SMTL ID : 6o0j.1

M.tb MenD with ThDP and Inhibitor bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-tetramer

Ligands

4 x DNA: 1,4-dihydroxy-2-naphthoic acid(Non-covalent)

DNA.1: 10 residues within 4Å: Chain A: Y.115, R.117, G.296, R.297, T.319, R.323, W.324, P.325 Chain B: G.135, A.136 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.115, A:R.297, A:R.323 Hydrogen bonds: A:N.114, A:G.296, A:R.323, A:R.323 Water bridges: A:R.117, A:R.117, A:G.321, A:R.323 Salt bridges: A:R.117 pi-Cation interactions: A:R.297 DNA.6: 10 residues within 4Å: Chain A: G.133, T.134, G.135 Chain B: Y.115, R.117, H.252, R.297, R.323, W.324, P.325 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:R.297, B:R.323 Hydrogen bonds: B:Y.115 Water bridges: B:R.117, B:H.252, B:T.319, B:R.323 Salt bridges: B:R.117 DNA.11: 10 residues within 4Å: Chain C: Y.115, R.117, H.252, G.253, R.297, T.319, R.323, W.324, P.325 Chain D: G.135 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:Y.115, C:R.297, C:R.297, C:R.323 Hydrogen bonds: C:N.114, C:G.296, C:R.323 Water bridges: C:A.116, C:R.117, C:R.117, C:G.321, C:R.323 Salt bridges: C:R.117 pi-Cation interactions: C:R.297 DNA.13: 9 residues within 4Å: Chain C: G.133, T.134, G.135 Chain D: Y.115, R.117, R.297, R.323, W.324, P.325 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:R.323, D:P.325 Hydrogen bonds: D:Y.115, D:R.323 Water bridges: D:G.321, D:R.323 Salt bridges: D:R.117

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: Y.129, L.143 Chain C: Y.129, L.143 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.155 Water bridges: A:Y.129 GOL.3: 4 residues within 4Å: Chain A: E.130, L.158 Chain C: E.130, L.158 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:E.130 Water bridges: A:L.158, A:L.158, C:E.130, C:L.158, C:L.158

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

ACT.4: 6 residues within 4Å: Chain A: T.26, E.160, A.162, P.163, T.166, W.173 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.26, A:T.166 Hydrogen bonds: A:A.162 ACT.8: 7 residues within 4Å: Chain A: N.137, Q.138 Chain B: A.396, S.397, R.401, R.419, A.422 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.422 Hydrogen bonds: B:S.397, A:N.137 Salt bridges: B:R.401, B:R.419 ACT.15: 7 residues within 4Å: Chain C: N.137 Chain D: A.396, S.397, R.401, R.419, A.422 Ligands: TPP.16 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:A.396 Hydrogen bonds: D:S.397, C:N.137 Salt bridges: D:R.401, D:R.419

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

FMT.5: 7 residues within 4Å: Chain A: G.48, S.49, R.50, T.98, R.127, Q.138 Ligands: TPP.9 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.49, A:R.50, A:T.98, A:R.127, A:Q.138 Water bridges: A:R.50 FMT.10: 1 residues within 4Å: Chain B: R.416 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.416, B:R.416 FMT.12: 5 residues within 4Å: Chain C: P.23, E.160, T.166, L.169, W.173 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.166

2 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 5 residues within 4Å: Chain B: D.460, D.489, G.491, G.493 Ligands: TPP.9 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.460, B:D.489, B:G.491, H2O.7 MG.14: 5 residues within 4Å: Chain D: D.460, D.489, G.491, G.493 Ligands: TPP.16 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.460, D:D.489, D:G.491, H2O.15

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.9: 26 residues within 4Å: Chain A: P.47, G.48, E.75, T.98, T.101, A.102, Q.138 Chain B: S.397, N.398, P.399, A.422, G.423, I.424, D.425, G.459, D.460, L.461, T.462, D.489, G.491, G.492, G.493, I.494, F.495 Ligands: FMT.5, MG.7 25 PLIP interactions: 21 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.424, B:I.424, B:D.425, B:L.461, B:F.495, A:P.47, A:T.98 Hydrogen bonds: B:S.397, B:S.397, B:N.398, B:N.398, B:A.422, B:I.424, B:D.460, B:D.460, B:L.461, B:T.462, B:G.493, B:I.494 Water bridges: B:T.462, B:D.489, B:D.489, A:A.102, A:A.102 pi-Stacking: B:F.495 TPP.16: 26 residues within 4Å: Chain C: P.47, G.48, E.75, T.98, T.101, A.102, Q.138 Chain D: S.397, N.398, P.399, A.422, G.423, I.424, D.425, G.459, D.460, L.461, T.462, D.489, G.491, G.492, G.493, I.494, F.495 Ligands: MG.14, ACT.15 19 PLIP interactions: 17 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:I.424, D:I.424, C:P.47, C:T.98 Hydrogen bonds: D:S.397, D:S.397, D:N.398, D:N.398, D:A.422, D:I.424, D:G.459, D:D.460, D:L.461, D:T.462, D:T.462, D:G.493, D:I.494 Water bridges: D:D.460 pi-Stacking: D:F.495

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bashiri, G. et al., Allosteric regulation of menaquinone (vitamin K2) biosynthesis in the human pathogenMycobacterium tuberculosis. J.Biol.Chem. (2020)

Release Date

2020-02-19

Peptides

2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
B

D
C

2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase

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