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2ISI
Biol. Unit 2
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Asym.Unit (140 KB)
Biol.Unit 1 (47 KB)
Biol.Unit 2 (47 KB)
Biol.Unit 3 (47 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF APE1 FROM HOMO SAPIENS IN A NEW CRYSTAL FORM COMPLEXED WITH A LIGAND
Authors
:
R. Agarwal, M. D. Naidu
Date
:
17 Oct 06 (Deposition) - 31 Oct 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.76
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Keywords
:
Ape1, Crystal Structure, Magnesium, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Agarwal, M. D. Naidu
Crystal Structure Of Hape1 In A New Crystal Form With A Bound Ligand: Implications On Catalytic Mechanism And Its Inhibition
To Be Published
(for further references see the
PDB file header
)
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
2a: PHOSPHATE ION (PO4a)
2b: PHOSPHATE ION (PO4b)
View:
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Label:
No.
Name
Count
Type
Full Name
1
MG
-1
Ligand/Ion
MAGNESIUM ION
2
PO4
1
Ligand/Ion
PHOSPHATE ION
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Sites
(2, 2)
Info
All Sites
1: AC2 (SOFTWARE)
2: AC4 (SOFTWARE)
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Label:
No.
Name
Evidence
Residues
Description
1
AC2
SOFTWARE
ASN B:174 , ASN B:212 , ALA B:230
BINDING SITE FOR RESIDUE PO4 B 401
2
AC4
SOFTWARE
ASP B:70 , GLU B:96
BINDING SITE FOR RESIDUE MG B 403
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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 (Q51H, chain B, )
2: VAR_014823 (I64V, chain B, )
3: VAR_019790 (D148E, chain B, )
View:
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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
Q
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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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
(1, 3)
Info
All SCOP Domains
1a: SCOP_d2isia_ (A:)
1b: SCOP_d2isic_ (C:)
1c: SCOP_d2isib_ (B:)
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)
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)
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)
Protein Domains
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(
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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
:
automated matches
(7)
Human (Homo sapiens) [TaxId: 9606]
(6)
1a
d2isia_
A:
1b
d2isic_
C:
1c
d2isib_
B:
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CATH Domains
(1, 3)
Info
all CATH domains
1a: CATH_2isiC00 (C:43-318)
1b: CATH_2isiA00 (A:43-318)
1c: CATH_2isiB00 (B:43-318)
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)
Homologous Superfamilies
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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)
Human (Homo sapiens)
(8)
1a
2isiC00
C:43-318
1b
2isiA00
A:43-318
1c
2isiB00
B:43-318
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Chain B
Asymmetric Unit 1
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