Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP39285
DateThu Jan 5 11:58:57 GMT 2012
Unique Job ID0106ad3fe443e7d2

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c2vv5D_
Top template information
PDB header:membrane protein
Chain: D: PDB Molecule:small-conductance mechanosensitive channel;
PDBTitle: the open structure of mscs
Confidence and coverage
Confidence:100.0% Coverage: 23%
251 residues ( 23% 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.
775 residues ( 70%) 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  MRLIITFLMAWCLSWGAYAATAPDSKQITQELEQAKAAKPAQPEVVEALQSALNALEERK
Secondary structure 



















SS confidence 



























































Disorder  ???










??????????








?????????

















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   .........70.........80.........90.........100.........110.........120
Sequence  GSLERIKQYQQVIDNYPKLSATLRAQLNNMRDEPRSVSPGMSTDALNQEILQVSSQLLDK
Secondary structure 











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Disorder 














?












?????????????













?


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   .........130.........140.........150.........160.........170.........180
Sequence  SRQAQQEQERAREIADSLNQLPQQQTDARRQLNEIERRLGTLTGNTPLNQAQNFALQSDS
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?















??????????????








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   .........190.........200.........210.........220.........230.........240
Sequence  ARLKALVDELELAQLSANNRQELARLRSELAEKESQQLDAYLQALRNQLNSQRQLEAERA
Secondary structure 




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?????









































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   .........250.........260.........270.........280.........290.........300
Sequence  LESTELLAENSADLPKDIVAQFKINRELSAALNQQAQRMDLVASQQRQAASQTLQVRQAL
Secondary structure 









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Disorder 



???????????












































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   .........310.........320.........330.........340.........350.........360
Sequence  NTLREQSQWLGSSNLLGEALRAQVARLPEMPKPQQLDTEMAQLRVQRLRYEDLLNKQPLL
Secondary structure 




















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Disorder 








?????













?
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???????
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   .........370.........380.........390.........400.........410.........420
Sequence  RQIHQADGQPLTAEQNRILEAQLRTQRELLNSLLQGGDTLLLELTKLKVSNGQLEDALKE
Secondary structure 















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Disorder  ?????????????????










































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   .........430.........440.........450.........460.........470.........480
Sequence  VNEATHRYLFWTSDVRPMTIAWPLEIAQDLRRLISLDTFSQLGKASVMMLTSKETILPLF
Secondary structure 












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???


















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???







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   .........490.........500.........510.........520.........530.........540
Sequence  GALILVGCSIYSRRYFTRFLERSAAKVGKVTQDHFWLTLRTLFWSILVASPLPVLWMTLG
Secondary structure 





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????
?

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   .........550.........560.........570.........580.........590.........600
Sequence  YGLREAWPYPLAVAIGDGVTATVPLLWVVMICATFARPNGLFIAHFGWPRERVSRGMRYY
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Disorder 

?

???



























???
???



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   .........610.........620.........630.........640.........650.........660
Sequence  LMSIGLIVPLIMALMMFDNLDDREFSGSLGRLCFILICGALAVVTLSLKKAGIPLYLNKE
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???????
?






















???????????
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   .........670.........680.........690.........700.........710.........720
Sequence  GSGDNITNHMLWNMMIGAPLVAILASAVGYLATAQALLARLETSVAIWFLLLVVYHVIRR
Secondary structure 




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   .........730.........740.........750.........760.........770.........780
Sequence  WMLIQRRRLAFDRAKHRRAEMLAQRARGEEEAHHHSSPEGAIEVDESEVDLDAISAQSLR
Secondary structure 
















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????????????????????????











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   .........790.........800.........810.........820.........830.........840
Sequence  LVRSILMLIALLSVIVLWSEIHSAFGFLENISLWDVTSTVQGVESLEPITLGAVLIAILV
Secondary structure 
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?????????
??










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   .........850.........860.........870.........880.........890.........900
Sequence  FIITTQLVRNLPALLELAILQHLDLTPGTGYAITTITKYLLMLIGGLVGFSMIGIEWSKL
Secondary structure 








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   .........910.........920.........930.........940.........950.........960
Sequence  QWLVAALGVGLGFGLQEIFANFISGLIILFEKPIRIGDTVTIRDLTGSVTKINTRATTIS
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   .........970.........980.........990.........1000.........1010.........1020
Sequence  DWDRKEIIVPNKAFITEQFINWSLSDSVTRVVLTIPAPADANSEEVTEILLTAARRCSLV
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?
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?

