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1R4N
Biol. Unit 1
Info
Asym.Unit (603 KB)
Biol.Unit 1 (156 KB)
Biol.Unit 2 (156 KB)
Biol.Unit 3 (156 KB)
Biol.Unit 4 (155 KB)
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(1)
Title
:
APPBP1-UBA3-NEDD8, AN E1-UBIQUITIN-LIKE PROTEIN COMPLEX WITH ATP
Authors
:
H. Walden, M. S. Podgorski, J. M. Holton, B. A. Schulman
Date
:
07 Oct 03 (Deposition) - 23 Dec 03 (Release) - 01 Feb 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.60
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,I (1x)
Biol. Unit 2: C,D,J (1x)
Biol. Unit 3: E,F,K (1x)
Biol. Unit 4: G,H,L (1x)
Keywords
:
Cell Cycle
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
H. Walden, M. S. Podgorski, D. T. Huang, D. W. Miller, R. J. Howard, D. L. Minor, J. M. Holton, B. A. Schulman
The Structure Of The Appbp1-Uba3-Nedd8-Atp Complex Reveals The Basis For Selective Ubiquitin-Like Protein Activation B An E1.
Mol. Cell V. 12 1427 2003
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
1b: ADENOSINE-5'-TRIPHOSPHATE (ATPb)
1c: ADENOSINE-5'-TRIPHOSPHATE (ATPc)
1d: ADENOSINE-5'-TRIPHOSPHATE (ATPd)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
2d: ZINC ION (ZNd)
View:
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Label:
No.
Name
Count
Type
Full Name
1
ATP
1
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
2
ZN
-1
Ligand/Ion
ZINC ION
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Sites
(1, 1)
Info
All Sites
1: AC5 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC5
SOFTWARE
ARG A:15 , ALA B:56 , GLY B:57 , ASP B:79 , MET B:80 , ASP B:81 , ARG B:90 , GLN B:91 , LYS B:103 , LYS B:126 , ILE B:127 , LEU B:145 , ASP B:146 , ALA B:150 , GLY I:176
BINDING SITE FOR RESIDUE ATP B 5
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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 A, )
View:
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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
A
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 (I:101-176)
2: UBIQUITIN_1 (I:127-152)
3: UBIQUITIN_ACTIVAT_2 (B: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
I:101-176
-
-
-
2
UBIQUITIN_1
PS00299
Ubiquitin domain signature.
NEDD8_HUMAN
27-52
1
I:127-152
-
-
-
3
UBIQUITIN_ACTIVAT_2
PS00865
Ubiquitin-activating enzyme active site.
UBA3_HUMAN
235-243
1
B:214-222
-
-
-
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Exons
(0, 0)
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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_d1r4ni_ (I:)
1b: SCOP_d1r4nj_ (J:)
1c: SCOP_d1r4nk_ (K:)
1d: SCOP_d1r4nl_ (L:)
2a: SCOP_d1r4na_ (A:)
2b: SCOP_d1r4nc_ (C:)
2c: SCOP_d1r4ne_ (E:)
2d: SCOP_d1r4ng_ (G:)
3a: SCOP_d1r4nb_ (B:)
3b: SCOP_d1r4nd_ (D:)
3c: SCOP_d1r4nf_ (F:)
3d: SCOP_d1r4nh_ (H:)
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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
d1r4ni_
I:
1b
d1r4nj_
J:
1c
d1r4nk_
K:
1d
d1r4nl_
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
d1r4na_
A:
2b
d1r4nc_
C:
2c
d1r4ne_
E:
2d
d1r4ng_
G:
Protein domain
:
UBA3
(12)
Human (Homo sapiens) [TaxId: 9606]
(12)
3a
d1r4nb_
B:
3b
d1r4nd_
D:
3c
d1r4nf_
F:
3d
d1r4nh_
H:
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CATH Domains
(4, 20)
Info
all CATH domains
1a: CATH_1r4nB01 (B:12-209,B:289-339)
1b: CATH_1r4nD01 (D:12-209,D:289-339)
1c: CATH_1r4nF01 (F:12-209,F:289-339)
1d: CATH_1r4nH01 (H:12-209,H:289-339)
1e: CATH_1r4nA01 (A:6-178,A:388-534)
1f: CATH_1r4nC01 (C:6-178,C:388-534)
1g: CATH_1r4nE01 (E:6-178,E:388-534)
1h: CATH_1r4nG01 (G:6-178,G:388-534)
2a: CATH_1r4nI00 (I:101-176)
2b: CATH_1r4nJ00 (J:101-176)
2c: CATH_1r4nK00 (K:101-176)
2d: CATH_1r4nL00 (L:101-176)
3a: CATH_1r4nB03 (B:340-602)
3b: CATH_1r4nD03 (D:340-602)
3c: CATH_1r4nF03 (F:340-602)
3d: CATH_1r4nH03 (H:340-602)
4a: CATH_1r4nB02 (B:212-288)
4b: CATH_1r4nD02 (D:212-288)
4c: CATH_1r4nF02 (F:212-288)
4d: CATH_1r4nH02 (H:212-288)
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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
1r4nB01
B:12-209,B:289-339
1b
1r4nD01
D:12-209,D:289-339
1c
1r4nF01
F:12-209,F:289-339
1d
1r4nH01
H:12-209,H:289-339
1e
1r4nA01
A:6-178,A:388-534
1f
1r4nC01
C:6-178,C:388-534
1g
1r4nE01
E:6-178,E:388-534
1h
1r4nG01
G:6-178,G:388-534
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)
2a
1r4nI00
I:101-176
2b
1r4nJ00
J:101-176
2c
1r4nK00
K:101-176
2d
1r4nL00
L:101-176
Homologous Superfamily
:
Ubiquitin activating enzymes (Uba3). Chain: B, domain 3
(8)
Human (Homo sapiens)
(8)
3a
1r4nB03
B:340-602
3b
1r4nD03
D:340-602
3c
1r4nF03
F:340-602
3d
1r4nH03
H:340-602
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)
4a
1r4nB02
B:212-288
4b
1r4nD02
D:212-288
4c
1r4nF02
F:212-288
4d
1r4nH02
H:212-288
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Pfam Domains
(0, 0)
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