a;
PDBTitle: crystal structure of pbpa from mycobacterium tuberculosis

Phyre2

PDB 3equ chain B

3D model

Region: 267 - 575
Aligned: 303
Modelled: 309
Confidence: 100.0%
Identity: 20%
PDB header:biosynthetic protein
Chain: B: PDB Molecule:penicillin-binding protein 2;
PDBTitle: crystal structure of penicillin-binding protein 2 from neisseria2 gonorrhoeae

Phyre2

PDB 3ue3 chain A

3D model

Region: 268 - 575
Aligned: 302
Modelled: 304
Confidence: 100.0%
Identity: 21%
PDB header:transferase
Chain: A: PDB Molecule:septum formation, penicillin binding protein 3,
PDBTitle: crystal structure of acinetobacter baumanni pbp3

Phyre2

PDB 3oc2 chain A

3D model

Region: 268 - 573
Aligned: 295
Modelled: 306
Confidence: 100.0%
Identity: 20%
PDB header:penicillin-binding protein
Chain: A: PDB Molecule:penicillin-binding protein 3;
PDBTitle: crystal structure of penicillin-binding protein 3 from pseudomonas2 aeruginosa

Phyre2

PDB 2olu chain A domain 1

3D model

Region: 38 - 253
Aligned: 198
Modelled: 216
Confidence: 100.0%
Identity: 25%
Fold: Lysozyme-like
Superfamily: Lysozyme-like
Family: PBP transglycosylase domain-like

Phyre2

PDB 1qmf chain A

3D model

Region: 268 - 566
Aligned: 291
Modelled: 299
Confidence: 100.0%
Identity: 16%
PDB header:peptidoglycan synthesis
Chain: A: PDB Molecule:penicillin-binding protein 2x;
PDBTitle: penicillin-binding protein 2x (pbp-2x) acyl-enzyme complex

Phyre2

PDB 3hzs chain A

3D model

Region: 45 - 243
Aligned: 198
Modelled: 199
Confidence: 100.0%
Identity: 23%
PDB header:transferase
Chain: A: PDB Molecule:monofunctional glycosyltransferase;
PDBTitle: s. aureus monofunctional glycosyltransferase (mtga)in complex with2 moenomycin

Phyre2

PDB 1pyy chain A domain 4

3D model

Region: 275 - 580
Aligned: 302
Modelled: 304
Confidence: 100.0%
Identity: 16%
Fold: beta-lactamase/transpeptidase-like
Superfamily: beta-lactamase/transpeptidase-like
Family: beta-Lactamase/D-ala carboxypeptidase

Phyre2

PDB 3pe9 chain D

3D model

Region: 692 - 770
Aligned: 74
Modelled: 74
Confidence: 97.7%
Identity: 15%
PDB header:unknown function
Chain: D: PDB Molecule:fibronectin(iii)-like module;
PDBTitle: structures of clostridium thermocellum cbha fibronectin(iii)-like2 modules

Phyre2

PDB 3pe9 chain B

3D model

Region: 692 - 770
Aligned: 74
Modelled: 74
Confidence: 97.2%
Identity: 15%
PDB header:unknown function
Chain: B: PDB Molecule:fibronectin(iii)-like module;
PDBTitle: structures of clostridium thermocellum cbha fibronectin(iii)-like2 modules

Phyre2

PDB 2e7c chain A

3D model

Region: 675 - 769
Aligned: 95
Modelled: 95
Confidence: 67.2%
Identity: 18%
PDB header:structural protein
Chain: A: PDB Molecule:myosin-binding protein c, fast-type;
PDBTitle: solution structure of the 6th ig-like domain from human2 myosin-binding protein c, fast-type