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   .........1030.........1040.........1050.........1060.........1070.........1080
Sequence  IDNPAPEVFLVDLQQGIQIFELRIYAAEMGHRMPLRHEIHQLILAGFHAHGIDMPFPPFQ
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   .........1090.........1100.......
Sequence  MRLESLNGKQTGRTLTSAGKGRQAGSL
Secondary structure 






















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Disorder 





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

Domain analysis 

Hover over an aligned region to see model and summary info

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

RankAligned region

PDB 2vv5 chain D

3D model

Region: 833 - 1086
Aligned: 251
Modelled: 254
Confidence: 100.0%
Identity: 20%
PDB header:membrane protein
Chain: D: PDB Molecule:small-conductance mechanosensitive channel;
PDBTitle: the open structure of mscs

Phyre2

PDB 2vv5 chain A domain 2

3D model

Region: 985 - 1086
Aligned: 101
Modelled: 102
Confidence: 99.6%
Identity: 20%
Fold: Ferredoxin-like
Superfamily: Mechanosensitive channel protein MscS (YggB), C-terminal domain
Family: Mechanosensitive channel protein MscS (YggB), C-terminal domain

Phyre2

PDB 2vv5 chain A domain 1

3D model

Region: 918 - 983
Aligned: 66
Modelled: 66
Confidence: 99.2%
Identity: 29%
Fold: Sm-like fold
Superfamily: Sm-like ribonucleoproteins
Family: Mechanosensitive channel protein MscS (YggB), middle domain

Phyre2

PDB 2vv5 chain A domain 3

3D model

Region: 833 - 916
Aligned: 83
Modelled: 84
Confidence: 98.7%
Identity: 12%
Fold: Mechanosensitive channel protein MscS (YggB), transmembrane region
Superfamily: Mechanosensitive channel protein MscS (YggB), transmembrane region
Family: Mechanosensitive channel protein MscS (YggB), transmembrane region

Phyre2

PDB 1cii chain A

3D model

Region: 19 - 576
Aligned: 515
Modelled: 521
Confidence: 98.7%
Identity: 12%
PDB header:transmembrane protein
Chain: A: PDB Molecule:colicin ia;
PDBTitle: colicin ia

Phyre2

PDB 1c1g chain A

3D model

Region: 26 - 310
Aligned: 282
Modelled: 285
Confidence: 98.5%
Identity: 12%
PDB header:contractile protein
Chain: A: PDB Molecule:tropomyosin;
PDBTitle: crystal structure of tropomyosin at 7 angstroms resolution2 in the spermine-induced crystal form

Phyre2

PDB 1yvl chain B

3D model

Region: 48 - 317
Aligned: 266
Modelled: 270
Confidence: 98.1%
Identity: 9%
PDB header:signaling protein
Chain: B: PDB Molecule:signal transducer and activator of transcription
PDBTitle: structure of unphosphorylated stat1

Phyre2

PDB 1sjj chain B

3D model

Region: 24 - 423
Aligned: 400
Modelled: 400
Confidence: 97.9%
Identity: 10%
PDB header:contractile protein
Chain: B: PDB Molecule:actinin;
PDBTitle: cryo-em structure of chicken gizzard smooth muscle alpha-2 actinin

Phyre2

PDB 2oev chain A

3D model

Region: 15 - 310
Aligned: 294
Modelled: 296
Confidence: 97.7%
Identity: 9%
PDB header:protein transport
Chain: A: PDB Molecule:programmed cell death 6-interacting protein;
PDBTitle: crystal structure of alix/aip1

Phyre2

PDB 1bf5 chain A

3D model

Region: 64 - 224
Aligned: 160
Modelled: 161
Confidence: 97.7%
Identity: 9%
PDB header:gene regulation/dna
Chain: A: PDB Molecule:signal transducer and activator of transcription
PDBTitle: tyrosine phosphorylated stat-1/dna complex

Phyre2

PDB 3oja chain B

3D model

Region: 23 - 165
Aligned: 143
Modelled: 143
Confidence: 97.5%
Identity: 12%
PDB header:protein binding
Chain: B: PDB Molecule:anopheles plasmodium-responsive leucine-rich repeat protein
PDBTitle: crystal structure of lrim1/apl1c complex

Phyre2

PDB 2oex chain B

3D model

Region: 13 - 310
Aligned: 296
Modelled: 298
Confidence: 97.3%
Identity: 8%
PDB header:protein transport
Chain: B: PDB Molecule:programmed cell death 6-interacting protein;
PDBTitle: structure of alix/aip1 v domain

Phyre2

PDB 1bg1 chain A

3D model

Region: 129 - 311
Aligned: 172
Modelled: 183
Confidence: 97.2%
Identity: 10%
PDB header:transcription/dna
Chain: A: PDB Molecule:protein (transcription factor stat3b);
PDBTitle: transcription factor stat3b/dna complex

