SMTL ID : 8tfg.1

1.88A CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS TOPOISOMERASE I

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

monomer

Ligands

11 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 8 residues within 4Å: Chain A: H.535, V.542, P.543, S.544, W.545, D.670, I.672, P.674 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.543, A:W.545 Water bridges: A:V.546 EDO.2: 7 residues within 4Å: Chain A: D.95, G.96, D.97, F.122, H.123, Y.326, E.371 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.96, A:E.371 Water bridges: A:D.95, A:F.122, A:Y.319 EDO.3: 4 residues within 4Å: Chain A: W.105, V.145, D.146, E.149 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.146, A:E.149 Water bridges: A:R.584 EDO.4: 6 residues within 4Å: Chain A: A.61, D.62, F.63, E.64, R.584, T.585 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.63, A:R.584, A:R.584 EDO.5: 7 residues within 4Å: Chain A: G.322, Y.323, A.379, T.382, F.383, A.384, Y.404 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.384, A:Y.404, A:Y.404 EDO.6: 7 residues within 4Å: Chain A: D.97, R.328, E.371, A.372, P.518, S.519 Ligands: EDO.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.97 Water bridges: A:S.519, A:S.519, A:S.519 EDO.7: 4 residues within 4Å: Chain A: G.598, V.599, P.600, R.605 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.605 Water bridges: A:G.598 EDO.8: 3 residues within 4Å: Chain A: A.384, A.388, E.392 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.392 Water bridges: A:T.385 EDO.9: 4 residues within 4Å: Chain A: T.11, Q.316, R.317, E.320 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.11 Water bridges: A:T.11, A:N.321 EDO.10: 7 residues within 4Å: Chain A: S.301, R.305, F.306, S.307, E.503, K.536, S.539 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.503, A:K.536 Water bridges: A:E.503 EDO.11: 7 residues within 4Å: Chain A: R.98, D.330, K.367, R.517, P.518, D.575 Ligands: EDO.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.98, A:D.330, A:D.575 Water bridges: A:R.98

7 x ACT: ACETATE ION(Non-functional Binders)

ACT.12: 4 residues within 4Å: Chain A: R.38, R.152, D.155, R.156 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.38, A:R.152, A:R.156 ACT.13: 6 residues within 4Å: Chain A: R.190, V.463, A.499, R.500, Y.501, S.505 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.463 Water bridges: A:T.502 Salt bridges: A:R.190 ACT.14: 5 residues within 4Å: Chain A: K.303, Q.409, A.454, Y.455, V.456 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:K.303, A:Y.455 Hydrogen bonds: A:V.456, A:V.456 Water bridges: A:K.303 Salt bridges: A:K.303 ACT.15: 5 residues within 4Å: Chain A: H.32, R.34, D.35, Q.148, R.152 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.148, A:R.152 Salt bridges: A:H.32, A:H.106 ACT.16: 3 residues within 4Å: Chain A: S.337, N.340, E.381 No protein-ligand interaction detected (PLIP) ACT.17: 4 residues within 4Å: Chain A: Q.529, D.530, R.531, G.532 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.532 ACT.18: 3 residues within 4Å: Chain A: D.269, G.270, I.485 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.270

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, K. et al., 1.88A CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS TOPOISOMERASE I. To Be Published

Release Date

2023-08-09

Peptides

DNA topoisomerase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA topoisomerase 1