Phyre2
1
c3dwkC_
2
c3fwlA_
3
c2olvA_
4
c3udiA_
5
c2jciA_
6
c2bg1A_
7
d2bg1a1
8
c2wadB_
9
d2c5wb1
10
d2olua2
11
c1pmdA_
12
c3pbqA_
13
c3lo7A_
14
c3equB_
15
c3ue3A_
16
c3oc2A_
17
d2olua1
18
c1qmfA_
19
c3hzsA_
20
d1pyya4
21
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24
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c3pe9D_
86
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c3pe9B_
91
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c2e7cA_
129
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3dwkC_
100.0 23 PDB header:transferase
Chain: C: PDB Molecule:penicillin-binding protein 2;
PDBTitle: identification of dynamic structural motifs involved in2 peptidoglycan glycosyltransfer
2c3fwlA_
100.0 25 PDB header:transferase, hydrolase
Chain: A: PDB Molecule:penicillin-binding protein 1b;
PDBTitle: crystal structure of the full-length transglycosylase pbp1b2 from escherichia coli
3c2olvA_
100.0 22 PDB header:transferase
Chain: A: PDB Molecule:penicillin-binding protein 2;
PDBTitle: structural insight into the transglycosylation step of bacterial cell2 wall biosynthesis : donor ligand complex
4c3udiA_
100.0 30 PDB header:penicillin-binding protein/antibiotic
Chain: A: PDB Molecule:penicillin-binding protein 1a;
PDBTitle: crystal structure of acinetobacter baumannii pbp1a in complex with2 penicillin g
5c2jciA_
100.0 19 PDB header:drug-binding protein
Chain: A: PDB Molecule:penicillin-binding protein 1b;
PDBTitle: structural insights into the catalytic mechanism and the2 role of streptococcus pneumoniae pbp1b
6c2bg1A_
100.0 19 PDB header:peptidoglycan
Chain: A: PDB Molecule:penicillin-binding protein 1b;
PDBTitle: active site restructuring regulates ligand recognition in2 classa penicillin-binding proteins (pbps)
7d2bg1a1
100.0 19 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
8c2wadB_
100.0 14 PDB header:peptide binding protein
Chain: B: PDB Molecule:penicillin-binding protein 2b;
PDBTitle: penicillin-binding protein 2b (pbp-2b) from streptococcus2 pneumoniae (strain 5204)
9d2c5wb1
100.0 24 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
10d2olua2
100.0 21 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
11c1pmdA_
100.0 15 PDB header:peptidoglycan synthesis
Chain: A: PDB Molecule:peptidoglycan synthesis multifunctional enzyme;
PDBTitle: penicillin-binding protein 2x (pbp-2x)
12c3pbqA_
100.0 18 PDB header:hydrolase/antibiotic
Chain: A: PDB Molecule:penicillin-binding protein 3;
PDBTitle: crystal structure of pbp3 complexed with imipenem
13c3lo7A_
100.0 20 PDB header:transferase
Chain: A: PDB Molecule:penicillin-binding protein a;
PDBTitle: crystal structure of pbpa from mycobacterium tuberculosis
14c3equB_
100.0 20 PDB header:biosynthetic protein
Chain: B: PDB Molecule:penicillin-binding protein 2;
PDBTitle: crystal structure of penicillin-binding protein 2 from neisseria2 gonorrhoeae
15c3ue3A_
100.0 21 PDB header:transferase
Chain: A: PDB Molecule:septum formation, penicillin binding protein 3,
PDBTitle: crystal structure of acinetobacter baumanni pbp3
16c3oc2A_
100.0 20 PDB header:penicillin-binding protein
Chain: A: PDB Molecule:penicillin-binding protein 3;
PDBTitle: crystal structure of penicillin-binding protein 3 from pseudomonas2 aeruginosa
17d2olua1
100.0 25 Fold:Lysozyme-like
Superfamily:Lysozyme-like
Family:PBP transglycosylase domain-like
18c1qmfA_
100.0 16 PDB header:peptidoglycan synthesis
Chain: A: PDB Molecule:penicillin-binding protein 2x;
PDBTitle: penicillin-binding protein 2x (pbp-2x) acyl-enzyme complex
19c3hzsA_
100.0 23 PDB header:transferase
Chain: A: PDB Molecule:monofunctional glycosyltransferase;
PDBTitle: s. aureus monofunctional glycosyltransferase (mtga)in complex with2 moenomycin
20d1pyya4
100.0 16 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
21d1rp5a4
