SMTL ID : 6ozw.1

Crystal structure of the 65-kilodalton amino-terminal fragment of DNA topoisomerase I from Streptococcus mutans

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

monomer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 1 residues within 4Å: Chain A: R.177 No protein-ligand interaction detected (PLIP) MG.2: 2 residues within 4Å: Chain A: R.178, R.182 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain A: M.313, R.338, A.512 No protein-ligand interaction detected (PLIP) MG.4: 5 residues within 4Å: Chain A: I.213, R.216, E.217, R.490, F.531 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:I.213, A:E.217, H2O.5 MG.5: 3 residues within 4Å: Chain A: R.177, D.181, R.204 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.181, H2O.10 MG.6: 3 residues within 4Å: Chain A: N.94, G.99, I.102 No protein-ligand interaction detected (PLIP)

14 x FMT: FORMIC ACID(Non-functional Binders)

FMT.7: 3 residues within 4Å: Chain A: D.122, R.338, S.509 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.122, A:S.509 Water bridges: A:R.123 FMT.8: 2 residues within 4Å: Chain A: K.583, K.587 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.587 FMT.9: 3 residues within 4Å: Chain A: R.216, A.489, Y.491 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.216, A:R.216, A:T.499 Water bridges: A:S.495 FMT.10: 4 residues within 4Å: Chain A: P.121, F.148, N.149, A.380 No protein-ligand interaction detected (PLIP) FMT.11: 3 residues within 4Å: Chain A: K.195, I.539, L.543 No protein-ligand interaction detected (PLIP) FMT.12: 7 residues within 4Å: Chain A: N.149, T.335, Y.336, T.339, H.381, E.382, A.383 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.149, A:T.335, A:Y.336, A:Y.336, A:H.381, A:E.382 FMT.13: 3 residues within 4Å: Chain A: K.311, K.402, D.403 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.311, A:K.402 FMT.14: 1 residues within 4Å: Chain A: K.221 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.221 FMT.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) FMT.16: 6 residues within 4Å: Chain A: E.89, M.168, D.172, Q.175, W.574, Q.575 No protein-ligand interaction detected (PLIP) FMT.17: 3 residues within 4Å: Chain A: E.56, G.60, R.61 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.60 FMT.18: 2 residues within 4Å: Chain A: H.134, D.137 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.134 FMT.19: 2 residues within 4Å: Chain A: P.346, Q.349 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.349 FMT.20: 2 residues within 4Å: Chain A: E.481, H.483 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jones, J.A. et al., Crystal structure of the 65-kilodalton amino-terminal fragment of DNA topoisomerase I from the gram-positive model organism Streptococcus mutans. Biochem.Biophys.Res.Commun. (2019)

Release Date

2019-06-26

Peptides

DNA topoisomerase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA topoisomerase 1