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2JF5
Asym. Unit
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Asym.Unit (35 KB)
Biol.Unit 1 (28 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF LYS63-LINKED DI-UBIQUITIN
Authors
:
D. Komander, P. Odenwaelder, D. Barford
Date
:
26 Jan 07 (Deposition) - 05 Feb 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.95
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Lys6, Lys63, Nf-Kb, Ubiquitin, Nuclear Protein, Signal Transduction, Signaling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Komander, F. Reyes-Turcu, J. D. F. Licchesi, P. Odenwaelder, K. D. Wilkinson, D. Barford
Molecular Discrimination Of Structurally Equivalent Lys 63-Linked And Linear Polyubiquitin Chains.
Embo Rep. V. 10 466 2009
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Hetero Components
(4, 6)
Info
All Hetero Components
1a: CADMIUM ION (CDa)
1b: CADMIUM ION (CDb)
2a: CHLORIDE ION (CLa)
3a: COBALT (II) ION (COa)
3b: COBALT (II) ION (COb)
4a: MAGNESIUM ION (MGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CD
2
Ligand/Ion
CADMIUM ION
2
CL
1
Ligand/Ion
CHLORIDE ION
3
CO
2
Ligand/Ion
COBALT (II) ION
4
MG
1
Ligand/Ion
MAGNESIUM ION
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU B:18 , ASP B:21 , LYS B:29 , CL B:1080
BINDING SITE FOR RESIDUE CD B1077
2
AC2
SOFTWARE
GLU A:18 , ASP A:21 , LYS A:29
BINDING SITE FOR RESIDUE CD A1076
3
AC3
SOFTWARE
MET B:1 , GLU B:16 , ASP B:32 , HOH B:2047
BINDING SITE FOR RESIDUE CO B1079
4
AC4
SOFTWARE
GLU B:18 , LYS B:29 , CD B:1077
BINDING SITE FOR RESIDUE CL B1080
5
AC5
SOFTWARE
MET A:1 , GLU A:16 , ASP A:32 , HOH A:2005
BINDING SITE FOR RESIDUE MG A1078
6
AC6
SOFTWARE
GLU B:64 , HIS B:68 , HOH B:2039 , HOH B:2043
BINDING SITE FOR RESIDUE CO B1081
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: UBIQUITIN_2 (A:1-75,B:1-76,A:1-75,B:1-76,-|-|A:...)
2: UBIQUITIN_1 (A:27-52,B:27-52,A:27-52,B:27-52,-|...)
;
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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
A:1-75
B:1-76
RL40_HUMAN
1-76
2
A:1-75
B:1-76
UBB_HUMAN
1-76
77-152
153-228
2
-
-
A:1-75
B:1-76
UBC_HUMAN
1-76
77-152
153-228
229-304
305-380
381-456
457-532
533-608
609-684
2
-
-
-
-
-
-
-
-
A:1-75
B:1-76
2
UBIQUITIN_1
PS00299
Ubiquitin domain signature.
RS27A_HUMAN
27-52
2
A:27-52
B:27-52
RL40_HUMAN
27-52
2
A:27-52
B:27-52
UBB_HUMAN
27-52
103-128
179-204
2
-
-
A:27-52
B:27-52
UBC_HUMAN
27-52
103-128
179-204
255-280
331-356
407-432
483-508
559-584
635-660
2
-
-
-
-
-
-
-
-
A:27-52
B:27-52
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Exons
(1, 2)
Info
All Exons
Exon 1.2 (A:1-75 | B:1-76)
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All Exon Boundaries
1: Boundary 1.1/1.2
2: Boundary 1.2/-
View:
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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
2
A:1-75
B:1-76
75
76
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SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2jf5a_ (A:)
1b: SCOP_d2jf5b_ (B:)
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Classes
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)
(
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Folds
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)
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)
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)
(
)
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
d2jf5a_
A:
1b
d2jf5b_
B:
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2jf5B00 (B:1-76)
1b: CATH_2jf5A00 (A:1-75)
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Classes
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(
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)
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)
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)
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)
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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
2jf5B00
B:1-76
1b
2jf5A00
A:1-75
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_ubiquitin_2jf5B01 (B:6-74)
1b: PFAM_ubiquitin_2jf5B02 (B:6-74)
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Clans
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)
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)
(
)
Clan
:
Ubiquitin
(279)
Family
:
ubiquitin
(99)
Homo sapiens (Human)
(67)
1a
ubiquitin-2jf5B01
B:6-74
1b
ubiquitin-2jf5B02
B:6-74
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Asymmetric Unit 1
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (35 KB)
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