Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionO13563
DateMon Jul 2 19:10:15 BST 2012
Unique Job IDd56708941e75af94

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c2kr0A_
Top template information
PDB header:protein binding
Chain: A: PDB Molecule:proteasomal ubiquitin receptor adrm1;
PDBTitle: a proteasome protein
Confidence and coverage
Confidence:100.0% Coverage: 88%
137 residues ( 88% 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  MSMSSTVIKFRAGVCEYNEDSRLCTPIPVQGEIEIKPNEEEELGFWDFEWRPTEKPVGRE
Secondary structure 
SS confidence 
Disorder  ???????
?
??????
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  LDPISLILIPGETMWVPIKSSKSGRIFALVFSSNERYFFWLQEKNSGNLPLNELSAKDKE
Secondary structure 
SS confidence 
Disorder  ?
??????
?
Disorder confidence 
 
   .........130.........140.........150......
Sequence  IYNKMIGVLNNSSESDEEESNDEKQKAQDVDVSMQD
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 2kr0 chain A

3D model

Region: 2 - 156
Aligned: 137
Modelled: 154
Confidence: 100.0%
Identity: 24%
PDB header:protein binding
Chain: A: PDB Molecule:proteasomal ubiquitin receptor adrm1;
PDBTitle: a proteasome protein

Phyre2

PDB 2z59 chain A

3D model

Region: 6 - 131
Aligned: 108
Modelled: 123
Confidence: 100.0%
Identity: 29%
PDB header:protein transport
Chain: A: PDB Molecule:protein adrm1;
PDBTitle: complex structures of mouse rpn13 (22-130aa) and ubiquitin

Phyre2

PDB 2r2y chain A

3D model

Region: 6 - 131
Aligned: 108
Modelled: 126
Confidence: 100.0%
Identity: 29%
PDB header:protein binding
Chain: A: PDB Molecule:protein adrm1;
PDBTitle: crystal structure of the proteasomal rpn13 pru-domain

Phyre2

PDB 2z4d chain A

3D model

Region: 6 - 101
Aligned: 96
Modelled: 96
Confidence: 100.0%
Identity: 100%
PDB header:nuclear protein
Chain: A: PDB Molecule:26s proteasome regulatory subunit rpn13;
PDBTitle: nmr structures of yeast proteasome component rpn13

Phyre2

PDB 2aj7 chain A domain 1

3D model

Region: 60 - 108
Aligned: 44
Modelled: 49
Confidence: 81.0%
Identity: 18%
Fold: BH3618-like
Superfamily: BH3618-like
Family: BH3618-like

Phyre2

PDB 1ddw chain A

3D model

Region: 5 - 93
Aligned: 81
Modelled: 49
Confidence: 51.3%
Identity: 15%
Fold: PH domain-like barrel
Superfamily: PH domain-like
Family: Enabled/VASP homology 1 domain (EVH1 domain)

Phyre2

PDB 1evh chain A

3D model

Region: 5 - 93
Aligned: 84
Modelled: 89
Confidence: 50.3%
Identity: 13%
Fold: PH domain-like barrel
Superfamily: PH domain-like
Family: Enabled/VASP homology 1 domain (EVH1 domain)

Phyre2

PDB 2l23 chain A

3D model

Region: 69 - 131
Aligned: 50
Modelled: 63
Confidence: 35.3%
Identity: 20%
PDB header:transcription
Chain: A: PDB Molecule:mediator of rna polymerase ii transcription subunit 25;
PDBTitle: nmr structure of the acid (activator interacting domain) of the human2 mediator med25 protein

Phyre2

PDB 2kc8 chain B

3D model

Region: 114 - 132
Aligned: 19
Modelled: 63
Confidence: 29.4%
Identity: 32%
PDB header:toxin/toxin repressor
Chain: B: PDB Molecule:antitoxin relb;
PDBTitle: structure of e. coli toxin rele (r81a/r83a) mutant in2 complex with antitoxin relbc (k47-l79) peptide

Phyre2

PDB 2hx0 chain A domain 1

3D model

Region: 80 - 95
Aligned: 16
Modelled: 16
Confidence: 22.0%
Identity: 19%
Fold: AF0104/ALDC/Ptd012-like
Superfamily: AF0104/ALDC/Ptd012-like
Family: AF0104-like

