SMTL ID : 9dtv.1

Structure of D141A mutant of M.tuberculosis MenD (SEPHCHC Synthase)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.42 Å

Oligo State

homo-tetramer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: R.117, G.253, G.296, R.297, T.319, R.323, W.324, P.325 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.117 GOL.9: 9 residues within 4Å: Chain C: R.117, H.252, G.296, R.297, T.319, T.320, R.323, W.324, P.325 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.117, C:T.320

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 5 residues within 4Å: Chain A: G.395, S.397, P.399, G.459, T.462 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain B: R.288 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain B: S.397, R.401, R.419, A.422 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain C: G.395, P.399, G.459, T.462 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain D: A.396, S.397, R.401, R.419, A.422 Ligand excluded by PLIP

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.3: 23 residues within 4Å: Chain A: P.47, E.75, T.98, T.101, A.102 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: MG.6 18 PLIP interactions: 15 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.397, B:N.398, B:N.398, B:A.422, B:I.424, B:G.459, B:D.460, B:D.460, B:L.461, B:T.462, B:T.462, B:G.493, B:I.494 Water bridges: B:D.489, B:D.489, A:T.101, A:A.102 Hydrophobic interactions: A:P.47 TPP.11: 22 residues within 4Å: Chain C: P.47, E.75, T.98, T.101, A.102 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 Ligands: MG.13 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.397, D:S.397, D:N.398, D:A.422, D:I.424, D:D.460, D:L.461, D:T.462, D:G.493, D:I.494 Water bridges: D:T.462 Hydrophobic interactions: C:P.47

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

DNA.4: 11 residues within 4Å: Chain A: G.133, T.134, G.135 Chain B: Y.115, R.117, H.252, G.296, R.297, R.323, W.324, P.325 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:R.297, B:R.323, B:R.323 Hydrogen bonds: B:Y.115, B:R.323 Water bridges: B:H.252, B:R.297 Salt bridges: B:R.117 DNA.12: 11 residues within 4Å: Chain C: G.133, T.134, G.135 Chain D: Y.115, R.117, H.252, G.296, R.297, R.323, W.324, P.325 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:R.297, D:R.323 Hydrogen bonds: D:Y.115, D:R.323 Water bridges: D:R.297 Salt bridges: D:R.117

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

EDO.5: 3 residues within 4Å: Chain B: D.239, F.316, A.333 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.239

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 5 residues within 4Å: Chain B: D.460, D.489, G.491, G.493 Ligands: TPP.3 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.460, B:D.489, B:G.491, H2O.2 MG.13: 5 residues within 4Å: Chain D: D.460, D.489, G.491, G.493 Ligands: TPP.11 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.460, D:D.489, D:G.491, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ho, N.A.T. et al., Apparent Reversal of Allosteric Response in Mycobacterium tuberculosis MenD Reveals Links to Half-of-Sites Reactivity. Chembiochem (2025)

Release Date

2025-04-16

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