SMTL ID : 1nop.1 (1 other biounit)

Crystal structure of human tyrosyl-DNA phosphodiesterase (Tdp1) in complex with vanadate, DNA and a human topoisomerase I-derived peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x DG- DT- DT: 5'-D(*AP*GP*AP*GP*TP*T)-3'(Non-covalent)

DG-DT-DT.1: 20 residues within 4Å: Chain A: Y.81, A.135, F.136, T.138, H.140, S.277, G.279, S.280, P.338, K.346, N.393, S.395, K.396, A.397, A.398, R.412, W.467 Ligands: LYS-LEU-ASN-TYR-LEU.2, LYS-LEU-ASN-TYR-LEU.2, VO4.3 Protein-ligand interaction information (PLIP) not available

1 x LYS- LEU- ASN- TYR- LEU: topoisomerase I-derived peptide(Non-covalent)

LYS-LEU-ASN-TYR-LEU.2: 15 residues within 4Å: Chain A: Y.81, C.82, F.83, D.84, D.107, Q.118, N.160, I.162, G.335, S.336, P.338, H.370, W.467 Ligands: DG-DT-DT.1, VO4.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.81, A:D.84, A:P.338 Hydrogen bonds: A:F.83, A:D.107, A:N.160, A:H.370

1 x VO4: VANADATE ION(Non-covalent)

VO4.3: 10 residues within 4Å: Chain A: Y.81, H.140, K.142, N.160, S.276, H.370, K.372, N.393 Ligands: DG-DT-DT.1, LYS-LEU-ASN-TYR-LEU.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.142, A:N.160, A:H.370, A:K.372, A:N.393

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Davies, D.R. et al., Crystal structure of a transition state mimic for Tdp1 assembled from vanadate, DNA, and a topoisomerase I-derived peptide. Chem.Biol. (2003)

Release Date

2003-03-11

Peptides

tyrosyl-DNA phosphodiesterase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

tyrosyl-DNA phosphodiesterase 1

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