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3U8U
Asym. Unit
Info
Asym.Unit (282 KB)
Biol.Unit 1 (52 KB)
Biol.Unit 2 (51 KB)
Biol.Unit 3 (50 KB)
Biol.Unit 4 (49 KB)
Biol.Unit 5 (50 KB)
Biol.Unit 6 (50 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN APURINIC/APYRIDINIMIC ENDONUCLEASE, APE1 IN A NEW CRYSTAL FORM
Authors
:
R. Agarwal, M. D. Naidu
Date
:
17 Oct 11 (Deposition) - 26 Oct 11 (Release) - 26 Oct 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.15
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Biol. Unit 5: E (1x)
Biol. Unit 6: F (1x)
Keywords
:
Endonuclease, Hydrolase, Lyase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
]
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Reference
:
R. Agarwal, M. D. Naidu
Crystal Structure Of Human Apurinic/Apyridinimic Endonuclease, Ape1 In A New Crystal Form
To Be Published
[
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Hetero Components
(2, 10)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
2e: MAGNESIUM ION (MGe)
2f: MAGNESIUM ION (MGf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
4
Ligand/Ion
CHLORIDE ION
2
MG
6
Ligand/Ion
MAGNESIUM ION
[
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Sites
(10, 10)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:70 , GLU A:96 , HOH A:670 , HOH A:689 , HOH A:708
BINDING SITE FOR RESIDUE MG A 319
02
AC2
SOFTWARE
ARG A:156 , TYR A:171 , ASN A:174
BINDING SITE FOR RESIDUE CL A 320
03
AC3
SOFTWARE
ASP B:70 , GLU B:96 , HOH B:714 , HOH B:733 , HOH B:779
BINDING SITE FOR RESIDUE MG B 319
04
AC4
SOFTWARE
ARG B:156 , ASN B:174
BINDING SITE FOR RESIDUE CL B 320
05
AC5
SOFTWARE
ASP C:70 , GLU C:96 , HOH C:656 , HOH C:657 , HOH C:700 , HOH C:876
BINDING SITE FOR RESIDUE MG C 319
06
AC6
SOFTWARE
ARG C:156 , ASN C:174
BINDING SITE FOR RESIDUE CL C 320
07
AC7
SOFTWARE
ASP D:70 , GLU D:96 , HOH D:717
BINDING SITE FOR RESIDUE MG D 319
08
AC8
SOFTWARE
ASP E:70 , GLU E:96 , HOH E:653 , HOH E:658 , HOH E:659 , HOH E:660
BINDING SITE FOR RESIDUE MG E 319
09
AC9
SOFTWARE
ASP F:70 , GLU F:96 , HOH F:662 , HOH F:663 , HOH F:664 , HOH F:665
BINDING SITE FOR RESIDUE MG F 319
10
BC1
SOFTWARE
ARG F:156 , ASN F:174 , HOH F:361
BINDING SITE FOR RESIDUE CL F 320
[
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SAPs(SNPs)/Variants
(3, 18)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_013455 (Q51H, chain A/B/C/D/E/F, )
2: VAR_014823 (I64V, chain A/B/C/D/E/F, )
3: VAR_019790 (D148E, chain A/B/C/D/E/F, )
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
A/B/C/D/E/F
Q
51
H
2
UniProt
VAR_014823
I
64
V
APEX1_HUMAN
Polymorphism
2307486
A/B/C/D/E/F
I
64
V
3
UniProt
VAR_019790
D
148
E
APEX1_HUMAN
Polymorphism
1130409
A/B/C/D/E/F
D
148
E
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(4, 24)
Info
All PROSITE Patterns/Profiles
1: AP_NUCLEASE_F1_4 (A:62-318,B:62-318,C:62-318,D:62-31...)
2: AP_NUCLEASE_F1_1 (A:89-98,B:89-98,C:89-98,D:89-98,E:...)
3: AP_NUCLEASE_F1_2 (A:251-267,B:251-267,C:251-267,D:25...)
4: AP_NUCLEASE_F1_3 (A:277-288,B:277-288,C:277-288,D:27...)
;
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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
6
A:62-318
B:62-318
C:62-318
D:62-318
E:62-318
F:62-318
2
AP_NUCLEASE_F1_1
PS00726
AP endonucleases family 1 signature 1.
APEX1_HUMAN
89-98
6
A:89-98
B:89-98
C:89-98
D:89-98
E:89-98
F:89-98
3
AP_NUCLEASE_F1_2
PS00727
AP endonucleases family 1 signature 2.
APEX1_HUMAN
251-267
6
A:251-267
B:251-267
C:251-267
D:251-267
E:251-267
F:251-267
4
AP_NUCLEASE_F1_3
PS00728
AP endonucleases family 1 signature 3.
APEX1_HUMAN
277-288
6
A:277-288
B:277-288
C:277-288
D:277-288
E:277-288
F:277-288
[
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]
Exons
(3, 18)
Info
All Exons
Exon 1.3a (A:44-82 | B:44-82 | C:44-82 | D:44...)
Exon 1.4 (A:83-147 | B:83-147 | C:83-147 | D...)
Exon 1.5a (A:147-318 | B:147-318 | C:147-318 ...)
View:
Select:
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All Exon Boundaries
1: Boundary 1.2/1.3a
2: Boundary 1.3a/1.4
3: Boundary 1.4/1.5a
4: Boundary 1.5a/-
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
1.1c
ENST00000398030
1c
ENSE00001531237
chr14:
20923400-20923497
98
APEX1_HUMAN
-
0
0
-
-
1.2
ENST00000398030
2
ENSE00000889014
chr14:
20923737-20923862
126
APEX1_HUMAN
1-20
20
0
-
-
1.3a
ENST00000398030
3a
ENSE00000652723
chr14:
20924073-20924260
188
APEX1_HUMAN
20-82
63
6
A:44-82
B:44-82
C:44-82
D:44-82
E:44-82
F:44-82
39
39
39
39
39
39
1.4
ENST00000398030
4
ENSE00000652726
chr14:
20924827-20925019
193
APEX1_HUMAN
83-147
65
6
A:83-147
B:83-147
C:83-147
D:83-147 (gaps)
E:83-147 (gaps)
F:83-147
65
65
65
65
65
65
1.5a
ENST00000398030
5a
ENSE00001842242
chr14:
20925150-20925895
746
APEX1_HUMAN
147-318
172
6
A:147-318
B:147-318
C:147-318
D:147-318
E:147-318
F:147-318
172
172
172
172
172
172
[
close EXON info
]
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d3u8ua_ (A:)
1b: SCOP_d3u8ub_ (B:)
1c: SCOP_d3u8uc_ (C:)
1d: SCOP_d3u8ud_ (D:)
1e: SCOP_d3u8ue_ (E:)
1f: SCOP_d3u8uf_ (F:)
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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
d3u8ua_
A:
1b
d3u8ub_
B:
1c
d3u8uc_
C:
1d
d3u8ud_
D:
1e
d3u8ue_
E:
1f
d3u8uf_
F:
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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Chain B
Chain C
Chain D
Chain E
Chain F
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Asym.Unit (282 KB)
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