SMTL ID : 9dqi.1

D306N Mutant of M.tuberculosis MenD (SEPHCHC Synthase)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: R.117, G.296, R.297, T.319, R.323, P.325 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.117, A:R.323 EDO.2: 2 residues within 4Å: Chain A: S.49 Chain B: L.498 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.49, A:Q.138 EDO.7: 1 residues within 4Å: Chain B: R.416 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.88, B:R.416, B:R.416 EDO.10: 6 residues within 4Å: Chain C: R.117, G.296, R.297, T.319, R.323, P.325 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.117

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

CL.3: 5 residues within 4Å: Chain A: G.395, S.397, P.399, G.459, T.462 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: P.204, L.205, V.206 Chain B: E.499 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain B: A.396, S.397, R.401, R.419, A.422 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain C: L.287, R.288, W.348, R.351 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain C: G.395, S.397, P.399, G.459, T.462 Ligand excluded by PLIP

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.5: 22 residues within 4Å: Chain A: P.47, E.75, 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.8 20 PLIP interactions: 3 interactions with chain A, 17 interactions with chain B Hydrophobic interactions: A:P.47, B:I.424, B:F.495 Water bridges: A:T.101, A:A.102, B:D.489, B:G.491 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 TPP.13: 23 residues within 4Å: Chain C: P.47, E.75, T.98, T.101, 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.15 16 PLIP interactions: 15 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:I.424, D:F.495, C:P.47 Hydrogen bonds: D:S.397, D:N.398, D:N.398, D:A.422, D:I.424, D:D.460, D:D.460, D:L.461, D:T.462, D:G.493, D:I.494 Water bridges: D:G.459, D:D.489

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

DNA.6: 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 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:R.297, B:R.323 Hydrogen bonds: B:Y.115, B:R.323 Water bridges: B:R.117, B:R.117, B:H.252, B:R.297, B:T.320, B:T.320 Salt bridges: B:R.117 DNA.14: 11 residues within 4Å: Chain C: G.133, G.135 Chain D: Y.115, R.117, H.252, G.253, G.296, R.297, R.323, W.324, P.325 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:R.297, D:R.323 Hydrogen bonds: D:Y.115, D:R.323 Salt bridges: D:R.117

2 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 4 residues within 4Å: Chain B: D.460, D.489, G.491 Ligands: TPP.5 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.460, B:D.489, B:G.491, H2O.3 MG.15: 4 residues within 4Å: Chain D: D.460, D.489, G.491 Ligands: TPP.13 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.460, D:D.489, D:G.491, H2O.7

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