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Asym. Unit
Info
Asym.Unit (125 KB)
Biol.Unit 1 (60 KB)
Biol.Unit 2 (60 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF CATALYTIC DOMAIN OF HUMAN POLY(ADP-RIBOSE) POLYMERASE WITH A NOVEL INHIBITOR
Authors
:
T. Kinoshita
Date
:
13 Aug 03 (Deposition) - 27 Jan 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Protein-Inhibitor Complex, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Kinoshita, I. Nakanishi, M. Warizaya, A. Iwashita, Y. Kido, K. Hattori, T. Fujii
Inhibitor-Induced Structural Change Of The Active Site Of Human Poly(Adp-Ribose) Polymerase.
Febs Lett. V. 556 43 2004
(for further references see the
PDB file header
)
[
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: 2-{3-[4-(4-FLUOROPHENYL)-3,6-DIHYD... (FRMa)
1b: 2-{3-[4-(4-FLUOROPHENYL)-3,6-DIHYD... (FRMb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FRM
2
Ligand/Ion
2-{3-[4-(4-FLUOROPHENYL)-3,6-DIHYDRO-1(2H)-PYRIDINYL]PROPYL}-8-METHYL-4(3H)-QUINAZOLINONE
[
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:105 , LEU A:108 , ASP A:109 , HIS A:201 , GLY A:202 , SER A:203 , ASN A:207 , ARG A:217 , TYR A:235 , SER A:243 , TYR A:246
BINDING SITE FOR RESIDUE FRM A 501
2
AC2
SOFTWARE
LEU B:108 , ASP B:109 , HIS B:201 , GLY B:202 , ARG B:217 , TYR B:235 , PHE B:236 , SER B:243 , TYR B:246 , GLU B:327 , HOH B:505
BINDING SITE FOR RESIDUE FRM B 502
[
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SAPs(SNPs)/Variants
(2, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_014715 (V101A, chain A/B, )
2: VAR_019173 (K279R, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_014715
V
762
A
PARP1_HUMAN
Polymorphism
1136410
A/B
V
101
A
2
UniProt
VAR_019173
K
940
R
PARP1_HUMAN
Polymorphism
3219145
A/B
K
279
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: PARP_ALPHA_HD (A:1-118,B:1-118)
2: PARP_CATALYTIC (A:127-350,B:127-350)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PARP_ALPHA_HD
PS51060
PARP alpha-helical domain profile.
PARP1_HUMAN
662-779
2
A:1-118
B:1-118
2
PARP_CATALYTIC
PS51059
PARP catalytic domain profile.
PARP1_HUMAN
788-1014
2
A:127-350
B:127-350
[
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]
Exons
(10, 20)
Info
All Exons
Exon 1.16 (A:1-29 | B:1-29)
Exon 1.17c (A:30-57 | B:30-57)
Exon 1.18 (A:58-98 | B:58-98)
Exon 1.19a (A:99-141 | B:99-141)
Exon 1.19c (A:142-174 | B:142-174)
Exon 1.20b (A:175-225 | B:175-225)
Exon 1.21b (A:226-268 | B:226-268)
Exon 1.22 (A:268-289 | B:268-289)
Exon 1.23b (A:289-327 | B:289-327)
Exon 1.24d (A:327-350 | B:327-350)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.15/1.16
02: Boundary 1.16/1.17c
03: Boundary 1.17c/1.18
04: Boundary 1.18/1.19a
05: Boundary 1.19a/1.19c
06: Boundary 1.19c/1.20b
07: Boundary 1.20b/1.21b
08: Boundary 1.21b/1.22
09: Boundary 1.22/1.23b
10: Boundary 1.23b/1.24d
11: Boundary 1.24d/-
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
1.1b
ENST00000366794
1b
ENSE00001697768
chr1:
226595774-226595511
264
PARP1_HUMAN
1-40
40
0
-
-
1.2a
ENST00000366794
2a
ENSE00000962007
chr1:
226590080-226589915
166
PARP1_HUMAN
41-96
56
0
-
-
1.5b
ENST00000366794
5b
ENSE00000962008
chr1:
226580015-226579900
116
PARP1_HUMAN
96-134
39
0
-
-
1.6
ENST00000366794
6
ENSE00000962009
chr1:
226578325-226578111
215
PARP1_HUMAN
135-206
72
0
-
-
1.7b
ENST00000366794
7b
ENSE00000962010
chr1:
226576456-226576357
100
PARP1_HUMAN
206-239
34
0
-
-
1.8
ENST00000366794
8
ENSE00000962011
chr1:
226574143-226574027
117
PARP1_HUMAN
240-278
39
0
-
-
1.9
ENST00000366794
9
ENSE00000962012
chr1:
226573381-226573205
177
PARP1_HUMAN
279-337
59
0
-
-
1.10
ENST00000366794
10
ENSE00000962013
chr1:
226570884-226570737
148
PARP1_HUMAN
338-387
50
0
-
-
1.11
ENST00000366794
11
ENSE00000962014
chr1:
226568909-226568769
141
PARP1_HUMAN
387-434
48
0
-
-
1.12
ENST00000366794
12
ENSE00000962015
chr1:
226567865-226567623
243
PARP1_HUMAN
434-515
82
0
-
-
1.13
ENST00000366794
13
ENSE00000962016
chr1:
226567342-226567274
69
PARP1_HUMAN
515-538
24
0
-
-
1.14
ENST00000366794
14
ENSE00000962017
chr1:
