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3A33
Asym. Unit
Info
Asym.Unit (43 KB)
Biol.Unit 1 (76 KB)
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(1)
Title
:
UBCH5B~UBIQUITIN CONJUGATE
Authors
:
E. Sakata, T. Satoh, S. Yamamoto, Y. Yamaguchi, M. Yagi-Utsumi, E. Kuri S. Wakatsuki, K. Kato
Date
:
08 Jun 09 (Deposition) - 24 Nov 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
E2 Ubiquitin-Conjugating Enzyme, Ubiquitin, Ligase, Ubl Conjugation Pathway, Isopeptide Bond, Nucleus
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Sakata, T. Satoh, S. Yamamoto, Y. Yamaguchi, M. Yagi-Utsumi, E. Kurimoto, K. Tanaka, S. Wakatsuki, K. Kato
Crystal Structure Of Ubch5B~Ubiquitin Intermediate: Insight Into The Formation Of The Self-Assembled E2~Ub Conjugates
Structure V. 18 138 2010
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
1
Ligand/Ion
GLYCEROL
[
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Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
PRO A:65 , LYS A:66 , VAL A:67 , SER A:83 , ILE A:84 , HOH A:171
BINDING SITE FOR RESIDUE GOL A 148
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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
(4, 4)
Info
All PROSITE Patterns/Profiles
1: UBIQUITIN_2 (B:1-76,B:1-76,-|-|B:1-76,-|-|-|-|-...)
2: UBIQUITIN_CONJUGAT_2 (A:4-136)
3: UBIQUITIN_1 (B:27-52,B:27-52,-|-|B:27-52,-|-|-|...)
4: UBIQUITIN_CONJUGAT_1 (A:74-89)
;
View:
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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
1
B:1-76
RL40_HUMAN
1-76
1
B:1-76
UBB_HUMAN
1-76
77-152
153-228
1
-
-
B:1-76
UBC_HUMAN
1-76
77-152
153-228
229-304
305-380
381-456
457-532
533-608
609-684
1
-
-
-
-
-
-
-
-
B:1-76
2
UBIQUITIN_CONJUGAT_2
PS50127
Ubiquitin-conjugating enzymes family profile.
UB2D2_HUMAN
4-136
1
A:4-136
3
UBIQUITIN_1
PS00299
Ubiquitin domain signature.
RS27A_HUMAN
27-52
1
B:27-52
RL40_HUMAN
27-52
1
B:27-52
UBB_HUMAN
27-52
103-128
179-204
1
-
-
B:27-52
UBC_HUMAN
27-52
103-128
179-204
255-280
331-356
407-432
483-508
559-584
635-660
1
-
-
-
-
-
-
-
-
B:27-52
4
UBIQUITIN_CONJUGAT_1
PS00183
Ubiquitin-conjugating enzymes active site.
UB2D2_HUMAN
74-89
1
A:74-89
[
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]
Exons
(8, 8)
Info
All Exons
Exon 1.2 (B:1-76)
Exon 2.2d (A:1-8)
Exon 2.6a (A:9-30)
Exon 2.7a (A:30-40)
Exon 2.8 (A:41-66)
Exon 2.9 (A:67-102)
Exon 2.10b (A:102-133)
Exon 2.11b (A:133-147)
View:
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All Exon Boundaries
01: Boundary 1.1/1.2
02: Boundary 1.2/-
03: Boundary -/2.2d
04: Boundary 2.2d/2.6a
05: Boundary 2.6a/2.7a
06: Boundary 2.7a/2.8
07: Boundary 2.8/2.9
08: Boundary 2.9/2.10b
09: Boundary 2.10b/2.11b
10: Boundary 2.11b/2.11f
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
1.1
ENST00000339647
1
ENSE00001257182
chr12:
125399577-125399133
445
UBC_HUMAN
-
0
0
-
-
1.2
ENST00000339647
2
ENSE00001406973
chr12:
125398320-125396194
2127
UBC_HUMAN
1-686
686
1
B:1-76
76
2.2d
ENST00000398734
2d
ENSE00002067174
chr5:
138941311-138941400
90
UB2D2_HUMAN
1-8
8
1
A:1-8
8
2.6a
ENST00000398734
6a
ENSE00001727928
chr5:
138979957-138980020
64
UB2D2_HUMAN
9-30
22
1
A:9-30
22
2.7a
ENST00000398734
7a
ENSE00000898561
chr5:
138994171-138994202
32
UB2D2_HUMAN
30-40
11
1
A:30-40
11
2.8
ENST00000398734
8
ENSE00001673964
chr5:
138994282-138994359
78
UB2D2_HUMAN
41-66
26
1
A:41-66
26
2.9
ENST00000398734
9
ENSE00001785808
chr5:
138994446-138994551
106
UB2D2_HUMAN
67-102
36
1
A:67-102
36
2.10b
ENST00000398734
10b
ENSE00001694979
chr5:
139002953-139003046
94
UB2D2_HUMAN
102-133
32
1
A:102-133
32
2.11b
ENST00000398734
11b
ENSE00002035469
chr5:
139006341-139006642
302
UB2D2_HUMAN
133-147
15
1
A:133-147
15
2.11f
ENST00000398734
11f
ENSE00002075824
chr5:
139007137-139007271
135
UB2D2_HUMAN
-
0
0
-
-
[
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SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d3a33b_ (B:)
2a: SCOP_d3a33a_ (A:)
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Classes
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(
)
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(
)
(
)
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
d3a33b_
B:
Fold
:
UBC-like
(176)
Superfamily
:
UBC-like
(176)
Family
:
UBC-related
(135)
Protein domain
:
automated matches
(40)
Human (Homo sapiens) [TaxId: 9606]
(25)
2a
d3a33a_
A:
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CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_3a33B00 (B:1-76)
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(
)
(
)
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
3a33B00
B:1-76
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Asymmetric Unit 1
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