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2B5L
Asym. Unit
Info
Asym.Unit (393 KB)
Biol.Unit 1 (195 KB)
Biol.Unit 2 (196 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF DDB1 IN COMPLEX WITH SIMIAN VIRUS 5 V PROTEIN
Authors
:
T. Li, X. Chen, K. C. Garbutt, P. Zhou, N. Zheng
Date
:
28 Sep 05 (Deposition) - 28 Feb 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.85
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C (1x)
Biol. Unit 2: B,D (1x)
Keywords
:
Ddb1, Sv5-V, Beta Propeller, Propeller Cluster, Zinc Finger, Protein Binding/Viral Protein Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Li, X. Chen, K. C. Garbutt, P. Zhou, N. Zheng
Structure Of Ddb1 In Complex With A Paramyxovirus V Protein: Viral Hijack Of A Propeller Cluster In Ubiquitin Ligase.
Cell(Cambridge, Mass. ) V. 124 105 2006
(for further references see the
PDB file header
)
[
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Hetero Components
(1, 4)
Info
All Hetero Components
1a: ZINC ION (ZNa)
1b: ZINC ION (ZNb)
1c: ZINC ION (ZNc)
1d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ZN
4
Ligand/Ion
ZINC ION
[
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS C:194 , CYS C:206 , CYS C:208 , CYS C:211
BINDING SITE FOR RESIDUE ZN C 3001
2
AC2
SOFTWARE
HIS C:171 , CYS C:190 , CYS C:215 , CYS C:218
BINDING SITE FOR RESIDUE ZN C 3002
3
AC3
SOFTWARE
CYS D:194 , CYS D:206 , CYS D:208 , CYS D:211
BINDING SITE FOR RESIDUE ZN D 3003
4
AC4
SOFTWARE
CYS D:190 , CYS D:215 , CYS D:218
BINDING SITE FOR RESIDUE ZN D 3004
[
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]
SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_023074 (L427F, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_023074
L
427
F
DDB1_HUMAN
Polymorphism
28720299
A/B
L
427
F
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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End label:
Sorry, no Info available
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Exons
(27, 54)
Info
All Exons
Exon 1.1a (A:1-21 | B:1-21)
Exon 1.2 (A:21-70 | B:21-70)
Exon 1.3c (A:71-109 | B:71-109)
Exon 1.4 (A:110-183 | B:110-183)
Exon 1.5 (A:184-222 | B:184-222)
Exon 1.6a (A:222-254 | B:222-254)
Exon 1.7 (A:255-307 | B:255-307)
Exon 1.8 (A:308-335 | B:308-335)
Exon 1.9 (A:336-374 | B:336-374)
Exon 1.10a (A:375-409 | B:375-409)
Exon 1.11 (A:409-434 | B:409-434)
Exon 1.12 (A:434-470 | B:434-470)
Exon 1.13 (A:471-530 | B:471-530)
Exon 1.14 (A:530-585 | B:530-585)
Exon 1.15 (A:585-621 | B:585-621)
Exon 1.16 (A:621-690 | B:621-690)
Exon 1.17 (A:690-722 | B:690-722)
Exon 1.18 (A:722-759 | B:722-759)
Exon 1.19 (A:760-801 (gaps) | B:760-801 (gaps...)
