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1R4M
Biol. Unit 3
Info
Asym.Unit (601 KB)
Biol.Unit 1 (155 KB)
Biol.Unit 2 (155 KB)
Biol.Unit 3 (155 KB)
Biol.Unit 4 (154 KB)
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(1)
Title
:
APPBP1-UBA3-NEDD8, AN E1-UBIQUITIN-LIKE PROTEIN COMPLEX
Authors
:
H. Walden, M. S. Podgorski, J. M. Holton, B. A. Schulman
Date
:
07 Oct 03 (Deposition) - 23 Dec 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
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:
[
Gene Ontology, PubMed, Web (Google)
]
)
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 By An E1.
Mol. Cell V. 12 1427 2003
(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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Label:
Sorry, no Info available
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Sites
(1, 1)
Info
All Sites
1: AC3 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC3
SOFTWARE
CYS F:199 , CYS F:202 , CYS F:343 , CYS F:346
BINDING SITE FOR RESIDUE ZN F 3
[
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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 E, )
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
E
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 (K:101-176)
2: UBIQUITIN_1 (K:127-152)
3: UBIQUITIN_ACTIVAT_2 (F:214-222)
;
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.
NEDD8_HUMAN
1-76
1
-
-
K:101-176
-
2
UBIQUITIN_1
PS00299
Ubiquitin domain signature.
NEDD8_HUMAN
27-52
1
-
-
K:127-152
-
3
UBIQUITIN_ACTIVAT_2
PS00865
Ubiquitin-activating enzyme active site.
UBA3_HUMAN
235-243
1
-
-
F:214-222
-
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
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_d1r4mi_ (I:)
1b: SCOP_d1r4mj_ (J:)
1c: SCOP_d1r4mk_ (K:)
1d: SCOP_d1r4ml_ (L:)
2a: SCOP_d1r4ma_ (A:)
2b: SCOP_d1r4mc_ (C:)
2c: SCOP_d1r4me_ (E:)
2d: SCOP_d1r4mg_ (G:)
3a: SCOP_d1r4mb_ (B:)
3b: SCOP_d1r4md_ (D:)
3c: SCOP_d1r4mf_ (F:)
3d: SCOP_d1r4mh_ (H:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
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
:
Nedd8
(14)
Human (Homo sapiens) [TaxId: 9606]
(14)
1a
d1r4mi_
I:
1b
d1r4mj_
J:
1c
d1r4mk_
K:
1d
d1r4ml_
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
d1r4ma_
A:
2b
d1r4mc_
C:
2c
d1r4me_
E:
2d
d1r4mg_
G:
Protein domain
:
UBA3
(12)
Human (Homo sapiens) [TaxId: 9606]
(12)
3a
d1r4mb_
B:
3b
d1r4md_
D:
3c
d1r4mf_
F:
3d
d1r4mh_
H:
[
close SCOP info
]
CATH Domains
(4, 20)
Info
all CATH domains
1a: CATH_1r4mB01 (B:12-209,B:289-339)
1b: CATH_1r4mD01 (D:12-209,D:289-339)
1c: CATH_1r4mF01 (F:12-209,F:289-339)
1d: CATH_1r4mH01 (H:12-209,H:289-339)
1e: CATH_1r4mA01 (A:6-178,A:388-534)
1f: CATH_1r4mC01 (C:6-178,C:388-534)
1g: CATH_1r4mE01 (E:6-178,E:388-534)
1h: CATH_1r4mG01 (G:6-178,G:388-534)
2a: CATH_1r4mI00 (I:101-176)
2b: CATH_1r4mJ00 (J:101-176)
2c: CATH_1r4mK00 (K:101-176)
2d: CATH_1r4mL00 (L:101-176)
3a: CATH_1r4mB03 (B:340-602)
3b: CATH_1r4mH03 (H:340-602)
3c: CATH_1r4mD03 (D:340-602)
3d: CATH_1r4mF03 (F:340-602)
4a: CATH_1r4mB02 (B:212-288)
4b: CATH_1r4mD02 (D:212-288)