Phyre2

PDB 2efr chain B

3D model

Region: 73 - 226
Aligned: 152
Modelled: 154
Confidence: 97.0%
Identity: 7%
PDB header:contractile protein
Chain: B: PDB Molecule:general control protein gcn4 and tropomyosin 1 alpha chain;
PDBTitle: crystal structure of the c-terminal tropomyosin fragment with n- and2 c-terminal extensions of the leucine zipper at 1.8 angstroms3 resolution

Phyre2

PDB 3na7 chain A

3D model

Region: 24 - 182
Aligned: 159
Modelled: 159
Confidence: 96.9%
Identity: 10%
PDB header:gene regulation, chaperone
Chain: A: PDB Molecule:hp0958;
PDBTitle: 2.2 angstrom structure of the hp0958 protein from helicobacter pylori2 ccug 17874

Phyre2

PDB 3cwg chain A

3D model

Region: 64 - 224
Aligned: 161
Modelled: 161
Confidence: 96.9%
Identity: 10%
PDB header:transcription
Chain: A: PDB Molecule:signal transducer and activator of transcription
PDBTitle: unphosphorylated mouse stat3 core fragment

Phyre2

PDB 3dtp chain A

3D model

Region: 112 - 229
Aligned: 118
Modelled: 118
Confidence: 96.5%
Identity: 12%
PDB header:contractile protein
Chain: A: PDB Molecule:myosin 2 heavy chain chimera of smooth and
PDBTitle: tarantula heavy meromyosin obtained by flexible docking to2 tarantula muscle thick filament cryo-em 3d-map

Phyre2

PDB 1f5n chain A

3D model

Region: 46 - 307
Aligned: 262
Modelled: 262
Confidence: 96.4%
Identity: 8%
PDB header:signaling protein
Chain: A: PDB Molecule:interferon-induced guanylate-binding protein 1;
PDBTitle: human guanylate binding protein-1 in complex with the gtp2 analogue, gmppnp.

Phyre2

PDB 1ei3 chain C

3D model

Region: 61 - 171
Aligned: 110
Modelled: 111
Confidence: 96.4%
Identity: 8%
PDB header:
PDB COMPND:

Phyre2

PDB 1g8x chain B

3D model

Region: 25 - 227
Aligned: 203
Modelled: 203
Confidence: 96.4%
Identity: 9%
PDB header:structural protein
Chain: B: PDB Molecule:myosin ii heavy chain fused to alpha-actinin 3;
PDBTitle: structure of a genetically engineered molecular motor

Phyre2
1

c2vv5D_
2

d2vv5a2
3

d2vv5a1
4

d2vv5a3
5

c1ciiA_
6

c1c1gA_
7

c1yvlB_
8

c1sjjB_
9

c2oevA_
10

c1bf5A_
11

c3ojaB_
12

c2oexB_
13

c1bg1A_
14

c2efrB_
15

c3na7A_
16

c3cwgA_
17

c3dtpA_
18

c1f5nA_
19

c1ei3C_
20

c1g8xB_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c2vv5D_



100.0 20 PDB header:membrane protein
Chain: D: PDB Molecule:small-conductance mechanosensitive channel;
PDBTitle: the open structure of mscs
2d2vv5a2



99.6 20 Fold:Ferredoxin-like
Superfamily:Mechanosensitive channel protein MscS (YggB), C-terminal domain
Family:Mechanosensitive channel protein MscS (YggB), C-terminal domain
3d2vv5a1



99.2 29 Fold:Sm-like fold
Superfamily:Sm-like ribonucleoproteins
Family:Mechanosensitive channel protein MscS (YggB), middle domain
4d2vv5a3



98.7 12 Fold:Mechanosensitive channel protein MscS (YggB), transmembrane region
Superfamily:Mechanosensitive channel protein MscS (YggB), transmembrane region
Family:Mechanosensitive channel protein MscS (YggB), transmembrane region
5c1ciiA_



98.7 12 PDB header:transmembrane protein
Chain: A: PDB Molecule:colicin ia;
PDBTitle: colicin ia
6c1c1gA_



98.5 12 PDB header:contractile protein
Chain: A: PDB Molecule:tropomyosin;
PDBTitle: crystal structure of tropomyosin at 7 angstroms resolution2 in the spermine-induced crystal form
7c1yvlB_



98.1 9 PDB header:signaling protein
Chain: B: PDB Molecule:signal transducer and activator of transcription
PDBTitle: structure of unphosphorylated stat1
8c1sjjB_



