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1NOP
Asym. Unit
Info
Asym.Unit (150 KB)
Biol.Unit 1 (75 KB)
Biol.Unit 2 (73 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN TYROSYL-DNA PHOSPHODIESTERASE (TDP1) IN COMPLEX WITH VANADATE, DNA AND A HUMAN TOPOISOMERASE I-DERIVED PEPTIDE
Authors
:
D. R. Davies, H. Interthal, J. J. Champoux, W. G. J. Hol
Date
:
16 Jan 03 (Deposition) - 11 Mar 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D,F
Biol. Unit 1: A,C,D (1x)
Biol. Unit 2: B,F (1x)
Keywords
:
Protein-Dna Complex, Vanadate Complex, Transition State Mimic, Hydrolase/Dna Complex
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
D. R. Davies, H. Interthal, J. J. Champoux, W. G. J. Hol
Crystal Structure Of A Transition State Mimic For Tdp1 Assembled From Vanadate, Dna, And A Topoisomerase I-Derived Peptide
Chem. Biol. V. 10 139 2003
(for further references see the
PDB file header
)
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: VANADATE ION (VO4a)
1b: VANADATE ION (VO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
VO4
2
Ligand/Ion
VANADATE ION
[
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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
HIS A:263 , LYS A:265 , ASN A:283 , HIS A:493 , LYS A:495 , ASN A:516 , HOH A:728 , TYR C:723 , DT D:806
BINDING SITE FOR RESIDUE VO4 A 699
2
AC2
SOFTWARE
TYR B:204 , HIS B:263 , LYS B:265 , ASN B:283 , HIS B:493 , LYS B:495 , ASN B:516 , DT F:806
BINDING SITE FOR RESIDUE VO4 B 699
[
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SAPs(SNPs)/Variants
(4, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_025820 (D187G, chain A/B, )
2: VAR_025821 (R304Q, chain A/B, )
3: VAR_017144 (H493R, chain A/B, )
4: VAR_025822 (T569A, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_025820
D
187
G
TYDP1_HUMAN
Polymorphism
35271143
A/B
D
187
G
2
UniProt
VAR_025821
R
304
Q
TYDP1_HUMAN
Polymorphism
34452707
A/B
R
304
Q
3
UniProt
VAR_017144
H
493
R
TYDP1_HUMAN
Disease (SCAN1)
---
A/B
H
493
R
4
UniProt
VAR_025822
T
569
A
TYDP1_HUMAN
Polymorphism
35973343
A/B
T
569
A
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
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Exons
(15, 30)
Info
All Exons
Exon 1.3 (A:162-187 | B:159-187)
Exon 1.4 (A:187-201 | B:187-201)
Exon 1.5 (A:202-220 | B:202-220)
Exon 1.6 (A:220-252 | B:220-252)
Exon 1.7 (A:253-264 | B:253-264)
Exon 1.8 (A:264-295 | B:264-295)
Exon 1.9 (A:295-351 | B:295-351)
Exon 1.10 (A:351-377 | B:351-377)
Exon 1.11 (A:378-439 (gaps) | B:378-439 (gaps...)
Exon 1.12 (A:440-456 | B:440-456)
Exon 1.13 (A:456-478 | B:456-478)
Exon 1.14 (A:478-514 | B:478-514)
Exon 1.15 (A:514-548 | B:514-548)
Exon 1.17 (A:549-585 (gaps) | B:549-585 (gaps...)