Phyre2

PDB 3fke chain B

3D model

Region: 24 - 42
Aligned: 19
Modelled: 16
Confidence: 19.7%
Identity: 16%
PDB header:rna binding protein
Chain: B: PDB Molecule:polymerase cofactor vp35;
PDBTitle: structure of the ebola vp35 interferon inhibitory domain

Phyre2

PDB 2h6l chain A domain 1

3D model

Region: 77 - 95
Aligned: 19
Modelled: 19
Confidence: 19.1%
Identity: 16%
Fold: AF0104/ALDC/Ptd012-like
Superfamily: AF0104/ALDC/Ptd012-like
Family: AF0104-like

Phyre2

PDB 2ns0 chain A domain 1

3D model

Region: 11 - 40
Aligned: 30
Modelled: 30
Confidence: 18.8%
Identity: 23%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: RHA1 ro06458-like

Phyre2

PDB 1qqg chain A domain 2

3D model

Region: 99 - 129
Aligned: 18
Modelled: 31
Confidence: 18.0%
Identity: 33%
Fold: PH domain-like barrel
Superfamily: PH domain-like
Family: Phosphotyrosine-binding domain (PTB)

Phyre2

PDB 1egx chain A

3D model

Region: 1 - 93
Aligned: 86
Modelled: 31
Confidence: 17.3%
Identity: 19%
Fold: PH domain-like barrel
Superfamily: PH domain-like
Family: Enabled/VASP homology 1 domain (EVH1 domain)

Phyre2

PDB 1bcr chain A

3D model

Region: 83 - 110
Aligned: 26
Modelled: 28
Confidence: 14.9%
Identity: 31%
PDB header:hydrolase/hydrolase inhibitor
Chain: A: PDB Molecule:serine carboxypeptidase ii;
PDBTitle: complex of the wheat serine carboxypeptidase, cpdw-ii, with the2 microbial peptide aldehyde inhibitor, antipain, and arginine at room3 temperature

Phyre2

PDB 2dt4 chain A

3D model

Region: 78 - 95
Aligned: 18
Modelled: 28
Confidence: 14.3%
Identity: 17%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein ph0802;
PDBTitle: crystal structure of pyrococcus horikoshii a plant- and prokaryote-2 conserved (ppc) protein at 1.60 resolution

Phyre2

PDB 3isy chain A

3D model

Region: 70 - 106
Aligned: 37
Modelled: 37
Confidence: 13.5%
Identity: 14%
PDB header:protein binding
Chain: A: PDB Molecule:intracellular proteinase inhibitor;
PDBTitle: crystal structure of an intracellular proteinase inhibitor (ipi,2 bsu11130) from bacillus subtilis at 2.61 a resolution

Phyre2

PDB 3apa chain A

3D model

Region: 32 - 100
Aligned: 67
Modelled: 37
Confidence: 13.5%
Identity: 18%
PDB header:sugar binding protein
Chain: A: PDB Molecule:zymogen granule membrane protein 16;
PDBTitle: crystal structure of human pancreatic secretory protein zg16p

Phyre2

PDB 1olm chain A domain 2

3D model

Region: 81 - 102
Aligned: 22
Modelled: 22
Confidence: 12.3%
Identity: 23%
Fold: Supernatant protein factor (SPF), C-terminal domain
Superfamily: Supernatant protein factor (SPF), C-terminal domain
Family: Supernatant protein factor (SPF), C-terminal domain

Phyre2
1
c2kr0A_
2
c2z59A_
3
c2r2yA_
4
c2z4dA_
5
d2aj7a1
6
d1ddwa_
7
d1evha_
8
c2l23A_
9
c2kc8B_
10
d2hx0a1
11
c3fkeB_
12
d2h6la1
13
d2ns0a1
14
d1qqga2
15
d1egxa_
16
c1bcrA_
17
c2dt4A_
18
c3isyA_
19
c3apaA_
20
d1olma2
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62



Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c2kr0A_
100.0 24 PDB header:protein binding
Chain: A: PDB Molecule:proteasomal ubiquitin receptor adrm1;
PDBTitle: a proteasome protein
2c2z59A_
100.0 29 PDB header:protein transport
Chain: A: PDB Molecule:protein adrm1;
PDBTitle: complex structures of mouse rpn13 (22-130aa) and ubiquitin
3c2r2yA_
100.0 29 PDB header:protein binding
Chain: A: PDB Molecule:protein adrm1;
PDBTitle: crystal structure of the proteasomal rpn13 pru-domain
4c2z4dA_
100.0 100 PDB header:nuclear protein
Chain: A: PDB Molecule:26s proteasome regulatory subunit rpn13;
PDBTitle: nmr structures of yeast proteasome component rpn13
5d2aj7a1
81.0 18 Fold:BH3618-like
Superfamily:BH3618-like
Family:BH3618-like
6d1ddwa_
51.3 15 Fold:PH domain-like barrel
Superfamily:PH domain-like
Family:Enabled/VASP homology 1 domain (EVH1 domain)
7d1evha_
50.3 13 Fold:PH domain-like barrel
Superfamily:PH domain-like
Family:Enabled/VASP homology 1 domain (EVH1 domain)
8c2l23A_
35.3 20 PDB header:transcription
Chain: A: PDB Molecule:mediator of rna polymerase ii transcription subunit 25;
PDBTitle: nmr structure of the acid (activator interacting domain) of the human2 mediator med25 protein
9c2kc8B_
29.4 32 PDB header:toxin/toxin repressor
Chain: B: PDB Molecule:antitoxin relb;
PDBTitle: structure of e. coli toxin rele (r81a/r83a) mutant in2 complex with antitoxin relbc (k47-l79) peptide
10d2hx0a1
22.0 19 Fold:AF0104/ALDC/Ptd012-like
Superfamily:AF0104/ALDC/Ptd012-like
Family:AF0104-like
11c3fkeB_
19.7 16 PDB header:rna binding protein
Chain: B: PDB Molecule:polymerase cofactor vp35;
PDBTitle: structure of the ebola vp35 interferon inhibitory domain
12d2h6la1
19.1 16 Fold:AF0104/ALDC/Ptd012-like
Superfamily:AF0104/ALDC/Ptd012-like
Family:AF0104-like
13d2ns0a1
18.8 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:RHA1 ro06458-like
14d1qqga2
18.0 33 Fold:PH domain-like barrel
Superfamily:PH domain-like
Family:Phosphotyrosine-binding domain (PTB)
15d1egxa_
17.3 19 Fold:PH domain-like barrel
Superfamily:PH domain-like
Family:Enabled/VASP homology 1 domain (EVH1 domain)
16c1bcrA_
14.9 31 PDB header:hydrolase/hydrolase inhibitor
Chain: A: PDB Molecule:serine carboxypeptidase ii;
PDBTitle: complex of the wheat serine carboxypeptidase, cpdw-ii, with the2 microbial peptide aldehyde inhibitor, antipain, and arginine at room3 temperature
17c2dt4A_
14.3 17 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein ph0802;
PDBTitle: crystal structure of pyrococcus horikoshii a plant- and prokaryote-2 conserved (ppc) protein at 1.60 resolution
18c3isyA_
13.5 14 PDB header:protein binding
Chain: A: PDB Molecule:intracellular proteinase inhibitor;
PDBTitle: crystal structure of an intracellular proteinase inhibitor (ipi,2 bsu11130) from bacillus subtilis at 2.61 a resolution
19c3apaA_
13.5 18 PDB header:sugar binding protein
Chain: A: PDB Molecule:zymogen granule membrane protein 16;
PDBTitle: crystal structure of human pancreatic secretory protein zg16p
20d1olma2
12.3 23 Fold:Supernatant protein factor (SPF), C-terminal domain
Superfamily:Supernatant protein factor (SPF), C-terminal domain
Family:Supernatant protein factor (SPF), C-terminal domain
21c3egbA_
not modelled 12.1 18 PDB header:protein binding
Chain: A: PDB Molecule:protein pellino homolog 2;
PDBTitle: structure of pellino2 fha domain at 3.3 angstroms resolution.
22c1z8rA_
not modelled 11.9 16 PDB header:hydrolase