97.9 10 PDB header:contractile protein
Chain: B: PDB Molecule:actinin;
PDBTitle: cryo-em structure of chicken gizzard smooth muscle alpha-2 actinin
9c2oevA_



97.7 9 PDB header:protein transport
Chain: A: PDB Molecule:programmed cell death 6-interacting protein;
PDBTitle: crystal structure of alix/aip1
10c1bf5A_



97.7 9 PDB header:gene regulation/dna
Chain: A: PDB Molecule:signal transducer and activator of transcription
PDBTitle: tyrosine phosphorylated stat-1/dna complex
11c3ojaB_



97.5 12 PDB header:protein binding
Chain: B: PDB Molecule:anopheles plasmodium-responsive leucine-rich repeat protein
PDBTitle: crystal structure of lrim1/apl1c complex
12c2oexB_



97.3 8 PDB header:protein transport
Chain: B: PDB Molecule:programmed cell death 6-interacting protein;
PDBTitle: structure of alix/aip1 v domain
13c1bg1A_



97.2 10 PDB header:transcription/dna
Chain: A: PDB Molecule:protein (transcription factor stat3b);
PDBTitle: transcription factor stat3b/dna complex
14c2efrB_



97.0 7 PDB header:contractile protein
Chain: B: PDB Molecule:general control protein gcn4 and tropomyosin 1 alpha chain;
PDBTitle: crystal structure of the c-terminal tropomyosin fragment with n- and2 c-terminal extensions of the leucine zipper at 1.8 angstroms3 resolution
15c3na7A_



96.9 10 PDB header:gene regulation, chaperone
Chain: A: PDB Molecule:hp0958;
PDBTitle: 2.2 angstrom structure of the hp0958 protein from helicobacter pylori2 ccug 17874
16c3cwgA_



96.9 10 PDB header:transcription
Chain: A: PDB Molecule:signal transducer and activator of transcription
PDBTitle: unphosphorylated mouse stat3 core fragment
17c3dtpA_



96.5 12 PDB header:contractile protein
Chain: A: PDB Molecule:myosin 2 heavy chain chimera of smooth and
PDBTitle: tarantula heavy meromyosin obtained by flexible docking to2 tarantula muscle thick filament cryo-em 3d-map
18c1f5nA_



96.4 8 PDB header:signaling protein
Chain: A: PDB Molecule:interferon-induced guanylate-binding protein 1;
PDBTitle: human guanylate binding protein-1 in complex with the gtp2 analogue, gmppnp.
19c1ei3C_



96.4 8 PDB header:
PDB COMPND:
20c1g8xB_



96.4 9 PDB header:structural protein
Chain: B: PDB Molecule:myosin ii heavy chain fused to alpha-actinin 3;
PDBTitle: structure of a genetically engineered molecular motor
21c3ghgK_



not modelled 96.1 9 PDB header:blood clotting
Chain: K: PDB Molecule:fibrinogen beta chain;
PDBTitle: crystal structure of human fibrinogen
22c3hizB_



not modelled 95.9 10 PDB header:transferase/oncoprotein
Chain: B: PDB Molecule:phosphatidylinositol 3-kinase regulatory subunit
PDBTitle: crystal structure of p110alpha h1047r mutant in complex with2 nish2 of p85alpha
23c2d3eD_



not modelled 95.6 9 PDB header:contractile protein
Chain: D: PDB Molecule:general control protein gcn4 and tropomyosin 1
PDBTitle: crystal structure of the c-terminal fragment of rabbit2 skeletal alpha-tropomyosin
24c2v71A_



not modelled 95.6 9 PDB header:nuclear protein
Chain: A: PDB Molecule:nuclear distribution protein nude-like 1;
PDBTitle: coiled-coil region of nudel
25c2ch7A_



not modelled 95.4 10 PDB header:chemotaxis
Chain: A: PDB Molecule:methyl-accepting chemotaxis protein;
PDBTitle: crystal structure of the cytoplasmic domain of a bacterial2 chemoreceptor from thermotoga maritima
26c1jchC_



not modelled 95.3 4 PDB header:ribosome inhibitor, hydrolase
Chain: C: PDB Molecule:colicin e3;
PDBTitle: crystal structure of colicin e3 in complex with its immunity protein
27c1ei3E_



not modelled 95.0 11 PDB header:
PDB COMPND:
28c3o0zD_



not modelled 94.9 14 PDB header:transferase
Chain: D: PDB Molecule:rho-associated protein kinase 1;
PDBTitle: crystal structure of a coiled-coil domain from human rock i
29c2fxmB_



