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3DBL
Biol. Unit 1
Info
Asym.Unit (665 KB)
Biol.Unit 1 (169 KB)
Biol.Unit 2 (171 KB)
Biol.Unit 3 (171 KB)
Biol.Unit 4 (173 KB)
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(1)
Title
:
STRUCTURAL DISSECTION OF A GATING MECHANISM PREVENTING MISACTIVATION OF UBIQUITIN BY NEDD8'S E1 (APPBP1-UBA3ARG190WT-NEDD8ALA72GLN)
Authors
:
J. Souphron, B. A. Schulman
Date
:
01 Jun 08 (Deposition) - 12 Aug 08 (Release) - 14 Jul 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: G,H,L (1x)
Biol. Unit 2: C,D,J (1x)
Biol. Unit 3: E,F,K (1x)
Biol. Unit 4: A,B,I (1x)
Keywords
:
Cell Cycle, Activating Enzyme, Apoptosis, Membrane, Ubl Conjugation Pathway, Atp-Binding, Ligase, Nucleotide- Binding, Polymorphism, Nucleus
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Souphron, M. B. Waddell, A. Paydar, Z. Tokgoz-Gromley, M. F. Roussel, B. A. Schulman
Structural Dissection Of A Gating Mechanism Preventing Misactivation Of Ubiquitin By Nedd8'S E1.
Biochemistry V. 47 8961 2008
(for further references see the
PDB file header
)
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Hetero Components
(0, 0)
Info
All Hetero Components
1a: ZINC ION (ZNa)
1b: ZINC ION (ZNb)
1c: ZINC ION (ZNc)
1d: ZINC ION (ZNd)
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Sites
(1, 1)
Info
All Sites
1: AC2 (SOFTWARE)
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Label:
No.
Name
Evidence
Residues
Description
1
AC2
SOFTWARE
CYS H:199 , CYS H:202 , CYS H:343 , CYS H:346
BINDING SITE FOR RESIDUE ZN H 2
[
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SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_052435 (S101F, chain G, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_052435
S
101
F
ULA1_HUMAN
Polymorphism
363212
G
S
101
F
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: UBIQUITIN_2 (L:101-176)
2: UBIQUITIN_1 (L:127-152)
3: UBIQUITIN_ACTIVAT_2 (H:214-222)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
UBIQUITIN_2
PS50053
Ubiquitin domain profile.
NEDD8_HUMAN
1-76
1
-
-
-
L:101-176
2
UBIQUITIN_1
PS00299
Ubiquitin domain signature.
NEDD8_HUMAN
27-52
1
-
-
-
L:127-152
3
UBIQUITIN_ACTIVAT_2
PS00865
Ubiquitin-activating enzyme active site.
UBA3_HUMAN
235-243
1
-
-
-
H:214-222
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Exons
(0, 0)
Info
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(3, 12)
Info
All SCOP Domains
1a: SCOP_d3dbli_ (I:)
1b: SCOP_d3dblj_ (J:)
1c: SCOP_d3dblk_ (K:)
1d: SCOP_d3dbll_ (L:)
2a: SCOP_d3dbla_ (A:)
2b: SCOP_d3dble_ (E:)
2c: SCOP_d3dblg_ (G:)
2d: SCOP_d3dblc_ (C:)
3a: SCOP_d3dblb_ (B:)
3b: SCOP_d3dbld_ (D:)
3c: SCOP_d3dblf_ (F:)
3d: SCOP_d3dblh_ (H:)
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)
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(
)
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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
:
Nedd8
(14)
Human (Homo sapiens) [TaxId: 9606]
(14)
1a
d3dbli_
I:
1b
d3dblj_
J:
1c
d3dblk_
K:
1d
d3dbll_
L:
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Activating enzymes of the ubiquitin-like proteins
(27)
Superfamily
:
Activating enzymes of the ubiquitin-like proteins
(27)
Family
:
Ubiquitin activating enzymes (UBA)
(21)
Protein domain
:
Amyloid beta precursor protein-binding protein 1, APPBP1
(9)
Human (Homo sapiens) [TaxId: 9606]
(9)
2a
d3dbla_
A:
2b
d3dble_
E:
2c
d3dblg_
G:
2d
d3dblc_
C:
Protein domain
:
UBA3
(12)
Human (Homo sapiens) [TaxId: 9606]
(12)
3a
d3dblb_
B:
3b
d3dbld_
D:
3c
d3dblf_
F:
3d
d3dblh_
H:
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CATH Domains
(3, 16)
Info
all CATH domains
1a: CATH_3dblB01 (B:11-209,B:289-339)
1b: CATH_3dblD01 (D:11-209,D:289-339)
1c: CATH_3dblF01 (F:11-209,F:289-339)
1d: CATH_3dblH01 (H:11-209,H:289-339)
1e: CATH_3dblA01 (A:6-178,A:388-534)
1f: CATH_3dblC01 (C:6-178,C:388-534)
1g: CATH_3dblE01 (E:6-178,E:388-534)
1h: CATH_3dblG01 (G:6-178,G:388-534)
2a: CATH_3dblB03 (B:340-400)
2b: CATH_3dblD03 (D:340-400)
2c: CATH_3dblF03 (F:340-400)
2d: CATH_3dblH03 (H:340-400)
3a: CATH_3dblB02 (B:212-288)
3b: CATH_3dblD02 (D:212-288)
3c: CATH_3dblF02 (F:212-288)
3d: CATH_3dblH02 (H:212-288)
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Homologous Superfamilies
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Human (Homo sapiens)
(188)
1a
3dblB01
B:11-209,B:289-339
1b
3dblD01
D:11-209,D:289-339
1c
3dblF01
F:11-209,F:289-339
1d
3dblH01
H:11-209,H:289-339
1e
3dblA01
A:6-178,A:388-534
1f
3dblC01
C:6-178,C:388-534
1g
3dblE01
E:6-178,E:388-534
1h
3dblG01
G:6-178,G:388-534
Architecture
:
Roll
(3276)
Topology
:
Ubiquitin-like (UB roll)
(674)
Homologous Superfamily
:
Ubiquitin activating enzymes (Uba3). Chain: B, domain 3
(8)
Human (Homo sapiens)
(8)
2a
3dblB03
B:340-400
2b
3dblD03
D:340-400
2c
3dblF03
F:340-400
2d
3dblH03
H:340-400
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Arc Repressor Mutant, subunit A
(1030)
Homologous Superfamily
:
Ubiquitin activating enzymes (Uba3). Chain: B, domain 2
(8)
Human (Homo sapiens)
(8)
3a
3dblB02
B:212-288
3b
3dblD02
D:212-288
3c
3dblF02
F:212-288
3d
3dblH02
H:212-288
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Pfam Domains
(0, 0)
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Asymmetric Unit 1
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Show PDB file:
Asym.Unit (665 KB)
Header - Asym.Unit
Biol.Unit 1 (169 KB)
Header - Biol.Unit 1
Biol.Unit 2 (171 KB)
Header - Biol.Unit 2
Biol.Unit 3 (171 KB)
Header - Biol.Unit 3
Biol.Unit 4 (173 KB)
Header - Biol.Unit 4
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