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1NH3
Asym. Unit
Info
Asym.Unit (99 KB)
Biol.Unit 1 (92 KB)
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(1)
Title
:
HUMAN TOPOISOMERASE I ARA-C COMPLEX
Authors
:
J. E. Chrencik, A. B. Burgin, Y. Pommier, L. Stewart, M. R. Redinbo
Date
:
18 Dec 02 (Deposition) - 04 Mar 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Ara-C, Protein-Dna Complex, Dna Damage, Isomerase, Isomerase/Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. E. Chrencik, A. B. Burgin, Y. Pommier, L. Stewart, M. R. Redinbo
Structural Impact Of The Leukemia Drug 1-Beta-D-Arabinofuranosylcytosine (Ara-C) On The Covalent Human Topoisomerase I-Dna Complex
J. Biol. Chem. V. 278 12461 2003
(for further references see the
PDB file header
)
[
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Hetero Components
(5, 18)
Info
All Hetero Components
1a: CYTOSINE ARABINOSE-5'-PHOSPHATE (CARa)
2a: (DUa)
2b: (DUb)
2c: (DUc)
2d: (DUd)
2e: (DUe)
2f: (DUf)
2g: (DUg)
2h: (DUh)
2i: (DUi)
2j: (DUj)
2k: (DUk)
2l: (DUl)
2m: (DUm)
2n: (DUn)
3a: 2'-DEOXY-GUANOSINE (GNGa)
4a: O-PHOSPHOTYROSINE (PTRa)
5a: 2',3'-DIDEOXY-URIDINE-5'-MONOPHOSP... (UBBa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CAR
1
Mod. Nucleotide
CYTOSINE ARABINOSE-5'-PHOSPHATE
2
DU
14
Mod. Residue
3
GNG
1
Mod. Nucleotide
2'-DEOXY-GUANOSINE
4
PTR
1
Mod. Amino Acid
O-PHOSPHOTYROSINE
5
UBB
1
Mod. Nucleotide
2',3'-DIDEOXY-URIDINE-5'-MONOPHOSPHATE
[
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Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
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]
SAPs(SNPs)/Variants
(6, 6)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_052592 (G214S, chain A, )
2: VAR_036555 (K326R, chain A, )
3: VAR_010666 (M370T, chain A, )
4: VAR_007530 (D533G, chain A, )
5: VAR_010667 (N722S, chain A, )
6: VAR_007531 (T729A, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_052592
G
214
S
TOP1_HUMAN
Polymorphism
6029542
A
G
214
S
2
UniProt
VAR_036555
K
326
R
TOP1_HUMAN
Unclassified
---
A
K
326
R
3
UniProt
VAR_010666
M
370
T
TOP1_HUMAN
Unclassified
---
A
M
370
T
4
UniProt
VAR_007530
D
533
G
TOP1_HUMAN
Unclassified
---
A
D
533
G
5
UniProt
VAR_010667
N
722
S
TOP1_HUMAN
Unclassified
---
A
N
722
S
6
UniProt
VAR_007531
T
729
A
TOP1_HUMAN
Unclassified
---
A
T
729
A
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: TOPOISOMERASE_I_EUK (A:719-728)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TOPOISOMERASE_I_EUK
PS00176
Eukaryotic DNA topoisomerase I active site.
TOP1_HUMAN
710-728
1
A:719-728
[
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]
Exons
(13, 13)
Info
All Exons
Exon 1.8 (A:203-205)
Exon 1.9 (A:205-244)
Exon 1.10 (A:244-284)
Exon 1.11 (A:285-325)
Exon 1.12 (A:326-388)
Exon 1.13 (A:388-436)
Exon 1.14 (A:437-484)
Exon 1.15 (A:485-546)
Exon 1.16 (A:547-569)
Exon 1.17 (A:570-608)
Exon 1.18 (A:608-626)
Exon 1.20 (A:719-732)
Exon 1.21 (A:732-765)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.7/1.8
02: Boundary 1.8/1.9
03: Boundary 1.9/1.10
04: Boundary 1.10/1.11
05: Boundary 1.11/1.12
06: Boundary 1.12/1.13
07: Boundary 1.13/1.14
08: Boundary 1.14/1.15
09: Boundary 1.15/1.16
10: Boundary 1.16/1.17
11: Boundary 1.17/1.18
12: Boundary 1.18/1.19
13: Boundary 1.19/1.20
14: Boundary 1.20/1.21
15: Boundary 1.21/-
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
1.1
ENST00000361337
1
ENSE00001174143
chr20:
39657458-39657740
283
TOP1_HUMAN
1-11
11
0
-
-
1.2
ENST00000361337
2
ENSE00001174139
chr20:
39658071-39658095
25
TOP1_HUMAN
12-20
9
0
-
-
1.3
ENST00000361337
3
ENSE00001159739
chr20:
39690034-39690130
97
TOP1_HUMAN
20-52
33
0
-
-
1.4
ENST00000361337
4
ENSE00001037776
chr20:
39704811-39704934
124
TOP1_HUMAN
52-93
42
0
-
-
1.5
ENST00000361337
5
ENSE00000844695
chr20:
39706222-39706277
56
TOP1_HUMAN
94-112
19
0
-
-
1.6
ENST00000361337
6
ENSE00000844696
chr20:
39708725-39708820
96
TOP1_HUMAN
112-144
33
0
-
-
1.7
ENST00000361337
7
ENSE00000844697
chr20:
39709805-39709880
76
TOP1_HUMAN
144-169
26
0
-
-
1.8
ENST00000361337
8
ENSE00000844698
chr20:
39713102-39713208
107
TOP1_HUMAN
170-205
36
1
A:203-205
3
1.9
ENST00000361337
9
ENSE00000844699
chr20:
39721112-39721227
116
TOP1_HUMAN
205-244
40
1
A:205-244
40
1.10
ENST00000361337
10
ENSE00000844700
chr20:
39725860-39725981
122
TOP1_HUMAN
244-284
41
1
A:244-284
41
1.11