Exon 1.18 (A:585-608 | B:585-607)
View:
Select:
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All Exon Boundaries
01: Boundary 1.1/1.3
02: Boundary 1.3/1.4
03: Boundary 1.4/1.5
04: Boundary 1.5/1.6
05: Boundary 1.6/1.7
06: Boundary 1.7/1.8
07: Boundary 1.8/1.9
08: Boundary 1.9/1.10
09: Boundary 1.10/1.11
10: Boundary 1.11/1.12
11: Boundary 1.12/1.13
12: Boundary 1.13/1.14
13: Boundary 1.14/1.15
14: Boundary 1.15/1.17
15: Boundary 1.17/1.18
16: Boundary 1.18/-
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
ENST00000393454
1
ENSE00001413418
chr14:
90422246-90422314
69
TYDP1_HUMAN
-
0
0
-
-
1.3
ENST00000393454
3
ENSE00002191997
chr14:
90429452-90430017
566
TYDP1_HUMAN
1-187
187
2
A:162-187
B:159-187
26
29
1.4
ENST00000393454
4
ENSE00001794647
chr14:
90432491-90432534
44
TYDP1_HUMAN
187-201
15
2
A:187-201
B:187-201
15
15
1.5
ENST00000393454
5
ENSE00001653050
chr14:
90433711-90433766
56
TYDP1_HUMAN
202-220
19
2
A:202-220
B:202-220
19
19
1.6
ENST00000393454
6
ENSE00001773975
chr14:
90437519-90437615
97
TYDP1_HUMAN
220-252
33
2
A:220-252
B:220-252
33
33
1.7
ENST00000393454
7
ENSE00000912013
chr14:
90442125-90442159
35
TYDP1_HUMAN
253-264
12
2
A:253-264
B:253-264
12
12
1.8
ENST00000393454
8
ENSE00001146713
chr14:
90446884-90446976
93
TYDP1_HUMAN
264-295
32
2
A:264-295
B:264-295
32
32
1.9
ENST00000393454
9
ENSE00001146704
chr14:
90450860-90451027
168
TYDP1_HUMAN
295-351
57
2
A:295-351
B:295-351
57
57
1.10
ENST00000393454
10
ENSE00001146697
chr14:
90451476-90451554
79
TYDP1_HUMAN
351-377
27
2
A:351-377
B:351-377
27
27
1.11
ENST00000393454
11
ENSE00001146688
chr14:
90455249-90455434
186
TYDP1_HUMAN
378-439
62
2
A:378-439 (gaps)
B:378-439 (gaps)
62
62
1.12
ENST00000393454
12
ENSE00001146680
chr14:
90456061-90456109
49
TYDP1_HUMAN
440-456
17
2
A:440-456
B:440-456
17
17
1.13
ENST00000393454
13
ENSE00001146670
chr14:
90458261-90458327
67
TYDP1_HUMAN
456-478
23
2
A:456-478
B:456-478
23
23
1.14
ENST00000393454
14
ENSE00001146662
chr14:
90459720-90459827
108
TYDP1_HUMAN
478-514
37
2
A:478-514
B:478-514
37
37
1.15
ENST00000393454
15
ENSE00001146656
chr14:
90485660-90485762
103
TYDP1_HUMAN
514-548
35
2
A:514-548
B:514-548
35
35
1.17
ENST00000393454
17
ENSE00001760418
chr14:
90499450-90499558
109
TYDP1_HUMAN
549-585
37
2
A:549-585 (gaps)
B:549-585 (gaps)
37
37
1.18
ENST00000393454
18
ENSE00001596585
chr14:
90509414-90511106
1693
TYDP1_HUMAN
585-608
24
2
A:585-608
B:585-607
24
23
[
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SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1nopa1 (A:162-350)
1b: SCOP_d1nopa2 (A:351-608)
1c: SCOP_d1nopb1 (B:159-350)
1d: SCOP_d1nopb2 (B:351-607)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Phospholipase D/nuclease
(33)
Superfamily
:
Phospholipase D/nuclease
(33)
Family
:
Tyrosyl-DNA phosphodiesterase TDP1
(17)
Protein domain
:
Tyrosyl-DNA phosphodiesterase TDP1
(13)
Human (Homo sapiens) [TaxId: 9606]
(12)
1a
d1nopa1
A:162-350
1b
d1nopa2
A:351-608
1c
d1nopb1
B:159-350
1d
d1nopb2
B:351-607
[
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1nopB01 (B:159-351)
1b: CATH_1nopA01 (A:162-351)
2a: CATH_1nopA02 (A:352-608)
2b: CATH_1nopB02 (B:352-607)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Endonuclease; Chain A
(28)
Homologous Superfamily
:
Endonuclease Chain A
(28)
[unclassified]
(8)
1a
1nopB01
B:159-351
1b
1nopA01
A:162-351
Homologous Superfamily
:
Phospholipase D/nuclease; domain 2
(13)
[unclassified]
(8)
2a
1nopA02
A:352-608
2b
1nopB02
B:352-607
[
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Tyr_DNA_phospho_1nopB01 (B:163-582)
1b: PFAM_Tyr_DNA_phospho_1nopB02 (B:163-582)
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Clan
:
PLD
(22)
Family
:
Tyr-DNA_phospho
(11)
Homo sapiens (Human)
(10)
1a
Tyr-DNA_phospho-1nopB01
B:163-582
1b
Tyr-DNA_phospho-1nopB02
B:163-582
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