not modelled 100.0 17 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
22d2oqoa1
not modelled 100.0 38 Fold:Lysozyme-like
Superfamily:Lysozyme-like
Family:PBP transglycosylase domain-like
23d1vqqa3
not modelled 100.0 15 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
24c1mwuA_
not modelled 100.0 15 PDB header:biosynthetic protein
Chain: A: PDB Molecule:penicillin-binding protein 2a;
PDBTitle: structure of methicillin acyl-penicillin binding protein 2a2 from methicillin resistant staphylococcus aureus strain3 27r at 2.60 a resolution.
25d1k25a4
not modelled 100.0 18 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
26c2iwdA_
not modelled 100.0 12 PDB header:antibiotic resistance
Chain: A: PDB Molecule:methicillin resistance mecr1 protein;
PDBTitle: oxacilloyl-acylated mecr1 extracellular antibiotic-sensor2 domain.
27d1k38a_
not modelled 100.0 16 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
28d1m6ka_
not modelled 100.0 13 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
29c3if6C_
not modelled 100.0 15 PDB header:hydrolase
Chain: C: PDB Molecule:oxa-46 oxacillinase;
PDBTitle: crystal structure of oxa-46 beta-lactamase from p.2 aeruginosa
30d1k55a_
not modelled 100.0 16 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
31c2jc7A_
not modelled 100.0 12 PDB header:hydrolase
Chain: A: PDB Molecule:beta-lactamase oxa-24;
PDBTitle: the crystal structure of the carbapenemase oxa-24 reveals2 new insights into the mechanism of carbapenem-hydrolysis
32d1nrfa_
not modelled 100.0 15 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
33d1xa1a_
not modelled 100.0 14 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
34c3hbrD_
not modelled 100.0 17 PDB header:hydrolase
Chain: D: PDB Molecule:oxa-48;
PDBTitle: crystal structure of oxa-48 beta-lactamase
35c2wuqB_
not modelled 99.9 16 PDB header:transcription
Chain: B: PDB Molecule:beta-lactamase regulatory protein blab;
PDBTitle: crystal structure of blab protein from streptomyces cacaoi
36c2qpnA_
not modelled 99.9 19 PDB header:hydrolase
Chain: A: PDB Molecule:beta-lactamase ges-1;
PDBTitle: ges-1 beta-lactamase
37d1g6aa_
not modelled 99.9 18 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
38d1dy6a_
not modelled 99.9 15 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
39c2xftA_
not modelled 99.9 11 PDB header:hydrolase
Chain: A: PDB Molecule:orf12;
PDBTitle: structural and mechanistic studies on a cephalosporin esterase from2 the clavulanic acid biosynthesis pathway
40c2wuqA_
not modelled 99.9 15 PDB header:transcription
Chain: A: PDB Molecule:beta-lactamase regulatory protein blab;
PDBTitle: crystal structure of blab protein from streptomyces cacaoi
41d2cc1a1
not modelled 99.9 20 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
42d1iysa_
not modelled 99.9 19 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
43c2j7vA_
not modelled 99.8 20 PDB header:hydrolase
Chain: A: PDB Molecule:tll2115 protein;
PDBTitle: structure of pbp-a
44c2ov5A_
not modelled 99.8 18 PDB header:hydrolase
Chain: A: PDB Molecule:carbapenemase;
PDBTitle: crystal structure of the kpc-2 carbapenemase
45d1e25a_
not modelled 99.8 15 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
46d1buea_
not modelled 99.8 16 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
47c3dw0B_
not modelled 99.8 19 PDB header:hydrolase
Chain: B: PDB Molecule:class a carbapenemase kpc-2;
PDBTitle: crystal structure of the class a carbapenemase kpc-2 at 1.62 angstrom resolution
48c3lezA_
not modelled 99.8 20 PDB header:hydrolase
Chain: A: PDB Molecule:beta-lactamase;
PDBTitle: crystal structure of a halotolerant bacterial beta-lactamase
49d1bsga_
not modelled 99.8 16 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
50d1o7ea_
not modelled 99.8 16 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