Exon 1.20 (A:801-856 | B:801-856)
Exon 1.21 (A:856-887 | B:856-887)
Exon 1.22 (A:888-944 | B:888-944)
Exon 1.23 (A:945-981 | B:945-981)
Exon 1.24 (A:981-1038 (gaps) | B:981-1038)
Exon 1.25 (A:1038-1072 | B:1038-1072)
Exon 1.26 (A:1072-1113 | B:1072-1113)
Exon 1.27b (A:1114-1140 | B:1114-1140)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1a
02: Boundary 1.1a/1.2
03: Boundary 1.2/1.3c
04: Boundary 1.3c/1.4
05: Boundary 1.4/1.5
06: Boundary 1.5/1.6a
07: Boundary 1.6a/1.7
08: Boundary 1.7/1.8
09: Boundary 1.8/1.9
10: Boundary 1.9/1.10a
11: Boundary 1.10a/1.11
12: Boundary 1.11/1.12
13: Boundary 1.12/1.13
14: Boundary 1.13/1.14
15: Boundary 1.14/1.15
16: Boundary 1.15/1.16
17: Boundary 1.16/1.17
18: Boundary 1.17/1.18
19: Boundary 1.18/1.19
20: Boundary 1.19/1.20
21: Boundary 1.20/1.21
22: Boundary 1.21/1.22
23: Boundary 1.22/1.23
24: Boundary 1.23/1.24
25: Boundary 1.24/1.25
26: Boundary 1.25/1.26
27: Boundary 1.26/1.27b
28: Boundary 1.27b/-
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
1.1a
ENST00000301764
1a
ENSE00001766096
chr11:
61100666-61100380
287
DDB1_HUMAN
1-21
21
2
A:1-21
B:1-21
21
21
1.2
ENST00000301764
2
ENSE00001244589
chr11:
61099163-61099015
149
DDB1_HUMAN
21-70
50
2
A:21-70
B:21-70
50
50
1.3c
ENST00000301764
3c
ENSE00001244580
chr11:
61097546-61097430
117
DDB1_HUMAN
71-109
39
2
A:71-109
B:71-109
39
39
1.4
ENST00000301764
4
ENSE00001244572
chr11:
61097056-61096835
222
DDB1_HUMAN
110-183
74
2
A:110-183
B:110-183
74
74
1.5
ENST00000301764
5
ENSE00001119057
chr11:
61094365-61094251
115
DDB1_HUMAN
184-222
39
2
A:184-222
B:184-222
39
39
1.6a
ENST00000301764
6a
ENSE00001119056
chr11:
61093180-61093083
98
DDB1_HUMAN
222-254
33
2
A:222-254
B:222-254
33
33
1.7
ENST00000301764
7
ENSE00001119058
chr11:
61091609-61091451
159
DDB1_HUMAN
255-307
53
2
A:255-307
B:255-307
53
53
1.8
ENST00000301764
8
ENSE00001119055
chr11:
61090566-61090483
84
DDB1_HUMAN
308-335
28
2
A:308-335
B:308-335
28
28
1.9
ENST00000301764
9
ENSE00001119053
chr11:
61089884-61089768
117
DDB1_HUMAN
336-374
39
2
A:336-374
B:336-374
39
39
1.10a
ENST00000301764
10a
ENSE00001119059
chr11:
61089169-61089067
103
DDB1_HUMAN
375-409
35
2
A:375-409
B:375-409
35
35
1.11
ENST00000301764
11
ENSE00001145160
chr11:
61084039-61083964
76
DDB1_HUMAN
409-434
26
2
A:409-434
B:409-434
26
26
1.12
ENST00000301764
12
ENSE00001145157
chr11:
61083865-61083757
109
DDB1_HUMAN
434-470
37
2
A:434-470
B:434-470
37
37
1.13
ENST00000301764
13
ENSE00001198138
chr11:
61081958-61081780
179
DDB1_HUMAN
471-530
60
2
A:471-530
B:471-530
60
60
1.14
ENST00000301764
14
ENSE00001063042
chr11:
61081682-61081519
164
DDB1_HUMAN
530-585
56
2
A:530-585
B:530-585
56
56
1.15
ENST00000301764
15
ENSE00001063027
chr11:
61081441-61081334
108
DDB1_HUMAN
585-621
37
2
A:585-621
B:585-621
37
37
1.16
ENST00000301764
16
ENSE00001063028
chr11:
61081178-61080971
208
DDB1_HUMAN
621-690
70
2
A:621-690
B:621-690
70
70
1.17
ENST00000301764
17
ENSE00001145124
chr11:
61079556-61079461
96
DDB1_HUMAN
690-722
33
2
A:690-722
B:690-722
33