not modelled 94.8 13 PDB header:contractile protein
Chain: B: PDB Molecule:myosin heavy chain, cardiac muscle beta isoform;
PDBTitle: structure of the human beta-myosin s2 fragment
30c3ojaA_



not modelled 94.7 11 PDB header:protein binding
Chain: A: PDB Molecule:leucine-rich immune molecule 1;
PDBTitle: crystal structure of lrim1/apl1c complex
31c4a55B_



not modelled 94.7 8 PDB header:transferase
Chain: B: PDB Molecule:phosphatidylinositol 3-kinase regulatory subunit alpha;
PDBTitle: crystal structure of p110alpha in complex with ish2 of p85alpha and2 the inhibitor pik-108
32c1y4cA_



not modelled 94.7 12 PDB header:de novo protein
Chain: A: PDB Molecule:maltose binding protein fused with designed
PDBTitle: designed helical protein fusion mbp
33c1deqF_



not modelled 94.5 5 PDB header:
PDB COMPND:
34c2dfsA_



not modelled 94.1 10 PDB header:contractile protein/transport protein
Chain: A: PDB Molecule:myosin-5a;
PDBTitle: 3-d structure of myosin-v inhibited state
35c2v1yB_



not modelled 94.0 7 PDB header:transferase
Chain: B: PDB Molecule:phosphatidylinositol 3-kinase regulatory subunit alpha;
PDBTitle: structure of a phosphoinositide 3-kinase alpha adaptor-2 binding domain (abd) in a complex with the ish2 domain3 from p85 alpha
36c2y3aB_



not modelled 93.9 13 PDB header:transferase
Chain: B: PDB Molecule:phosphatidylinositol 3-kinase regulatory subunit beta;
PDBTitle: crystal structure of p110beta in complex with icsh2 of p85beta and2 the drug gdc-0941
37c1deqO_



not modelled 93.8 9 PDB header:
PDB COMPND:
38c2b9cA_



not modelled 93.6 12 PDB header:contractile protein
Chain: A: PDB Molecule:striated-muscle alpha tropomyosin;
PDBTitle: structure of tropomyosin's mid-region: bending and binding2 sites for actin
39c2j69D_



not modelled 92.1 10 PDB header:hydrolase
Chain: D: PDB Molecule:bacterial dynamin-like protein;
PDBTitle: bacterial dynamin-like protein bdlp
40c3u59C_



not modelled 91.2 15 PDB header:contractile protein
Chain: C: PDB Molecule:tropomyosin beta chain;
PDBTitle: n-terminal 98-aa fragment of smooth muscle tropomyosin beta
41c1hciB_



not modelled 91.1 11 PDB header:triple-helix coiled coil
Chain: B: PDB Molecule:alpha-actinin 2;
PDBTitle: crystal structure of the rod domain of alpha-actinin
42c3ipkA_



not modelled 89.6 12 PDB header:cell adhesion
Chain: A: PDB Molecule:agi/ii;
PDBTitle: crystal structure of a3vp1 of agi/ii of streptococcus mutans
43c1deqD_



not modelled 87.8 10 PDB header:
PDB COMPND:
44d2ap3a1



not modelled 87.4 11 Fold:Four-helical up-and-down bundle
Superfamily:MW0975(SA0943)-like
Family:MW0975(SA0943)-like
45c3hnwB_



not modelled 84.8 20 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of a basic coiled-coil protein of unknown function2 from eubacterium eligens atcc 27750
46c2zkrt_



not modelled 84.8 24 PDB header:ribosomal protein/rna
Chain: T: PDB Molecule:rna expansion segment es39 part iii;
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
47c3ol1A_



not modelled 84.8 12 PDB header:structural protein
Chain: A: PDB Molecule:vimentin;
PDBTitle: crystal structure of vimentin (fragment 144-251) from homo sapiens,2 northeast structural genomics consortium target hr4796b
48c2v66C_



not modelled 84.5 11 PDB header:structural protein
Chain: C: PDB Molecule:nuclear distribution protein nude-like 1;
PDBTitle: crystal structure of the coiled-coil domain of ndel1 (a.a.2 58 to 169)c
49c3r6nA_



not modelled 84.1 5 PDB header:cell adhesion
Chain: A: PDB Molecule:desmoplakin;
PDBTitle: crystal structure of a rigid four spectrin repeat fragment of the2 human desmoplakin plakin domain
50c2gl2B_



not modelled 83.5 10 PDB header:cell adhesion
Chain: B: PDB Molecule:adhesion a;
PDBTitle: crystal structure of the tetra muntant (t66g,r67g,f68g,2 y69g) of bacterial adhesin fada
51c3g67A_