51d1m40a_
not modelled 99.8 19 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
52d1djaa_
not modelled 99.8 12 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
53d1n9ba_
not modelled 99.8 21 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
54c2v20A_
not modelled 99.7 18 PDB header:hydrolase
Chain: A: PDB Molecule:beta-lactamase tem;
PDBTitle: structure of a tem-1 beta-lactamase insertant2 allosterically regulated by kanamycin and anions. complex3 with sulfate.
55d1hzoa_
not modelled 99.7 17 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
56c1w7fB_
not modelled 99.7 17 PDB header:hydrolase
Chain: B: PDB Molecule:beta-lactamase;
PDBTitle: crystal structure of the class a beta-lactamase bs32 inhibited with isocitrate
57c3qhyA_
not modelled 99.7 19 PDB header:hydrolase/hydrolase inhibitor
Chain: A: PDB Molecule:beta-lactamase;
PDBTitle: structural, thermodynamic and kinetic analysis of the picomolar2 binding affinity interaction of the beta-lactamase inhibitor protein-3 ii (blip-ii) with class a beta-lactamases
58d1alqa_
not modelled 99.6 13 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
59c3cg5A_
not modelled 99.6 20 PDB header:hydrolase
Chain: A: PDB Molecule:beta-lactamase;
PDBTitle: crystal structure of the covalent adduct formed between tb2 b-lactamase and clavulanate
60d1i2sa_
not modelled 99.6 17 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
61c1i2sA_
not modelled 99.6 17 PDB header:hydrolase
Chain: A: PDB Molecule:beta-lactamase;
PDBTitle: beta-lactamase from bacillus licheniformis bs3
62c3p09B_
not modelled 99.6 14 PDB header:hydrolase
Chain: B: PDB Molecule:beta-lactamase;
PDBTitle: crystal structure of beta-lactamase from francisella tularensis
63c3cjmA_
not modelled 99.4 14 PDB header:hydrolase
Chain: A: PDB Molecule:putative beta-lactamase;
PDBTitle: crystal structure of putative beta-lactamase (np_815223.1) from2 enterococcus faecalis v583 at 1.50 a resolution
64c3p09A_
not modelled 99.4 14 PDB header:hydrolase
Chain: A: PDB Molecule:beta-lactamase;
PDBTitle: crystal structure of beta-lactamase from francisella tularensis
65d3beca2
not modelled 98.8 16 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
66d1xp4a2
not modelled 98.8 15 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
67d1w79a1
not modelled 98.6 21 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:Dac-like
68d1es5a_
not modelled 98.6 13 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
69c2bcfA_
not modelled 98.4 18 PDB header:hydrolase
Chain: A: PDB Molecule:probable d-alanyl-d-alanine carboxypeptidase
PDBTitle: crystal structure of a evolved putative penicillin-binding2 protein homolog, rv2911, from mycobacterium tuberculosis.
70c1xp4C_
not modelled 98.3 14 PDB header:hydrolase
Chain: C: PDB Molecule:d-alanyl-d-alanine carboxypeptidase;
PDBTitle: crystal structure of a peptidoglycan synthesis regulatory2 factor (pbp3) from streptococcus pneumoniae
71d1tvfa2
not modelled 98.3 11 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
72c1z6fA_
not modelled 98.3 18 PDB header:hydrolase
Chain: A: PDB Molecule:penicillin-binding protein 5;
PDBTitle: crystal structure of penicillin-binding protein 5 from e. coli in2 complex with a boronic acid inhibitor
73d2ex2a1
not modelled 98.2 22 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:Dac-like
74d1w5da1
not modelled 98.2 24 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:Dac-like
75c2pbyB_
not modelled 98.1 22 PDB header:hydrolase
Chain: B: PDB Molecule:glutaminase;
PDBTitle: probable glutaminase from geobacillus kaustophilus hta426
76c3uo9B_
not modelled 98.1 15 PDB header:hydrolase/hydrolase inhibitor
Chain: B: PDB Molecule:glutaminase kidney isoform, mitochondrial;
PDBTitle: crystal structure of human gac in complex with glutamate and bptes