33
1.18
ENST00000301764
18
ENSE00001198106
chr11:
61079367-61079256
112
DDB1_HUMAN
722-759
38
2
A:722-759
B:722-759
38
38
1.19
ENST00000301764
19
ENSE00001063044
chr11:
61077890-61077767
124
DDB1_HUMAN
760-801
42
2
A:760-801 (gaps)
B:760-801 (gaps)
42
42
1.20
ENST00000301764
20
ENSE00001063040
chr11:
61077432-61077268
165
DDB1_HUMAN
801-856
56
2
A:801-856
B:801-856
56
56
1.21
ENST00000301764
21
ENSE00001063041
chr11:
61076549-61076455
95
DDB1_HUMAN
856-887
32
2
A:856-887
B:856-887
32
32
1.22
ENST00000301764
22
ENSE00001145096
chr11:
61071507-61071337
171
DDB1_HUMAN
888-944
57
2
A:888-944
B:888-944
57
57
1.23
ENST00000301764
23
ENSE00001145090
chr11:
61070627-61070518
110
DDB1_HUMAN
945-981
37
2
A:945-981
B:945-981
37
37
1.24
ENST00000301764
24
ENSE00001198074
chr11:
61070223-61070054
170
DDB1_HUMAN
981-1038
58
2
A:981-1038 (gaps)
B:981-1038
58
58
1.25
ENST00000301764
25
ENSE00001506453
chr11:
61069831-61069729
103
DDB1_HUMAN
1038-1072
35
2
A:1038-1072
B:1038-1072
35
35
1.26
ENST00000301764
26
ENSE00001506452
chr11:
61068404-61068281
124
DDB1_HUMAN
1072-1113
42
2
A:1072-1113
B:1072-1113
42
42
1.27b
ENST00000301764
27b
ENSE00001798842
chr11:
61067691-61066920
772
DDB1_HUMAN
1114-1140
27
2
A:1114-1140
B:1114-1140
27
27
[
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SCOP Domains
(3, 10)
Info
All SCOP Domains
1a: SCOP_d2b5la3 (A:1044-1140)
1b: SCOP_d2b5lb3 (B:1044-1140)
2a: SCOP_d2b5la1 (A:14-354)
2b: SCOP_d2b5la2 (A:1-13,A:355-392,A:708-1043)
2c: SCOP_d2b5la4 (A:393-707)
2d: SCOP_d2b5lb1 (B:14-354)
2e: SCOP_d2b5lb2 (B:1-13,B:355-392,B:708-1043)
2f: SCOP_d2b5lb4 (B:393-707)
3a: SCOP_d2b5lc_ (C:)
3b: SCOP_d2b5ld_ (D:)
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Protein Domains
(
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(
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Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
DDB1 C-terminal-like
(2)
Superfamily
:
DDB1 C-terminal-like
(2)
Family
:
DDB1 C-terminal-like
(2)
Protein domain
:
DDB1 C-terminal domain
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d2b5la3
A:1044-1140
1b
d2b5lb3
B:1044-1140
Class
:
All beta proteins
(24004)
Fold
:
7-bladed beta-propeller
(245)
Superfamily
:
WD40 repeat-like
(95)
Family
:
DDB1-like
(2)
Protein domain
:
DDB1
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
2a
d2b5la1
A:14-354
2b
d2b5la2
A:1-13,A:355-392,A:708-1043
2c
d2b5la4
A:393-707
2d
d2b5lb1
B:14-354
2e
d2b5lb2
B:1-13,B:355-392,B:708-1043
2f
d2b5lb4
B:393-707
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
SV5-V core-like
(2)
Superfamily
:
SV5-V core-like
(2)
Family
:
SV5-V core-like
(2)
Protein domain
:
SV5-V core
(2)
Simian virus 5 [TaxId: 11207]
(2)
3a
d2b5lc_
C:
3b
d2b5ld_
D:
[
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
(0, 0)
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Asym.Unit (393 KB)
Header - Asym.Unit
Biol.Unit 1 (195 KB)
Header - Biol.Unit 1
Biol.Unit 2 (196 KB)
Header - Biol.Unit 2
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