SMTL ID : 9foy.1

Ternary complex of a Mycobacterium tuberculosis DNA gyrase core fusion with DNA and the inhibitor AMK32b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x DA- DG- DC- DC- DG- DT- DA- DG: DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*G)-3')(Non-covalent)

DA-DG-DC-DC-DG-DT-DA-DG.1: 30 residues within 4Å: Chain A: E.37, R.60, G.61, K.62, D.114, R.291, K.301, V.303, H.304, H.337, H.339, G.340, S.343, S.347, R.350, S.356, G.431, I.433, N.531, N.534 Chain B: R.380 Chain C: G.1 Chain D: C.5, T.6, A.7, C.8, G.9, G.10, C.11, T.12 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.39, A:D.39, A:S.40, A:R.60 Salt bridges: A:K.19, A:R.60, B:R.380 DA-DG-DC-DC-DG-DT-DA-DG.2: 30 residues within 4Å: Chain A: R.380 Chain B: E.37, R.60, G.61, K.62, D.114, K.189, R.291, K.301, V.303, H.304, H.337, H.339, G.340, S.343, S.347, R.350, S.356, I.433, N.531, N.534 Chain C: C.5, T.6, A.7, C.8, G.9, G.10, C.11, T.12 Chain D: G.1 11 PLIP interactions: 1 interactions with chain A, 10 interactions with chain B Salt bridges: A:K.19, B:K.68, B:K.68, B:R.73, B:R.73, B:H.117, B:R.237 Hydrophobic interactions: B:I.433 Hydrogen bonds: B:N.65, B:N.65, B:G.436

1 x 01: (1~{S})-2-[4-[[4-bromanyl-3,5-bis(fluoranyl)phenyl]methylamino]cyclohexyl]-1-(6-methoxy-1,5-naphthyridin-4-yl)ethanol

01.3: 13 residues within 4Å: Chain A: A.326, A.330, M.333, D.341, M.379 Chain B: M.333, D.341, M.379 Chain C: T.2, A.3 Chain D: T.2, A.3 Ligands: 02.4 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:D.341, A:D.341

1 x 02: (1~{R})-2-[4-[[4-bromanyl-3,5-bis(fluoranyl)phenyl]methylamino]cyclohexyl]-1-(6-methoxy-1,5-naphthyridin-4-yl)ethanol

02.4: 13 residues within 4Å: Chain A: A.326, M.333, D.341, M.379 Chain B: A.330, M.333, D.341, M.379 Chain C: T.2, A.3 Chain D: T.2, A.3 Ligands: 01.3 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:D.341, A:D.341

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kokot, M. et al., Unraveling the Mycobacterium tuberculosis DNA gyrase-DNA-NBTI complex. To be published

Release Date

2024-08-07

Peptides

DNA gyrase subunit B,DNA gyrase subunit A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA gyrase subunit B,DNA gyrase subunit A