77c3czdA_
not modelled 98.1 16 PDB header:hydrolase
Chain: A: PDB Molecule:glutaminase kidney isoform;
PDBTitle: crystal structure of human glutaminase in complex with l-glutamate
78c2dfwA_
not modelled 98.0 16 PDB header:hydrolase
Chain: A: PDB Molecule:salt-tolerant glutaminase;
PDBTitle: crystal structure of a major fragment of the salt-tolerant2 glutaminase from micrococcus luteus k-3
79c3ih9A_
not modelled 98.0 18 PDB header:hydrolase
Chain: A: PDB Molecule:salt-tolerant glutaminase;
PDBTitle: crystal structure analysis of mglu in its tris form
80d1u60a_
not modelled 98.0 17 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:Glutaminase
81c3ss4C_
not modelled 97.9 16 PDB header:hydrolase
Chain: C: PDB Molecule:glutaminase c;
PDBTitle: crystal structure of mouse glutaminase c, phosphate-bound form
82c3a3jA_
not modelled 97.8 19 PDB header:hydrolase
Chain: A: PDB Molecule:pbp5;
PDBTitle: crystal structures of penicillin binding protein 5 from2 haemophilus influenzae
83c3it9B_
not modelled 97.8 17 PDB header:hydrolase
Chain: B: PDB Molecule:d-alanyl-d-alanine carboxypeptidase dacc;
PDBTitle: crystal structure of penicillin-binding protein 6 (pbp6)2 from e. coli in apo state
84d1mkia_
not modelled 97.7 17 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:Glutaminase
85c3pe9D_
97.7 15 PDB header:unknown function
Chain: D: PDB Molecule:fibronectin(iii)-like module;
PDBTitle: structures of clostridium thermocellum cbha fibronectin(iii)-like2 modules
86c3humB_
not modelled 97.6 13 PDB header:hydrolase/antibiotics
Chain: B: PDB Molecule:penicillin-binding protein 4;
PDBTitle: crystal structure of penicillin binding protein 4 from2 staphylococcus aureus col in complex with cefotaxime
87c3mfdB_
not modelled 97.6 22 PDB header:hydrolase
Chain: B: PDB Molecule:d-alanyl-d-alanine carboxypeptidase dacb;
PDBTitle: the structure of the beta-lactamase superfamily domain of d-alanyl-d-2 alanine carboxypeptidase from bacillus subtilis
88c1tvfA_
not modelled 97.5 12 PDB header:penicillin binding
Chain: A: PDB Molecule:penicillin binding protein 4;
PDBTitle: crystal structure of penicillin-binding protein 4 (pbp4)2 from staphylococcus aureus
89c1zkjA_
not modelled 97.2 16 PDB header:hydrolase
Chain: A: PDB Molecule:extended-spectrum beta-lactamase;
PDBTitle: structural basis for the extended substrate spectrum of cmy-2 10, a plasmid-encoded class c beta-lactamase
90c3pe9B_
97.2 15 PDB header:unknown function
Chain: B: PDB Molecule:fibronectin(iii)-like module;
PDBTitle: structures of clostridium thermocellum cbha fibronectin(iii)-like2 modules
91d2dcfa1
not modelled 97.2 21 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
92d1ci9a_
not modelled 97.1 19 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
93d1onha_
not modelled 97.0 18 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
94c3ozhA_
not modelled 97.0 20 PDB header:hydrolase
Chain: A: PDB Molecule:beta-lactamase/d-alanine carboxypeptidase;
PDBTitle: crystal structure of beta-lactamase/d-alanine carboxypeptidase from2 yersinia pestis
95c3pe9A_
not modelled 96.9 17 PDB header:unknown function
Chain: A: PDB Molecule:fibronectin(iii)-like module;
PDBTitle: structures of clostridium thermocellum cbha fibronectin(iii)-like2 modules
96c3pe9C_
not modelled 96.9 19 PDB header:unknown function
Chain: C: PDB Molecule:fibronectin(iii)-like module;
PDBTitle: structures of clostridium thermocellum cbha fibronectin(iii)-like2 modules
97d1rgya_
not modelled 96.9 17 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
98c2wzzA_
not modelled 96.8 18 PDB header:hydrolase
Chain: A: PDB Molecule:beta-lactamase;
PDBTitle: amp-c beta-lactamase (pseudomonas aeruginosa)in complex2 with compound m-03
99c2qmiH_
not modelled 96.6 17 PDB header:hydrolase
Chain: H: PDB Molecule:pbp related beta-lactamase;
