SMTL ID : 5esd.1

Crystal Structure of M. tuberculosis MenD bound to ThDP and Mn2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-tetramer

Ligands

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 5 residues within 4Å: Chain A: D.460, D.489, G.491, G.493 Ligands: TPP.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.460, A:D.489, A:G.491, H2O.2 MN.4: 4 residues within 4Å: Chain B: D.460, D.489, G.491 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.6 MN.6: 6 residues within 4Å: Chain C: D.460, D.489, G.491, G.492, G.493 Ligands: TPP.5 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.460, C:D.489, C:G.491, H2O.11 MN.8: 5 residues within 4Å: Chain D: D.460, D.489, G.491, G.493 Ligands: TPP.7 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.460, D:D.489, D:G.491, H2O.14

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.2: 17 residues within 4Å: Chain A: S.397, N.398, P.399, I.424, G.459, D.460, L.461, T.462, D.489, G.491, G.492, G.493, I.494, F.513 Chain D: G.48, S.49 Ligands: MN.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.461, A:F.513 Hydrogen bonds: A:S.397, A:N.398, A:D.460, A:L.461, A:T.462, A:T.462, A:G.493, A:I.494 Water bridges: A:N.398, A:N.398, A:G.459, A:D.489, A:D.489 TPP.3: 16 residues within 4Å: Chain B: S.397, N.398, P.399, I.424, G.459, D.460, L.461, T.462, D.489, G.491, G.492, G.493, F.513 Chain C: P.47, G.48 Ligands: MN.4 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.424, B:L.461, B:F.513 Hydrogen bonds: B:S.397, B:S.397, B:N.398, B:D.460, B:L.461, B:T.462, B:G.493 Water bridges: B:N.398, B:N.398 TPP.5: 25 residues within 4Å: Chain B: P.47, E.75, T.98, T.101, A.102, Q.138 Chain C: 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: MN.6 22 PLIP interactions: 19 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:I.424, C:I.424, C:L.461, C:F.495, C:F.495, 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.489, B:A.102 pi-Stacking: C:F.495 TPP.7: 25 residues within 4Å: Chain A: P.47, 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, H.465, D.489, G.491, G.492, G.493, I.494, F.495 Ligands: MN.8 20 PLIP interactions: 18 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:L.461, D:F.495, A:P.47 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:G.493, D:I.494 Water bridges: D:D.402, D:T.462, D:D.489, A:A.102 pi-Stacking: D:F.495

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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