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3IHP
Asym. Unit
Info
Asym.Unit (422 KB)
Biol.Unit 1 (207 KB)
Biol.Unit 2 (208 KB)
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(1)
Title
:
COVALENT UBIQUITIN-USP5 COMPLEX
Authors
:
J. R. Walker, G. V. Avvakumov, S. Xue, C. Butler-Cole, J. Weigelt, C. Bountra, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, S. Dhe- Paganon, Structural Genomics Consortium (Sgc)
Date
:
30 Jul 09 (Deposition) - 29 Dec 09 (Release) - 29 Dec 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C (1x)
Biol. Unit 2: B,D (1x)
Keywords
:
Hydrolase, Protease, Thiol Protease, Ubl Conjugation Pathway, Metal-Binding, Zinc-Finger, Structural Genomics, Structural Genomics Consortium, Sgc, Acetylation, Alternative Splicing, Phosphoprotein, Zinc, Cytoplasm, Isopeptide Bond, Nucleus, Ubl Conjugation
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. R. Walker, G. V. Avvakumov, S. Xue, C. Butler-Cole, J. Weigelt, C. Bountra, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, S. Dhe-Paganon
Covalent Ubiquitin-Usp5 Complex
To Be Published
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 5)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
2a: ETHANAMINE (NEHa)
2b: ETHANAMINE (NEHb)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
1
Ligand/Ion
CHLORIDE ION
2
NEH
2
Ligand/Ion
ETHANAMINE
3
ZN
2
Ligand/Ion
ZINC ION
[
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]
Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN A:333 , CYS A:335 , GLN A:433 , GLY A:794 , GLY C:75
BINDING SITE FOR RESIDUE NEH C 76
2
AC2
SOFTWARE
ASN B:333 , CYS B:335 , GLN B:433 , GLY B:794 , GLY D:75
BINDING SITE FOR RESIDUE NEH D 76
3
AC3
SOFTWARE
ARG D:74
BINDING SITE FOR RESIDUE CL D 77
4
AC4
SOFTWARE
CYS A:199 , CYS A:202 , CYS A:219 , HIS A:232
BINDING SITE FOR RESIDUE ZN A 836
5
AC5
SOFTWARE
CYS B:199 , CYS B:202 , CYS B:219 , HIS B:232
BINDING SITE FOR RESIDUE ZN B 836
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(7, 16)
Info
All PROSITE Patterns/Profiles
1: UBIQUITIN_2 (C:1-75,D:1-75,C:1-75,D:1-75,-|-|C:...)
2: UBIQUITIN_1 (C:27-52,D:27-52,C:27-52,D:27-52,-|...)
3: ZF_UBP (A:197-269,B:197-269)
4: USP_3 (A:326-833,B:326-833)
5: USP_1 (A:327-342,B:327-342)
6: UBA (A:634-672,B:632-672|A:698-738,B:69...)
7: USP_2 (A:778-796,B:778-796)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
UBIQUITIN_2
PS50053
Ubiquitin domain profile.
RS27A_HUMAN
1-76
2
C:1-75
D:1-75
RL40_HUMAN
1-76
2
C:1-75
D:1-75
UBB_HUMAN
1-76
77-152
153-228
2
-
-
C:1-75
D:1-75
UBC_HUMAN
1-76
77-152
153-228
229-304
305-380
381-456
457-532
533-608
609-684
2
-
-
-
-
-
-
-
-
C:1-75
D:1-75
2
UBIQUITIN_1
PS00299
Ubiquitin domain signature.
RS27A_HUMAN
27-52
2
C:27-52
D:27-52
RL40_HUMAN
27-52
2
C:27-52
D:27-52
UBB_HUMAN
27-52
103-128
179-204
2
-
-
C:27-52
D:27-52
UBC_HUMAN
27-52
103-128
179-204
255-280
331-356
407-432
483-508
559-584
635-660
2
-
-
-
-
-
-
-
-
C:27-52
D:27-52
3
ZF_UBP
PS50271
Zinc finger UBP-type profile.