Chain: A: PDB Molecule:coxsackievirus b4 polyprotein;
PDBTitle: 2a cysteine proteinase from human coxsackievirus b4 (strain2 jvb / benschoten / new york / 51)
23c3hwuA_
not modelled 11.5 14 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative dna-binding protein;
PDBTitle: crystal structure of putative dna-binding protein (yp_299413.1) from2 ralstonia eutropha jmp134 at 1.30 a resolution
24d2hrva_
not modelled 10.8 8 Fold:Trypsin-like serine proteases
Superfamily:Trypsin-like serine proteases
Family:Viral cysteine protease of trypsin fold
25c1qqgA_
not modelled 9.3 33 PDB header:signal transduction
Chain: A: PDB Molecule:insulin receptor substrate 1;
PDBTitle: crystal structure of the ph-ptb targeting region of irs-1
26c1gxsC_
not modelled 9.0 20 PDB header:lyase
Chain: C: PDB Molecule:p-(s)-hydroxymandelonitrile lyase chain a;
PDBTitle: crystal structure of hydroxynitrile lyase from sorghum2 bicolor in complex with inhibitor benzoic acid: a novel3 cyanogenic enzyme
27d1xoub_
not modelled 8.6 35 Fold:EspA/CesA-like
Superfamily:EspA/CesA-like
Family:EspA chaperone CesA
28d1zaka2
not modelled 8.6 40 Fold:Rubredoxin-like
Superfamily:Microbial and mitochondrial ADK, insert "zinc finger" domain
Family:Microbial and mitochondrial ADK, insert "zinc finger" domain
29d1i2ha_
not modelled 8.5 11 Fold:PH domain-like barrel
Superfamily:PH domain-like
Family:Enabled/VASP homology 1 domain (EVH1 domain)
30d2a6sa1
not modelled 7.7 19 Fold:RelE-like
Superfamily:RelE-like
Family:YoeB/Txe-like
31d1xr0b_
not modelled 7.2 20 Fold:PH domain-like barrel
Superfamily:PH domain-like
Family:Phosphotyrosine-binding domain (PTB)
32d2gdta1
not modelled 7.2 24 Fold:SARS Nsp1-like
Superfamily:SARS Nsp1-like
Family:SARS Nsp1-like
33d1usma_
not modelled 7.1 24 Fold:DCoH-like
Superfamily:PCD-like
Family:PCD-like
34c1jmuD_
not modelled 7.0 19 PDB header:viral protein
Chain: D: PDB Molecule:protein mu-1;
PDBTitle: crystal structure of the reovirus mu1/sigma3 complex
35c3htnA_
not modelled 6.9 14 PDB header:metal binding protein
Chain: A: PDB Molecule:putative dna binding protein;
PDBTitle: crystal structure of a putative dna binding protein (bt_1116) from2 bacteroides thetaiotaomicron vpi-5482 at 1.50 a resolution
36d1r9wa_
not modelled 6.7 11 Fold:Origin of replication-binding domain, RBD-like
Superfamily:Origin of replication-binding domain, RBD-like
Family:Replication initiation protein E1
37d1oqka_
not modelled 6.6 13 Fold:Rof/RNase P subunit-like
Superfamily:Rof/RNase P subunit-like
Family:RNase P subunit p29-like
38d1gpca_
not modelled 6.5 23 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Phage ssDNA-binding proteins
39d1bqua2
not modelled 6.4 13 Fold:Immunoglobulin-like beta-sandwich
Superfamily:Fibronectin type III
Family:Fibronectin type III
40c3oeiH_
not modelled 6.4 10 PDB header:toxin, protein binding
Chain: H: PDB Molecule:relk (toxin rv3358);
PDBTitle: crystal structure of mycobacterium tuberculosis reljk (rv3357-rv3358-2 relbe3)
41c2odxA_
not modelled 6.2 18 PDB header:oxidoreductase
Chain: A: PDB Molecule:cytochrome c oxidase polypeptide iv;
PDBTitle: solution structure of zn(ii)cox4
42d3bwuc1
not modelled 6.2 18 Fold:Immunoglobulin-like beta-sandwich
Superfamily:PapD-like
Family:Pilus chaperone
43c3ewgA_
not modelled 6.1 8 PDB header:transcription
Chain: A: PDB Molecule:putative transcription antitermination protein nusg;
PDBTitle: crystal structure of the n-terminal domain of nusg (ngn) from2 methanocaldococcus jannaschii