4c: CATH_1r4mF02 (F:212-288)
4d: CATH_1r4mH02 (H:212-288)
View:
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(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
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
1r4mB01
B:12-209,B:289-339
1b
1r4mD01
D:12-209,D:289-339
1c
1r4mF01
F:12-209,F:289-339
1d
1r4mH01
H:12-209,H:289-339
1e
1r4mA01
A:6-178,A:388-534
1f
1r4mC01
C:6-178,C:388-534
1g
1r4mE01
E:6-178,E:388-534
1h
1r4mG01
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
1r4mI00
I:101-176
2b
1r4mJ00
J:101-176
2c
1r4mK00
K:101-176
2d
1r4mL00
L:101-176
Homologous Superfamily
:
Ubiquitin activating enzymes (Uba3). Chain: B, domain 3
(8)
Human (Homo sapiens)
(8)
3a
1r4mB03
B:340-602
3b
1r4mH03
H:340-602
3c
1r4mD03
D:340-602
3d
1r4mF03
F: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
1r4mB02
B:212-288
4b
1r4mD02
D:212-288
4c
1r4mF02
F:212-288
4d
1r4mH02
H:212-288
[
close CATH info
]
Pfam Domains
(5, 24)
Info
all PFAM domains
1a: PFAM_ThiF_1r4mH01 (H:47-192)
1b: PFAM_ThiF_1r4mH02 (H:47-192)
1c: PFAM_ThiF_1r4mH03 (H:47-192)
1d: PFAM_ThiF_1r4mH04 (H:47-192)
1e: PFAM_ThiF_1r4mG01 (G:29-165)
1f: PFAM_ThiF_1r4mG02 (G:29-165)
1g: PFAM_ThiF_1r4mG03 (G:29-165)
1h: PFAM_ThiF_1r4mG04 (G:29-165)
2a: PFAM_ubiquitin_1r4mL01 (L:106-174)
2b: PFAM_ubiquitin_1r4mL02 (L:106-174)
2c: PFAM_ubiquitin_1r4mL03 (L:106-174)
2d: PFAM_ubiquitin_1r4mL04 (L:106-174)
3a: PFAM_E2_bind_1r4mH05 (H:353-917)
3b: PFAM_E2_bind_1r4mH06 (H:353-917)
3c: PFAM_E2_bind_1r4mH07 (H:353-917)
3d: PFAM_E2_bind_1r4mH08 (H:353-917)
4a: PFAM_UBACT_1r4mH09 (H:248-314)
4b: PFAM_UBACT_1r4mH10 (H:248-314)
4c: PFAM_UBACT_1r4mH11 (H:248-314)
4d: PFAM_UBACT_1r4mH12 (H:248-314)
5a: PFAM_UBA_e1_thiolCys_1r4mH13 (H:195-241)
5b: PFAM_UBA_e1_thiolCys_1r4mH14 (H:195-241)
5c: PFAM_UBA_e1_thiolCys_1r4mH15 (H:195-241)
5d: PFAM_UBA_e1_thiolCys_1r4mH16 (H:195-241)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
NADP_Rossmann
(1239)
Family
:
ThiF
(14)
Homo sapiens (Human)
(8)
1a
ThiF-1r4mH01
H:47-192
1b
ThiF-1r4mH02
H:47-192
1c
ThiF-1r4mH03
H:47-192
1d
ThiF-1r4mH04
H:47-192
1e
ThiF-1r4mG01
G:29-165
1f
ThiF-1r4mG02
G:29-165
1g
ThiF-1r4mG03
G:29-165
1h
ThiF-1r4mG04
G:29-165
Clan
:
Ubiquitin
(279)
Family
:
ubiquitin
(99)
Homo sapiens (Human)
(67)
2a
ubiquitin-1r4mL01
L:106-174
2b
ubiquitin-1r4mL02
L:106-174
2c
ubiquitin-1r4mL03
L:106-174
2d
ubiquitin-1r4mL04
L:106-174
Clan
:
no clan defined [family: E2_bind]
(5)
Family
:
E2_bind
(5)
Homo sapiens (Human)
(5)
3a
E2_bind-1r4mH05
H:353-917
3b
E2_bind-1r4mH06
H:353-917
3c
E2_bind-1r4mH07
H:353-917
3d
E2_bind-1r4mH08
H:353-917
Clan
:
no clan defined [family: UBACT]
(10)
Family
:
UBACT
(10)
Homo sapiens (Human)
(9)
4a
UBACT-1r4mH09
H:248-314
4b
UBACT-1r4mH10
H:248-314
4c
UBACT-1r4mH11
H:248-314
4d
UBACT-1r4mH12
H:248-314
Clan
:
no clan defined [family: UBA_e1_thiolCys]
(10)
Family
:
UBA_e1_thiolCys
(10)
Homo sapiens (Human)
(9)
5a
UBA_e1_thiolCys-1r4mH13
H:195-241
5b
UBA_e1_thiolCys-1r4mH14
H:195-241
5c
UBA_e1_thiolCys-1r4mH15
H:195-241
5d
UBA_e1_thiolCys-1r4mH16
H:195-241
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