not modelled 83.3 7 PDB header:signaling protein
Chain: A: PDB Molecule:methyl-accepting chemotaxis protein;
PDBTitle: crystal structure of a soluble chemoreceptor from thermotoga2 maritima
52c3l9oA_



not modelled 80.6 13 PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent rna helicase dob1;
PDBTitle: crystal structure of mtr4, a co-factor of the nuclear exosome
53d2hqha1



not modelled 80.5 33 Fold:SH3-like barrel
Superfamily:Cap-Gly domain
Family:Cap-Gly domain
54d2cqaa1



not modelled 79.8 32 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:TIP49 domain
55c2rd0B_



not modelled 77.6 10 PDB header:transferase/oncoprotein
Chain: B: PDB Molecule:phosphatidylinositol 3-kinase regulatory subunit alpha;
PDBTitle: structure of a human p110alpha/p85alpha complex
56c3edvB_



not modelled 76.3 10 PDB header:structural protein
Chain: B: PDB Molecule:spectrin beta chain, brain 1;
PDBTitle: crystal structure of repeats 14-16 of beta2-spectrin
57c1l8dB_



not modelled 74.4 7 PDB header:replication
Chain: B: PDB Molecule:dna double-strand break repair rad50 atpase;
PDBTitle: rad50 coiled-coil zn hook
58c2zv4O_



not modelled 74.3 13 PDB header:structural protein
Chain: O: PDB Molecule:major vault protein;
PDBTitle: the structure of rat liver vault at 3.5 angstrom resolution
59d2cp6a1



not modelled 74.2 30 Fold:SH3-like barrel
Superfamily:Cap-Gly domain
Family:Cap-Gly domain
60d1nz9a_



not modelled 74.0 35 Fold:SH3-like barrel
Superfamily:Translation proteins SH3-like domain
Family:N-utilization substance G protein NusG, C-terminal domain
61c3kbtA_



not modelled 73.9 9 PDB header:structural protein
Chain: A: PDB Molecule:spectrin beta chain, erythrocyte;
PDBTitle: crystal structure of the ankyrin binding domain of human erythroid2 beta spectrin (repeats 13-15) in complex with the spectrin binding3 domain of human erythroid ankyrin (zu5-ank)
62d1nppa2



not modelled 72.0 22 Fold:SH3-like barrel
Superfamily:Translation proteins SH3-like domain
Family:N-utilization substance G protein NusG, C-terminal domain
63c2wpqA_



not modelled 71.6 9 PDB header:membrane protein
Chain: A: PDB Molecule:trimeric autotransporter adhesin fragment;
PDBTitle: salmonella enterica sada 479-519 fused to gcn4 adaptors (2 sadak3, in-register fusion)
64c2kvqG_



not modelled 70.9 18 PDB header:transcription
Chain: G: PDB Molecule:transcription antitermination protein nusg;
PDBTitle: solution structure of nuse:nusg-ctd complex
65c2jvvA_



not modelled 70.9 18 PDB header:transcription
Chain: A: PDB Molecule:transcription antitermination protein nusg;
PDBTitle: solution structure of e. coli nusg carboxyterminal domain
66c4a1cS_



not modelled 70.5 40 PDB header:ribosome
Chain: S: PDB Molecule:rpl26;
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 4.
67d1vqot1



not modelled 68.6 15 Fold:SH3-like barrel
Superfamily:Translation proteins SH3-like domain
Family:Ribosomal proteins L24p and L21e
68c3iz5Y_



not modelled 67.0 35 PDB header:ribosome
Chain: Y: PDB Molecule:60s ribosomal protein l26 (l24p);
PDBTitle: localization of the large subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome
69c3lssA_



not modelled 66.5 13 PDB header:ligase
Chain: A: PDB Molecule:seryl-trna synthetase;
PDBTitle: trypanosoma brucei seryl-trna synthetase in complex with atp
70c2e6zA_



not modelled 66.0 20 PDB header:transcription
Chain: A: PDB Molecule:transcription elongation factor spt5;
PDBTitle: solution structure of the second kow motif of human2 transcription elongation factor spt5
71d1whka_



not modelled 65.9 13 Fold:SH3-like barrel
Superfamily:Cap-Gly domain
Family:Cap-Gly domain
72d2plsa1



not modelled 65.2 17 Fold:FAD-binding/transporter-associated domain-like
Superfamily:FAD-binding/transporter-associated domain-like
Family:CorC/HlyC domain-like
73c2vfyA_



not modelled 65.0 16 PDB header:hydrolase
Chain: A: PDB Molecule:akap18 delta;
PDBTitle: akap18 delta central domain
74d1whma_



