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1DE9
Biol. Unit 2
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Asym.Unit (108 KB)
Biol.Unit 1 (53 KB)
Biol.Unit 2 (53 KB)
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(1)
Title
:
HUMAN APE1 ENDONUCLEASE WITH BOUND ABASIC DNA AND MN2+ ION
Authors
:
C. D. Mol, T. Izumi, S. Mitra, J. A. Tainer
Date
:
13 Nov 99 (Deposition) - 02 Feb 00 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,U,V,W,X,Y,Z
Biol. Unit 1: A,X,Y,Z (1x)
Biol. Unit 2: B,U,V,W (1x)
Keywords
:
Enzyme:Dna Complex, Dna Repair Abasic Site, Ap Endonuclease, Lyase/Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. D. Mol, T. Izumi, S. Mitra, J. A. Tainer
Dna-Bound Structures And Mutants Reveal Abasic Dna Binding By Ape1 And Dna Repair Coordination
Nature V. 403 451 2000
(for further references see the
PDB file header
)
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSP... (3DRa)
1b: 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSP... (3DRb)
2a: MANGANESE (II) ION (MNa)
2b: MANGANESE (II) ION (MNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3DR
1
Mod. Nucleotide
1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2
MN
-1
Ligand/Ion
MANGANESE (II) ION
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Sites
(1, 1)
Info
All Sites
1: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC2
SOFTWARE
GLU B:96 , ASP B:308 , DC U:5 , 3DR V:6
BINDING SITE FOR RESIDUE MN B 1001
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SAPs(SNPs)/Variants
(3, 3)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_013455 (H51H, chain B, )
2: VAR_014823 (I64V, chain B, )
3: VAR_019790 (D148E, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_013455
Q
51
H
APEX1_HUMAN
Polymorphism
1048945
B
H
51
H
2
UniProt
VAR_014823
I
64
V
APEX1_HUMAN
Polymorphism
2307486
B
I
64
V
3
UniProt
VAR_019790
D
148
E
APEX1_HUMAN
Polymorphism
1130409
B
D
148
E
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(4, 4)
Info
All PROSITE Patterns/Profiles
1: AP_NUCLEASE_F1_4 (B:62-318)
2: AP_NUCLEASE_F1_1 (B:89-98)
3: AP_NUCLEASE_F1_2 (B:251-267)
4: AP_NUCLEASE_F1_3 (B:277-288)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
AP_NUCLEASE_F1_4
PS51435
AP endonucleases family 1 profile.
APEX1_HUMAN
62-318
1
-
B:62-318
2
AP_NUCLEASE_F1_1
PS00726
AP endonucleases family 1 signature 1.
APEX1_HUMAN
89-98
1
-
B:89-98
3
AP_NUCLEASE_F1_2
PS00727
AP endonucleases family 1 signature 2.
APEX1_HUMAN
251-267
1
-
B:251-267
4
AP_NUCLEASE_F1_3
PS00728
AP endonucleases family 1 signature 3.
APEX1_HUMAN
277-288
1
-
B:277-288
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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.
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SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1de9a_ (A:)
1b: SCOP_d1de9b_ (B:)
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Classes
(
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(
)
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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
:
DNase I-like
(70)
Superfamily
:
DNase I-like
(70)
Family
:
DNase I-like
(31)
Protein domain
:
DNA repair endonuclease Hap1
(7)
Human (Homo sapiens) [TaxId: 9606]
(7)
1a
d1de9a_
A:
1b
d1de9b_
B:
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1de9A00 (A:43-318)
1b: CATH_1de9B00 (B:43-318)
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
4-Layer Sandwich
(459)
Topology
:
Deoxyribonuclease I; Chain A
(35)
Homologous Superfamily
:
[code=3.60.10.10, no name defined]
(35)
[unclassified]
(5)
1a
1de9A00
A:43-318
1b
1de9B00
B:43-318
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Asymmetric Unit 1
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Asym.Unit (108 KB)
Header - Asym.Unit
Biol.Unit 1 (53 KB)
Header - Biol.Unit 1
Biol.Unit 2 (53 KB)
Header - Biol.Unit 2
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