UBP5_HUMAN
197-269
2
A:197-269
B:197-269
4
USP_3
PS50235
Ubiquitin specific protease (USP) domain profile.
UBP5_HUMAN
326-856
2
A:326-833
B:326-833
5
USP_1
PS00972
Ubiquitin specific protease (USP) domain signature 1.
UBP5_HUMAN
327-342
2
A:327-342
B:327-342
6
UBA
PS50030
Ubiquitin-associated domain (UBA) profile.
UBP5_HUMAN
654-695
722-762
4
A:634-672
B:632-672
A:698-738
B:699-739
7
USP_2
PS00973
Ubiquitin specific protease (USP) domain signature 2.
UBP5_HUMAN
801-819
2
A:778-796
B:778-796
[
close PROSITE info
]
Exons
(20, 40)
Info
All Exons
Exon 1.1a (A:1-37 | B:1-37)
Exon 1.2 (A:38-76 | B:38-76)
Exon 1.4 (A:117-146 | B:117-146)
Exon 1.5 (A:147-195 (gaps) | B:147-195 (gaps...)
Exon 1.6 (A:195-257 (gaps) | B:195-257)
Exon 1.7 (A:257-283 | B:257-283)
Exon 1.8 (A:319-353 | B:316-353)
Exon 1.9 (A:353-377 | B:353-377)
Exon 1.10 (A:377-388 | B:377-388)
Exon 1.11 (A:410-448 | B:411-448)
Exon 1.12 (A:449-500 | B:449-500)
Exon 1.13 (A:500-558 | B:500-558)
Exon 1.14 (A:558-588 | B:558-588)
Exon 1.15b (A:588-617 | B:588-617)
Exon 1.16 (A:634-677 | B:632-677)
Exon 1.17 (A:677-724 (gaps) | B:677-725 (gaps...)
Exon 1.18 (A:725-777 (gaps) | B:726-777 (gaps...)
Exon 1.19 (A:777-805 | B:777-805)
Exon 1.20 (A:805-834 | B:805-835)
Exon 2.2 (C:1-75 | D:1-75)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1a
02: Boundary 1.1a/1.2
03: Boundary 1.2/1.3
04: Boundary 1.3/1.4
05: Boundary 1.4/1.5
06: Boundary 1.5/1.6
07: Boundary 1.6/1.7
08: Boundary 1.7/1.8
09: Boundary 1.8/1.9
10: Boundary 1.9/1.10
11: Boundary 1.10/1.11
12: Boundary 1.11/1.12
13: Boundary 1.12/1.13
14: Boundary 1.13/1.14
15: Boundary 1.14/1.15b
16: Boundary 1.15b/1.16
17: Boundary 1.16/1.17
18: Boundary 1.17/1.18
19: Boundary 1.18/1.19
20: Boundary 1.19/1.20
21: Boundary 1.20/-
22: Boundary 2.1/2.2
23: Boundary 2.2/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1a
ENST00000229268
1a
ENSE00001603691
chr12:
6961285-6961454
170
UBP5_HUMAN
1-37
37
2
A:1-37
B:1-37
37
37
1.2
ENST00000229268
2
ENSE00000716138
chr12:
6964565-6964690
126
UBP5_HUMAN
38-79
42
2
A:38-76
B:38-76
39
39
1.3
ENST00000229268
3
ENSE00000716140
chr12:
6964919-6964985
67
UBP5_HUMAN
80-102
23
0
-
-
1.4
ENST00000229268
4
ENSE00000716141
chr12:
6965181-6965314
134
UBP5_HUMAN
102-146
45
2
A:117-146
B:117-146
30
30
1.5
ENST00000229268
5
ENSE00000716142
chr12:
6965469-6965614
146
UBP5_HUMAN
147-195
49
2
A:147-195 (gaps)
B:147-195 (gaps)
49
49
1.6
ENST00000229268
6
ENSE00000716143
chr12:
6965871-6966055
185
UBP5_HUMAN
195-257
63
2
A:195-257 (gaps)
B:195-257
63
63
1.7
ENST00000229268
7
ENSE00000716144
chr12:
6966793-6966887
95
UBP5_HUMAN
257-288
32
2
A:257-283
B:257-283
27
27
1.8
ENST00000229268
8
ENSE00000716145
chr12:
6967588-6967781
194
UBP5_HUMAN
289-353
65
2
A:319-353