not modelled 63.3 23 Fold:SH3-like barrel
Superfamily:Cap-Gly domain
Family:Cap-Gly domain
75d2coya1



not modelled 63.2 27 Fold:SH3-like barrel
Superfamily:Cap-Gly domain
Family:Cap-Gly domain
76c2i1jA_



not modelled 62.8 11 PDB header:cell adhesion, membrane protein
Chain: A: PDB Molecule:moesin;
PDBTitle: moesin from spodoptera frugiperda at 2.1 angstroms resolution
77d2cp5a1



not modelled 62.5 20 Fold:SH3-like barrel
Superfamily:Cap-Gly domain
Family:Cap-Gly domain
78d1t9ha1



not modelled 61.5 33 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
79d2coza1



not modelled 60.8 27 Fold:SH3-like barrel
Superfamily:Cap-Gly domain
Family:Cap-Gly domain
80c2e7sM_



not modelled 60.8 7 PDB header:endocytosis/exocytosis
Chain: M: PDB Molecule:rab guanine nucleotide exchange factor sec2;
PDBTitle: crystal structure of the yeast sec2p gef domain
81c1i84V_



not modelled 60.6 18 PDB header:contractile protein
Chain: V: PDB Molecule:smooth muscle myosin heavy chain;
PDBTitle: cryo-em structure of the heavy meromyosin subfragment of2 chicken gizzard smooth muscle myosin with regulatory light3 chain in the dephosphorylated state. only c alphas4 provided for regulatory light chain. only backbone atoms5 provided for s2 fragment.
82c1l2fA_



not modelled 60.6 19 PDB header:transcription
Chain: A: PDB Molecule:n utilization substance protein a;
PDBTitle: crystal structure of nusa from thermotoga maritima: a2 structure-based role of the n-terminal domain
83d2cp2a1



not modelled 60.5 20 Fold:SH3-like barrel
Superfamily:Cap-Gly domain
Family:Cap-Gly domain
84c2qihA_



not modelled 60.5 15 PDB header:cell adhesion
Chain: A: PDB Molecule:protein uspa1;
PDBTitle: crystal structure of 527-665 fragment of uspa1 protein from2 moraxella catarrhalis
85c3cnrA_



not modelled 59.6 23 PDB header:unknown function
Chain: A: PDB Molecule:type iv fimbriae assembly protein;
PDBTitle: crystal structure of pilz (xac1133) from xanthomonas2 axonopodis pv citri
86d1yeza1



not modelled 59.5 21 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:TRAM domain
87c2jeeA_



not modelled 59.5 9 PDB header:cell cycle
Chain: A: PDB Molecule:yiiu;
PDBTitle: xray structure of e. coli yiiu
88d1whja_



not modelled 59.4 24 Fold:SH3-like barrel
Superfamily:Cap-Gly domain
Family:Cap-Gly domain
89d2e3ha1



not modelled 59.4 30 Fold:SH3-like barrel
Superfamily:Cap-Gly domain
Family:Cap-Gly domain
90c2k52A_



not modelled 58.8 16 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein mj1198;
PDBTitle: structure of uncharacterized protein mj1198 from2 methanocaldococcus jannaschii. northeast structural3 genomics target mjr117b
91d2do3a1



not modelled 57.1 28 Fold:SH3-like barrel
Superfamily:Translation proteins SH3-like domain
Family:SPT5 KOW domain-like
92d2p13a1



not modelled 57.0 17 Fold:FAD-binding/transporter-associated domain-like
Superfamily:FAD-binding/transporter-associated domain-like
Family:CorC/HlyC domain-like
93c2no2A_



not modelled 56.9 12 PDB header:cell adhesion
Chain: A: PDB Molecule:huntingtin-interacting protein 1;
PDBTitle: crystal structure of the dllrkn-containing coiled-coil2 domain of huntingtin-interacting protein 1
94c2e4hA_



not modelled 56.6 27 PDB header:structural protein
Chain: A: PDB Molecule:restin;
PDBTitle: solution structure of cytoskeletal protein in complex with2 tubulin tail
95d2e3ia1



not modelled 56.3 20 Fold:SH3-like barrel
Superfamily:Cap-Gly domain
Family:Cap-Gly domain
96c2rcnA_



not modelled 55.3 21 PDB header:hydrolase
Chain: A: PDB Molecule:probable gtpase engc;
PDBTitle: crystal structure of the ribosomal interacting gtpase yjeq from the2 enterobacterial species salmonella typhimurium.
97c1e0tD_



not modelled 55.2 18 PDB header:phosphotransferase
Chain: D: PDB Molecule:pyruvate kinase;
PDBTitle: r292d mutant of e. coli pyruvate kinase
98c2zdiA_



