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2NYT
Asym. Unit
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Asym.Unit (128 KB)
Biol.Unit 1 (123 KB)
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(1)
Title
:
THE APOBEC2 CRYSTAL STRUCTURE AND FUNCTIONAL IMPLICATIONS FOR AID
Authors
:
C. Prochnow, R. Bransteitter, M. Klein, M. Goodman, X. Chen
Date
:
21 Nov 06 (Deposition) - 09 Jan 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Cytidine Deaminase, Zinc-Ion Binding, Apobec, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Prochnow, R. Bransteitter, M. G. Klein, M. F. Goodman, X. S. Chen
The Apobec-2 Crystal Structure And Functional Implications For The Deaminase Aid.
Nature V. 445 447 2007
(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)
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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
GLU A:60 , HIS A:98 , CYS A:128 , CYS A:131
BINDING SITE FOR RESIDUE ZN A 2000
2
AC2
SOFTWARE
HIS B:98 , CYS B:128 , CYS B:131
BINDING SITE FOR RESIDUE ZN B 2001
3
AC3
SOFTWARE
GLU C:60 , HIS C:98 , CYS C:128 , CYS C:131
BINDING SITE FOR RESIDUE ZN C 2002
4
AC4
SOFTWARE
HIS D:98 , CYS D:128 , CYS D:131
BINDING SITE FOR RESIDUE ZN D 2003
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SAPs(SNPs)/Variants
(1, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_024406 (I136T, chain A/B/C/D, )
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dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_024406
I
136
T
ABEC2_HUMAN
Polymorphism
2076472
A/B/C/D
I
136
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: CYT_DCMP_DEAMINASES_2 (A:64-169,B:64-169,C:64-169,D:64-16...)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CYT_DCMP_DEAMINASES_2
PS51747
Cytidine and deoxycytidylate deaminases domain profile.
ABEC2_HUMAN
64-169
4
A:64-169
B:64-169
C:64-169
D:64-169
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Exons
(2, 8)
Info
All Exons
Exon 1.1b (A:36-44 (gaps) | B:35-44 (gaps) | ...)
Exon 1.2b (A:44-224 (gaps) | B:44-224 | C:44-...)
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1: Boundary -/1.1b
2: Boundary 1.1b/1.2b
3: Boundary 1.2b/1.3
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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
1.1b
ENST00000244669
1b
ENSE00000849850
chr6:
41021043-41021217
175
ABEC2_HUMAN
1-44
44
4
A:36-44 (gaps)
B:35-44 (gaps)
C:40-44
D:40-44
30
31
5
5
1.2b
ENST00000244669
2b
ENSE00000849851
chr6:
41029067-41029631
565
ABEC2_HUMAN
44-224
181
4
A:44-224 (gaps)
B:44-224
C:44-224
D:44-224 (gaps)
181
181
181
181
1.3
ENST00000244669
3
ENSE00000849852
chr6:
41031840-41032250
411
ABEC2_HUMAN
-
0
0
-
-
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SCOP Domains
(0, 0)
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_APOBEC_C_2nytD01 (D:159-216)
1b: PFAM_APOBEC_C_2nytD02 (D:159-216)
1c: PFAM_APOBEC_C_2nytD03 (D:159-216)
1d: PFAM_APOBEC_C_2nytD04 (D:159-216)
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Clan
:
CDA
(39)
Family
:
APOBEC_C
(1)
Homo sapiens (Human)
(1)
1a
APOBEC_C-2nytD01
D:159-216
1b
APOBEC_C-2nytD02
D:159-216
1c
APOBEC_C-2nytD03
D:159-216
1d
APOBEC_C-2nytD04
D:159-216
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