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2GFO
Asym. Unit
Info
Asym.Unit (69 KB)
Biol.Unit 1 (61 KB)
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(1)
Title
:
STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 8
Authors
:
J. R. Walker, G. V Avvakumov, S. Xue, E. M. Newman, P. J. Finerty Jr. , C. Cole, J. Weigelt, M. Sundstrom, C. Arrowsmith, A. Edwards, A. Bochkar Paganon, Structural Genomics Consortium (Sgc)
Date
:
22 Mar 06 (Deposition) - 04 Apr 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Hydrolase, Protease, Thiol Protease, Ubl Conjugation Pathway, Deubiquitinating Enzyme, Dub, Zinc Ribbon, Structural Genomics Consortium, Sgc
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. V. Avvakumov, J. R. Walker, S. Xue, P. J. Finerty Jr. , F. Mackenzie, E. M. Newman, S. Dhe-Paganon
Amino-Terminal Dimerization, Nrdp1-Rhodanese Interaction, And Inhibited Catalytic Domain Conformation Of The Ubiquitin-Specific Protease 8 (Usp8).
J. Biol. Chem. V. 281 38061 2006
[
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Hetero Components
(2, 5)
Info
All Hetero Components
1a: SELENOMETHIONINE (MSEa)
1b: SELENOMETHIONINE (MSEb)
1c: SELENOMETHIONINE (MSEc)
1d: SELENOMETHIONINE (MSEd)
2a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MSE
4
Mod. Amino Acid
SELENOMETHIONINE
2
ZN
1
Ligand/Ion
ZINC ION
[
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]
Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS A:936 , CYS A:939 , CYS A:985 , CYS A:988
BINDING SITE FOR RESIDUE ZN A 1200
[
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SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_017797 (A827G, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_017797
A
827
G
UBP8_HUMAN
Polymorphism
1056577
A
A
827
G
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: USP_3 (A:777-1109)
2: USP_1 (A:778-793)
3: USP_2 (A:1051-1068)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
USP_3
PS50235
Ubiquitin specific protease (USP) domain profile.
UBP8_HUMAN
777-1109
1
A:777-1109
2
USP_1
PS00972
Ubiquitin specific protease (USP) domain signature 1.
UBP8_HUMAN
778-793
1
A:778-793
3
USP_2
PS00973
Ubiquitin specific protease (USP) domain signature 2.
UBP8_HUMAN
1051-1068
1
A:1051-1068
[
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Exons
(6, 6)
Info
All Exons
Exon 1.16a (A:762-816)
Exon 1.20a (A:816-886)
Exon 1.21b (A:887-965 (gaps))
Exon 1.22 (A:966-1013)
Exon 1.23 (A:1013-1057)
Exon 1.24b (A:1058-1109)
View:
Select:
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All Exon Boundaries
1: Boundary 1.15/1.16a
2: Boundary 1.16a/1.20a
3: Boundary 1.20a/1.21b
4: Boundary 1.21b/1.22
5: Boundary 1.22/1.23
6: Boundary 1.23/1.24b
7: Boundary 1.24b/-
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
1.1b
ENST00000396444
1b
ENSE00001524965
chr15:
50716579-50716851
273
UBP8_HUMAN
-
0
0
-
-
1.3
ENST00000396444
3
ENSE00000931366
chr15:
50731206-50731374
169
UBP8_HUMAN
1-35
35
0
-
-
1.4
ENST00000396444
4
ENSE00000931367
chr15:
50733546-50733690
145
UBP8_HUMAN
35-83
49
0
-
-
1.5
ENST00000396444
5
ENSE00000931368
chr15:
50741597-50741682
86
UBP8_HUMAN
84-112
29
0
-
-
1.6
ENST00000396444
6
ENSE00000931369
chr15:
50751197-50751359
163
UBP8_HUMAN
112-166
55
0
-
-
1.7
ENST00000396444
7
ENSE00000931370
chr15:
50754477-50754519
43
UBP8_HUMAN
167-181
15
0
-
-
1.8
ENST00000396444
8
ENSE00000931371
chr15:
50757244-50757388
145
UBP8_HUMAN
181-229
49
0
-
-
1.9
ENST00000396444
9
ENSE00000931372
chr15:
50763830-50763992
163
UBP8_HUMAN
229-283
55
0
-
-
1.10
ENST00000396444
10
ENSE00000931373
chr15:
50769046-50769190
145
UBP8_HUMAN
284-332
49
0
-
-
1.11
ENST00000396444
11
ENSE00000931374
chr15:
50769473-50769696
224
UBP8_HUMAN
332-406
75
0
-
-
1.12
ENST00000396444
12
ENSE00000931375
chr15:
50773678-50774262
585
UBP8_HUMAN
407-601
195
0
-
-
1.13
ENST00000396444
13
ENSE00000931376
chr15:
50776472-50776558
87
UBP8_HUMAN
602-630
29
0
-
-
1.14
ENST00000396444
14
ENSE00000931377
chr15:
50781998-50782078
81
UBP8_HUMAN
631-657
27
0
-
-
1.15
ENST00000396444
15
ENSE00000931378
chr15:
50782460-50782722
263
UBP8_HUMAN
658-745
88
0
-
-
1.16a
ENST00000396444
16a
ENSE00000931379
chr15:
50784898-50785110
213
UBP8_HUMAN
745-816
72
1
A:762-816
55
1.20a
ENST00000396444
20a
ENSE00000931380
chr15:
50786267-50786477
211
UBP8_HUMAN
816-886
71
1
A:816-886
71
1.21b
ENST00000396444
21b
ENSE00000931381
chr15:
50788045-50788281
237
UBP8_HUMAN
887-965
79
1
A:887-965 (gaps)
79
1.22
ENST00000396444
22
ENSE00000884623
chr15:
50789286-50789428
143
UBP8_HUMAN
966-1013
48
1
A:966-1013
48
1.23
ENST00000396444
23
ENSE00000931382
chr15:
50790793-50790925
133
UBP8_HUMAN
1013-1057
45
1
A:1013-1057
45
1.24b
ENST00000396444
24b
ENSE00001904826
chr15:
50791100-50793280
2181
UBP8_HUMAN
1058-1118
61
1
A:1058-1109
52
[
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SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2gfoa1 (A:762-1109)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Cysteine proteinases
(392)
Superfamily
:
Cysteine proteinases
(392)
Family
:
Ubiquitin carboxyl-terminal hydrolase, UCH
(14)
Protein domain
:
Ubiquitin carboxyl-terminal hydrolase 8
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d2gfoa1
A:762-1109
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
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Pfam Domains
(0, 0)
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Sorry, no Info available
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Chain A
Asymmetric Unit 1
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