PDBTitle: structure of the octameric penicillin-binding protein2 homologue from pyrococcus abyssi
100c2qz6A_
not modelled 96.5 16 PDB header:hydrolase
Chain: A: PDB Molecule:beta-lactamase;
PDBTitle: first crystal structure of a psychrophile class c beta-2 lactamase
101c3pdgA_
not modelled 96.3 8 PDB header:unknown function
Chain: A: PDB Molecule:fibronectin(iii)-like module;
PDBTitle: structures of clostridium thermocellum cbha fibronectin(iii)-like2 modules
102d2drwa1
not modelled 96.1 11 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
103d2hdsa1
not modelled 96.0 18 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
104c3a3eB_
not modelled 95.8 19 PDB header:hydrolase
Chain: B: PDB Molecule:penicillin-binding protein 4;
PDBTitle: crystal structure of penicillin binding protein 4 (dacb)2 from haemophilus influenzae, complexed with novel beta-3 lactam (cmv)
105d1yqsa1
not modelled 94.7 19 Fold:beta-lactamase/transpeptidase-like
Superfamily:beta-lactamase/transpeptidase-like
Family:beta-Lactamase/D-ala carboxypeptidase
106c3tg9A_
not modelled 93.4 14 PDB header:penicillin binding protein
Chain: A: PDB Molecule:penicillin-binding protein;
PDBTitle: the crystal structure of penicillin binding protein from bacillus2 halodurans
107d1rhfa2
not modelled 93.2 14 Fold:Immunoglobulin-like beta-sandwich
Superfamily:Immunoglobulin
Family:I set domains
108c3hleA_
not modelled 93.1 11 PDB header:transferase
Chain: A: PDB Molecule:transesterase;
PDBTitle: simvastatin synthase (lovd), from aspergillus terreus, s5 mutant, s76a2 mutant, complex with monacolin j acid
109c3i7jB_
not modelled 93.0 21 PDB header:hydrolase
Chain: B: PDB Molecule:beta-lactamase mb2281c;
PDBTitle: crystal structure of a beta-lactamase (mb2281c) from2 mycobacterium bovis, northeast structural genomics3 consortium target mbr246
110c3o3vB_
not modelled 88.9 18 PDB header:hydrolase
Chain: B: PDB Molecule:beta-lactamase;
PDBTitle: crystal structure of clbp peptidase domain
111c2e6pA_
not modelled 88.7 16 PDB header:structural protein
Chain: A: PDB Molecule:obscurin-like protein 1;
PDBTitle: solution structure of the ig-like domain (714-804) from2 human obscurin-like protein 1
112d2oz4a3
not modelled 88.5 17 Fold:Immunoglobulin-like beta-sandwich
Superfamily:Immunoglobulin
Family:I set domains
113c3pddA_
not modelled 87.0 8 PDB header:unknown function
Chain: A: PDB Molecule:glycoside hydrolase, family 9;
PDBTitle: structures of clostridium thermocellum cbha fibronectin(iii)-like2 modules
114c2cknA_
not modelled 83.3 14 PDB header:transferase
Chain: A: PDB Molecule:basic fibroblast growth factor receptor 1;
PDBTitle: nmr structure of the first ig module of mouse fgfr1
115d1cs6a1
not modelled 82.8 15 Fold:Immunoglobulin-like beta-sandwich
Superfamily:Immunoglobulin
Family:I set domains
116c2v5mA_
not modelled 82.1 19 PDB header:cell adhesion
Chain: A: PDB Molecule:dscam;
PDBTitle: structural basis for dscam isoform specificity
117c2v5rB_
not modelled 80.9 21 PDB header:cell adhesion
Chain: B: PDB Molecule:dscam;
PDBTitle: structural basis for dscam isoform specificity
118c3b43A_
not modelled 79.9 14 PDB header:structural protein
Chain: A: PDB Molecule:titin;
PDBTitle: i-band fragment i65-i70 from titin
119c2dltA_
not modelled 79.4 22 PDB header:contractile protein
Chain: A: PDB Molecule:myosin binding protein c, fast-type;
PDBTitle: solution structure of the ig-like domain(433- 525) of2 murine myosin-binding protein c, fast-type
120d1f00i2
not modelled 79.3 21 Fold:Immunoglobulin-like beta-sandwich
Superfamily:Invasin/intimin cell-adhesion fragments
Family:Invasin/intimin cell-adhesion fragments

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
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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