B:316-353
35
38
1.9
ENST00000229268
9
ENSE00000866969
chr12:
6968634-6968705
72
UBP5_HUMAN
353-377
25
2
A:353-377
B:353-377
25
25
1.10
ENST00000229268
10
ENSE00000716147
chr12:
6969315-6969402
88
UBP5_HUMAN
377-406
30
2
A:377-388
B:377-388
12
12
1.11
ENST00000229268
11
ENSE00000716148
chr12:
6969530-6969655
126
UBP5_HUMAN
407-448
42
2
A:410-448
B:411-448
39
38
1.12
ENST00000229268
12
ENSE00000716149
chr12:
6970117-6970270
154
UBP5_HUMAN
449-500
52
2
A:449-500
B:449-500
52
52
1.13
ENST00000229268
13
ENSE00000716150
chr12:
6970607-6970781
175
UBP5_HUMAN
500-558
59
2
A:500-558
B:500-558
59
59
1.14
ENST00000229268
14
ENSE00000716151
chr12:
6971634-6971722
89
UBP5_HUMAN
558-588
31
2
A:558-588
B:558-588
31
31
1.15b
ENST00000229268
15b
ENSE00000866970
chr12:
6972350-6972541
192
UBP5_HUMAN
588-652
65
2
A:588-617
B:588-617
30
30
1.16
ENST00000229268
16
ENSE00000716153
chr12:
6972994-6973137
144
UBP5_HUMAN
652-700
49
2
A:634-677
B:632-677
44
46
1.17
ENST00000229268
17
ENSE00000716154
chr12:
6973214-6973359
146
UBP5_HUMAN
700-748
49
2
A:677-724 (gaps)
B:677-725 (gaps)
49
49
1.18
ENST00000229268
18
ENSE00000716155
chr12:
6973886-6974039
154
UBP5_HUMAN
749-800
52
2
A:725-777 (gaps)
B:726-777 (gaps)
53
52
1.19
ENST00000229268
19
ENSE00000716156
chr12:
6974328-6974412
85
UBP5_HUMAN
800-828
29
2
A:777-805
B:777-805
29
29
1.20
ENST00000229268
20
ENSE00001164806
chr12:
6975148-6975793
646
UBP5_HUMAN
828-858
31
2
A:805-834
B:805-835
30
31
2.1
ENST00000339647
1
ENSE00001257182
chr12:
125399577-125399133
445
UBC_HUMAN
-
0
0
-
-
2.2
ENST00000339647
2
ENSE00001406973
chr12:
125398320-125396194
2127
UBC_HUMAN
1-686
686
2
C:1-75
D:1-75
75
75
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3ihpc_ (C:)
1b: SCOP_d3ihpd_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
beta-Grasp (ubiquitin-like)
(1032)
Superfamily
:
Ubiquitin-like
(546)
Family
:
Ubiquitin-related
(337)
Protein domain
:
Ubiquitin
(162)
Human (Homo sapiens) [TaxId: 9606]
(121)
1a
d3ihpc_
C:
1b
d3ihpd_
D:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_3ihpC00 (C:1-75)
1b: CATH_3ihpD00 (D:1-75)
View:
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Classes
(
)
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Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Roll
(3276)
Topology
:
Ubiquitin-like (UB roll)
(674)
Homologous Superfamily
:
Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
(286)
Human (Homo sapiens)
(177)
1a
3ihpC00
C:1-75
1b
3ihpD00
D:1-75
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Atom Selection
(currently selected atoms:
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Chain C
Chain D
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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