not modelled 55.1 12 PDB header:chaperone
Chain: A: PDB Molecule:prefoldin subunit beta;
PDBTitle: crystal structure of prefoldin from pyrococcus horikoshii2 ot3
99d2cp3a1



not modelled 54.5 35 Fold:SH3-like barrel
Superfamily:Cap-Gly domain
Family:Cap-Gly domain
100d1h6za2



not modelled 54.3 38 Fold:The "swivelling" beta/beta/alpha domain
Superfamily:Phosphohistidine domain
Family:Pyruvate phosphate dikinase, central domain
101d1vqoq1



not modelled 54.1 27 Fold:SH3-like barrel
Superfamily:Translation proteins SH3-like domain
Family:Ribosomal proteins L24p and L21e
102c2p03A_



not modelled 54.1 10 PDB header:cell adhesion
Chain: A: PDB Molecule:alpha-2-macroglobulin receptor-associated
PDBTitle: the structure of receptor-associated protein(rap)
103c2z0wA_



not modelled 53.7 20 PDB header:protein binding
Chain: A: PDB Molecule:cap-gly domain-containing linker protein 4;
PDBTitle: crystal structure of the 2nd cap-gly domain in human restin-2 like protein 2 reveals a swapped-dimer
104d2cowa1



not modelled 53.7 32 Fold:SH3-like barrel
Superfamily:Cap-Gly domain
Family:Cap-Gly domain
105c1q46A_



not modelled 53.3 18 PDB header:translation
Chain: A: PDB Molecule:translation initiation factor 2 alpha subunit;
PDBTitle: crystal structure of the eif2 alpha subunit from2 saccharomyces cerevisia
106c2v4hA_



not modelled 52.9 12 PDB header:transcription
Chain: A: PDB Molecule:nf-kappa-b essential modulator;
PDBTitle: nemo cc2-lz domain - 1d5 darpin complex
107c3b7kA_



not modelled 52.7 21 PDB header:hydrolase
Chain: A: PDB Molecule:acyl-coenzyme a thioesterase 12;
PDBTitle: human acyl-coenzyme a thioesterase 12
108c2wctC_



not modelled 52.7 37 PDB header:rna-binding protein
Chain: C: PDB Molecule:non-structural protein 3;
PDBTitle: human sars coronavirus unique domain (triclinic form)
109d2essa1



not modelled 52.1 15 Fold:Thioesterase/thiol ester dehydrase-isomerase
Superfamily:Thioesterase/thiol ester dehydrase-isomerase
Family:Acyl-ACP thioesterase-like
110c1hh2P_



not modelled 52.0 20 PDB header:transcription regulation
Chain: P: PDB Molecule:n utilization substance protein a;
PDBTitle: crystal structure of nusa from thermotoga maritima
111d1yvca1



not modelled 51.9 19 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:TRAM domain
112d1ppje2



not modelled 51.5 22 Fold:Single transmembrane helix
Superfamily:ISP transmembrane anchor
Family:ISP transmembrane anchor
113c3iz5U_



not modelled 51.4 24 PDB header:ribosome
Chain: U: PDB Molecule:60s ribosomal protein l21 (l21e);
PDBTitle: localization of the large subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome
114d2o1ra1



not modelled 51.3 21 Fold:FAD-binding/transporter-associated domain-like
Superfamily:FAD-binding/transporter-associated domain-like
Family:CorC/HlyC domain-like
115d1whha_



not modelled 51.3 24 Fold:SH3-like barrel
Superfamily:Cap-Gly domain
Family:Cap-Gly domain
116c4a1aP_



not modelled 51.2 28 PDB header:ribosome
Chain: P: PDB Molecule:60s ribosomal protein l21;
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 3.
117c3a7pB_



not modelled 50.9 8 PDB header:protein transport
Chain: B: PDB Molecule:autophagy protein 16;
PDBTitle: the crystal structure of saccharomyces cerevisiae atg16
118d2f9ha1



not modelled 50.8 26 Fold:PTSIIA/GutA-like
Superfamily:PTSIIA/GutA-like
Family:PTSIIA/GutA-like
119c3dedB_



not modelled 50.4 8 PDB header:membrane protein
Chain: B: PDB Molecule:probable hemolysin;
PDBTitle: c-terminal domain of probable hemolysin from chromobacterium violaceum
120d1y7ua1



not modelled 50.4 13 Fold:Thioesterase/thiol ester dehydrase-isomerase
Superfamily:Thioesterase/thiol ester dehydrase-isomerase
Family:4HBT-like

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