44c2zkro_
not modelled 6.0 15 PDB header:ribosomal protein/rna
Chain: O: PDB Molecule:rna expansion segment es30;
PDBTitle: structure of a mammalian ribosomal 60s subunit within an 80s complex2 obtained by docking homology models of the rna and proteins into an3 8.7 a cryo-em map
45d2hg6a1
not modelled 6.0 33 Fold:PA1123-like
Superfamily:PA1123-like
Family:PA1123-like
46d1jl1a_
not modelled 5.9 14 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Ribonuclease H
47c3pjyB_
not modelled 5.9 8 PDB header:transcription regulator
Chain: B: PDB Molecule:hypothetical signal peptide protein;
PDBTitle: crystal structure of a putative transcription regulator (r01717) from2 sinorhizobium meliloti 1021 at 1.55 a resolution
48c2ktrA_
not modelled 5.7 18 PDB header:signaling protein, transport protein
Chain: A: PDB Molecule:sequestosome-1;
PDBTitle: nmr structure of p62 pb1 dimer determined based on pcs
49c2cseB_
not modelled 5.4 19 PDB header:virus
Chain: B: PDB Molecule:major outer-capsid protein mu1;
PDBTitle: features of reovirus outer-capsid protein mu1 revealed by2 electron and image reconstruction of the virion at 7.0-a3 resolution
50d1eeta1
not modelled 5.4 24 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Ribonuclease H
51c2lhkB_
not modelled 5.3 30 PDB header:chaperone
Chain: B: PDB Molecule:l0052;
PDBTitle: structural analysis of a chaperone in type iii secretion system
52d1mu2a1
not modelled 5.3 24 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Ribonuclease H
53c3ddcB_
not modelled 5.2 18 PDB header:hydrolase/apoptosis
Chain: B: PDB Molecule:ras association domain-containing family protein 5;
PDBTitle: crystal structure of nore1a in complex with ras
54c3u22B_
not modelled 5.2 6 PDB header:heme binding protein
Chain: B: PDB Molecule:putative hmuy_like heme binding protein;
PDBTitle: crystal structure of a putative hmuy_like heme binding protein2 (bvu_2192) from bacteroides vulgatus atcc 8482 at 2.12 a resolution
55d1qc6a_
not modelled 5.2 18 Fold:PH domain-like barrel
Superfamily:PH domain-like
Family:Enabled/VASP homology 1 domain (EVH1 domain)
56d1f08a_
not modelled 5.2 22 Fold:Origin of replication-binding domain, RBD-like
Superfamily:Origin of replication-binding domain, RBD-like
Family:Replication initiation protein E1
57c3ks8D_
not modelled 5.2 12 PDB header:viral protein/rna
Chain: D: PDB Molecule:polymerase cofactor vp35;
PDBTitle: crystal structure of reston ebolavirus vp35 rna binding2 domain in complex with 18bp dsrna
58c3iz5D_
not modelled 5.1 15 PDB header:ribosome
Chain: D: PDB Molecule:60s ribosomal protein l4 (l4p);
PDBTitle: localization of the large subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome
59c3dwvB_
not modelled 5.1 18 PDB header:oxidoreductase
Chain: B: PDB Molecule:glutathione peroxidase-like protein;
PDBTitle: glutathione peroxidase-type tryparedoxin peroxidase,2 oxidized form
60d1fltx_
not modelled 5.1 19 Fold:Immunoglobulin-like beta-sandwich
Superfamily:Immunoglobulin
Family:I set domains
61d2r4qa1
not modelled 5.1 13 Fold:Phosphotyrosine protein phosphatases I-like
Superfamily:PTS system IIB component-like
Family:PTS system, Fructose specific IIB subunit-like
62c3q6kA_
not modelled 5.0 12 PDB header:protein binding
Chain: A: PDB Molecule:43.2 kda salivary protein;
PDBTitle: salivary protein from lutzomyia longipalpis

Binding site prediction 

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