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1RGU
Biol. Unit 2
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Asym.Unit (152 KB)
Biol.Unit 1 (75 KB)
Biol.Unit 2 (75 KB)
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(1)
Title
:
THE CRYSTAL STRUCTURE OF HUMAN TYROSYL-DNA PHOSPHODIESTERASE COMPLEXED WITH VANADATE, OCTOPAMINE, AND TETRANUCLEOTIDE AGTG
Authors
:
D. R. Davies, H. Interthal, J. J. Champoux, W. G. Hol
Date
:
13 Nov 03 (Deposition) - 02 Mar 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.22
Chains
:
Asym. Unit : A,B,D,F
Biol. Unit 1: A,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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Reference
:
D. R. Davies, H. Interthal, J. J. Champoux, W. G. Hol
Explorations Of Peptide And Oligonucleotide Binding Sites Of Tyrosyl-Dna Phosphodiesterase Using Vanadate Complexes.
J. Med. Chem. V. 47 829 2004
(for further references see the
PDB file header
)
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Hetero Components
(2, 2)
Info
All Hetero Components
1a: 4-(2S-AMINO-1-HYDROXYETHYL)PHENOL (OTSa)
1b: 4-(2S-AMINO-1-HYDROXYETHYL)PHENOL (OTSb)
2a: SPERMINE (SPMa)
3a: VANADATE ION (VO4a)
3b: VANADATE ION (VO4b)
View:
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Label:
No.
Name
Count
Type
Full Name
1
OTS
1
Ligand/Ion
4-(2S-AMINO-1-HYDROXYETHYL)PHENOL
2
SPM
-1
Ligand/Ion
SPERMINE
3
VO4
1
Ligand/Ion
VANADATE ION
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Sites
(3, 3)
Info
All Sites
1: AC2 (SOFTWARE)
2: AC3 (SOFTWARE)
3: AC5 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC2
SOFTWARE
HIS B:263 , LYS B:265 , ASN B:283 , HIS B:493 , LYS B:495 , ASN B:516 , OTS B:996 , DG F:806
BINDING SITE FOR RESIDUE VO4 B 699
2
AC3
SOFTWARE
ASN A:591 , TRP A:605 , VAL A:606 , PRO A:607 , THR B:449 , SER B:450 , LEU B:451 , THR B:600
BINDING SITE FOR RESIDUE SPM A 999
3
AC5
SOFTWARE
TYR B:204 , GLY B:458 , SER B:459 , HIS B:493 , HOH B:676 , VO4 B:699 , DG F:806
BINDING SITE FOR RESIDUE OTS B 996
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SAPs(SNPs)/Variants
(4, 4)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_025820 (D187G, chain B, )
2: VAR_025821 (R304Q, chain B, )
3: VAR_017144 (H493R, chain B, )
4: VAR_025822 (T569A, chain B, )
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dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_025820
D
187
G
TYDP1_HUMAN
Polymorphism
35271143
B
D
187
G
2
UniProt
VAR_025821
R
304
Q
TYDP1_HUMAN
Polymorphism
34452707
B
R
304
Q
3
UniProt
VAR_017144
H
493
R
TYDP1_HUMAN
Disease (SCAN1)
---
B
H
493
R
4
UniProt
VAR_025822
T
569
A
TYDP1_HUMAN
Polymorphism
35973343
B
T
569
A
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(, 0)
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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.
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SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1rgua1 (A:162-350)
1b: SCOP_d1rgua2 (A:351-608)
1c: SCOP_d1rgub1 (B:162-350)
1d: SCOP_d1rgub2 (B:351-607)
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Protein Domains
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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
d1rgua1
A:162-350
1b
d1rgua2
A:351-608
1c
d1rgub1
B:162-350
1d
d1rgub2
B:351-607
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1rguA01 (A:162-351)
1b: CATH_1rguB01 (B:162-351)
2a: CATH_1rguB02 (B:352-607)
2b: CATH_1rguA02 (A:352-608)
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Organisms
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)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Endonuclease; Chain A
(28)
Homologous Superfamily
:
Endonuclease Chain A
(28)
[unclassified]
(8)
1a
1rguA01
A:162-351
1b
1rguB01
B:162-351
Homologous Superfamily
:
Phospholipase D/nuclease; domain 2
(13)
[unclassified]
(8)
2a
1rguB02
B:352-607
2b
1rguA02
A:352-608
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Tyr_DNA_phospho_1rguB01 (B:163-582)
1b: PFAM_Tyr_DNA_phospho_1rguB02 (B:163-582)
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Clan
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PLD
(22)
Family
:
Tyr-DNA_phospho
(11)
Homo sapiens (Human)
(10)
1a
Tyr-DNA_phospho-1rguB01
B:163-582
1b
Tyr-DNA_phospho-1rguB02
B:163-582
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Asymmetric Unit 1
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