SMTL ID : 5eso.1

Crystal Structure of M. tuberculosis MenD with ThDP, Mg2+ and Isochorismate bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: D.460, D.489 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.460, A:D.489, H2O.6, H2O.8, H2O.8 MG.6: 4 residues within 4Å: Chain B: D.460, D.489, G.491 Ligands: FMT.9 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.460, B:D.489, B:G.491, H2O.9, H2O.15 MG.11: 5 residues within 4Å: Chain C: D.460, D.489, G.491, G.493 Ligands: TPP.15 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.460, C:D.489, C:G.491, H2O.18 MG.17: 5 residues within 4Å: Chain D: D.460, D.489, G.491, G.493 Ligands: TPP.18 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.460, D:D.489, D:G.491, H2O.27

2 x ISC: (5S,6S)-5-[(1-carboxyethenyl)oxy]-6-hydroxycyclohexa-1,3-diene-1-carboxylic acid(Non-covalent)

ISC.2: 11 residues within 4Å: Chain A: G.48, S.49, R.50, T.98, R.127, N.137, Q.138 Chain D: R.302, R.401, L.498 Ligands: TPP.18 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:S.49, A:R.50, A:T.98, A:R.127, A:R.127, A:N.137, A:Q.138, A:Q.138 Water bridges: A:S.49 Salt bridges: A:R.127, D:R.302 ISC.7: 11 residues within 4Å: Chain B: G.48, S.49, R.50, T.98, R.127, N.137, Q.138 Chain C: R.302, R.401, L.498 Ligands: TPP.15 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:S.49, B:R.50, B:R.127, B:R.127, B:N.137, B:Q.138 Water bridges: B:S.49 Salt bridges: B:R.127, C:R.302

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

FMT.3: 6 residues within 4Å: Chain A: R.117, G.296, R.297, T.319, R.323, P.325 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.117, A:G.296 Water bridges: A:G.296, A:T.320, A:T.320 FMT.8: 5 residues within 4Å: Chain B: P.23, E.160, A.162, T.166, W.173 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.162 FMT.9: 8 residues within 4Å: Chain B: S.397, N.398, G.459, D.460, L.461, T.462, G.491 Ligands: MG.6 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.397, B:S.397, B:G.459, B:L.461, B:T.462 Water bridges: B:T.462 FMT.12: 6 residues within 4Å: Chain B: N.137 Chain C: A.396, S.397, R.401, R.419, A.422 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:S.397, C:R.401, C:R.401, C:R.419, C:R.419, B:N.137 FMT.13: 2 residues within 4Å: Chain C: R.414, R.416 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.414, C:R.416, C:R.416 FMT.14: 5 residues within 4Å: Chain C: T.270, I.413, R.414, V.415, R.416 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.415, C:R.416

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: T.265, V.266, A.267, R.273, P.278, L.279, H.280 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.267, A:R.273, A:L.279, A:L.279 GOL.5: 9 residues within 4Å: Chain A: P.23, T.26, A.159, E.160, A.162, P.163, T.166, L.169, W.173 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.26, A:E.160, A:E.160, A:A.162 GOL.10: 6 residues within 4Å: Chain B: T.265, V.266, A.267, R.273, P.278, L.279 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.267, B:R.273, B:L.279, B:L.279 Water bridges: B:R.273, B:L.408

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.15: 24 residues within 4Å: Chain B: P.47, E.75, T.98, T.101, A.102 Chain C: 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: ISC.7, MG.11 23 PLIP interactions: 18 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:I.424, C:I.424, B:P.47, B:T.98 Hydrogen bonds: C:S.397, C:N.398, C:N.398, C:A.422, C:I.424, C:G.459, C:D.460, C:L.461, C:T.462, C:T.462, C:G.493, C:I.494 Water bridges: C:D.460, C:S.487, C:G.491, B:E.75, B:T.101, B:T.101 pi-Stacking: C:F.495 TPP.18: 25 residues within 4Å: Chain A: 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, H.465, D.489, G.491, G.492, G.493, I.494, F.495 Ligands: ISC.2, MG.17 22 PLIP interactions: 17 interactions with chain D, 5 interactions with chain A Hydrophobic interactions: D:I.424, D:F.495, A:P.47, A:T.98 Hydrogen bonds: D:S.397, D:N.398, D:N.398, D:A.422, D:I.424, D:G.459, D:D.460, D:D.460, D:L.461, D:T.462, D:D.489, D:G.493, D:I.494 Water bridges: D:D.489, A:E.75, A:A.102, A:Q.138 pi-Stacking: D:F.495

2 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.16: 9 residues within 4Å: Chain C: L.45, C.46, E.75, A.78, V.95, A.96, M.97, A.102, L.106 No protein-ligand interaction detected (PLIP) BME.19: 10 residues within 4Å: Chain D: L.45, C.46, E.75, A.78, V.95, A.96, M.97, T.98, A.102, L.106 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.98, D:T.98

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jirgis, E.N. et al., Structural Views along the Mycobacterium tuberculosis MenD Reaction Pathway Illuminate Key Aspects of Thiamin Diphosphate-Dependent Enzyme Mechanisms. Structure (2016)

Release Date

2016-06-22

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

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

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