ENST00000361337
11
ENSE00000844701
chr20:
39726855-39726977
123
TOP1_HUMAN
285-325
41
1
A:285-325
41
1.12
ENST00000361337
12
ENSE00000844702
chr20:
39728696-39728883
188
TOP1_HUMAN
326-388
63
1
A:326-388
63
1.13
ENST00000361337
13
ENSE00000844703
chr20:
39729849-39729993
145
TOP1_HUMAN
388-436
49
1
A:388-436
49
1.14
ENST00000361337
14
ENSE00000844704
chr20:
39741422-39741565
144
TOP1_HUMAN
437-484
48
1
A:437-484
48
1.15
ENST00000361337
15
ENSE00000844706
chr20:
39742610-39742795
186
TOP1_HUMAN
485-546
62
1
A:485-546
62
1.16
ENST00000361337
16
ENSE00000844709
chr20:
39744011-39744079
69
TOP1_HUMAN
547-569
23
1
A:547-569
23
1.17
ENST00000361337
17
ENSE00000844711
chr20:
39744918-39745032
115
TOP1_HUMAN
570-608
39
1
A:570-608
39
1.18
ENST00000361337
18
ENSE00000844712
chr20:
39746809-39746936
128
TOP1_HUMAN
608-650
43
1
A:608-626
19
1.19
ENST00000361337
19
ENSE00000844716
chr20:
39750336-39750430
95
TOP1_HUMAN
651-682
32
0
-
-
1.20
ENST00000361337
20
ENSE00000844717
chr20:
39750646-39750795
150
TOP1_HUMAN
682-732
51
1
A:719-732
14
1.21
ENST00000361337
21
ENSE00001159738
chr20:
39751835-39753127
1293
TOP1_HUMAN
732-765
34
1
A:732-765
34
[
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]
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d1nh3a1 (A:431-626,A:719-765)
2a: SCOP_d1nh3a2 (A:203-430)
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Classes
(
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Folds
(
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Superfamilies
(
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(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
DNA breaking-rejoining enzymes
(47)
Superfamily
:
DNA breaking-rejoining enzymes
(47)
Family
:
Eukaryotic DNA topoisomerase I, catalytic core
(16)
Protein domain
:
Eukaryotic DNA topoisomerase I, catalytic core
(16)
Human (Homo sapiens) [TaxId: 9606]
(15)
1a
d1nh3a1
A:431-626,A:719-765
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment
(16)
Superfamily
:
Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment
(16)
Family
:
Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment
(16)
Protein domain
:
Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment
(16)
Human (Homo sapiens) [TaxId: 9606]
(15)
2a
d1nh3a2
A:203-430
[
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]
CATH Domains
(4, 4)
Info
all CATH domains
1a: CATH_1nh3A03 (A:431-580)
2a: CATH_1nh3A01 (A:236-319)
3a: CATH_1nh3A04 (A:591-626,A:719-764)
4a: CATH_1nh3A02 (A:320-430)
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Architectures
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Topologies
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)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Topoisomerase I; Chain A, domain 3
(16)
Homologous Superfamily
:
Topoisomerase I; Chain A, domain 3
(16)
[unclassified]
(15)
1a
1nh3A03
A:431-580
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Arc Repressor Mutant, subunit A
(1030)
Homologous Superfamily
:
Yeast DNA topoisomerase - domain 1
(16)
[unclassified]
(15)
2a
1nh3A01
A:236-319
Topology
:
Topoisomerase I; Chain A, domain 4
(31)
Homologous Superfamily
:
[code=1.10.132.10, no name defined]
(15)
[unclassified]
(15)
3a
1nh3A04
A:591-626,A:719-764
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Complex
(381)
Topology
:
DNA Topoisomerase I; domain 2
(16)
Homologous Superfamily
:
DNA Topoisomerase I, domain 2
(16)
[unclassified]
(15)
4a
1nh3A02
A:320-430
[
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]
Pfam Domains
(3, 3)
Info
all PFAM domains
1a: PFAM_Topoisom_I_1nh3A01 (A:431-626)
2a: PFAM_Topo_C_assoc_1nh3A02 (A:719-764)
3a: PFAM_Topoisom_I_N_1nh3A03 (A:215-429)
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Clans
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)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
DNA-mend
(28)
Family
:
Topoisom_I
(12)
Homo sapiens (Human)
(10)
1a
Topoisom_I-1nh3A01
A:431-626
Clan
:
no clan defined [family: Topo_C_assoc]
(10)
Family
:
Topo_C_assoc
(10)
Homo sapiens (Human)
(10)
2a
Topo_C_assoc-1nh3A02
A:719-764
Clan
:
no clan defined [family: Topoisom_I_N]
(11)
Family
:
Topoisom_I_N
(11)
Homo sapiens (Human)
(10)
3a
Topoisom_I_N-1nh3A03
A:215-429
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Asym.Unit (99 KB)
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