226566975-226566843
133
PARP1_HUMAN
538-582
45
0
-
-
1.15
ENST00000366794
15
ENSE00000962018
chr1:
226565004-226564809
196
PARP1_HUMAN
582-647
66
0
-
-
1.16
ENST00000366794
16
ENSE00000962019
chr1:
226562055-226561927
129
PARP1_HUMAN
648-690
43
2
A:1-29
B:1-29
29
29
1.17c
ENST00000366794
17c
ENSE00000962020
chr1:
226558218-226558135
84
PARP1_HUMAN
691-718
28
2
A:30-57
B:30-57
28
28
1.18
ENST00000366794
18
ENSE00000962021
chr1:
226556022-226555900
123
PARP1_HUMAN
719-759
41
2
A:58-98
B:58-98
41
41
1.19a
ENST00000366794
19a
ENSE00000962022
chr1:
226555309-226555181
129
PARP1_HUMAN
760-802
43
2
A:99-141
B:99-141
43
43
1.19c
ENST00000366794
19c
ENSE00000962023
chr1:
226553753-226553655
99
PARP1_HUMAN
803-835
33
2
A:142-174
B:142-174
33
33
1.20b
ENST00000366794
20b
ENSE00000962024
chr1:
226552855-226552703
153
PARP1_HUMAN
836-886
51
2
A:175-225
B:175-225
51
51
1.21b
ENST00000366794
21b
ENSE00000962025
chr1:
226551771-226551644
128
PARP1_HUMAN
887-929
43
2
A:226-268
B:226-268
43
43
1.22
ENST00000366794
22
ENSE00000962026
chr1:
226550861-226550800
62
PARP1_HUMAN
929-950
22
2
A:268-289
B:268-289
22
22
1.23b
ENST00000366794
23b
ENSE00000962027
chr1:
226549784-226549670
115
PARP1_HUMAN
950-988
39
2
A:289-327
B:289-327
39
39
1.24d
ENST00000366794
24d
ENSE00001442633
chr1:
226549242-226548392
851
PARP1_HUMAN
988-1014
27
2
A:327-350
B:327-350
24
24
[
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]
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1uk0a1 (A:1-137)
1b: SCOP_d1uk0b1 (B:1-137)
2a: SCOP_d1uk0a2 (A:138-350)
2b: SCOP_d1uk0b2 (B:138-350)
View:
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Classes
(
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(
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Folds
(
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)
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(
)
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)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Domain of poly(ADP-ribose) polymerase
(38)
Superfamily
:
Domain of poly(ADP-ribose) polymerase
(38)
Family
:
Domain of poly(ADP-ribose) polymerase
(16)
Protein domain
:
Domain of poly(ADP-ribose) polymerase
(16)
Human (Homo sapiens) [TaxId: 9606]
(8)
1a
d1uk0a1
A:1-137
1b
d1uk0b1
B:1-137
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
ADP-ribosylation
(157)
Superfamily
:
ADP-ribosylation
(157)
Family
:
Poly(ADP-ribose) polymerase, C-terminal domain
(18)
Protein domain
:
Poly(ADP-ribose) polymerase, C-terminal domain
(16)
Human (Homo sapiens) [TaxId: 9606]
(8)
2a
d1uk0a2
A:138-350
2b
d1uk0b2
B:138-350
[
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]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1uk0A02 (A:137-349)
1b: CATH_1uk0B02 (B:137-349)
2a: CATH_1uk0A01 (A:1-136)
2b: CATH_1uk0B01 (B:1-136)
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)
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)
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(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Phosphoenolpyruvate Carboxykinase; domain 3
(62)
Homologous Superfamily
:
[code=3.90.228.10, no name defined]
(20)
Human (Homo sapiens)
(12)
1a
1uk0A02
A:137-349
1b
1uk0B02
B:137-349
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Poly(ADP-ribose) Polymerase; domain 1
(21)
Homologous Superfamily
:
Poly(ADP-ribose) Polymerase, domain 1
(21)
Human (Homo sapiens)
(12)
2a
1uk0A01
A:1-136
2b
1uk0B01
B:1-136
[
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]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_PARP_1uk0B01 (B:136-346)
1b: PFAM_PARP_1uk0B02 (B:136-346)
2a: PFAM_PARP_reg_1uk0B03 (B:1-134)
2b: PFAM_PARP_reg_1uk0B04 (B:1-134)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
ADP-ribosyl
(56)
Family
:
PARP
(21)
Homo sapiens (Human)
(18)
1a
PARP-1uk0B01
B:136-346
1b
PARP-1uk0B02
B:136-346
Clan
:
no clan defined [family: PARP_reg]
(10)
Family
:
PARP_reg
(10)
Homo sapiens (Human)
(7)
2a
PARP_reg-1uk0B03
B:1-134
2b
PARP_reg-1uk0B04
B:1-134
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