SMTL ID : 6o0g.1

M.tb MenD bound to Intermediate I and Inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

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

DNA.1: 8 residues within 4Å: Chain A: Y.115, R.117, G.296, R.297, T.319, R.323, W.324, P.325 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:R.297, A:R.323 Hydrogen bonds: A:Y.115, A:R.323 Water bridges: A:R.117, A:R.117, A:T.320, A:T.320 Salt bridges: A:R.117 DNA.11: 11 residues within 4Å: Chain A: G.133, T.134, G.135 Chain B: Y.115, R.117, G.296, R.297, T.319, R.323, W.324, P.325 10 PLIP interactions: 10 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:R.297, B:T.319, B:G.321, B:R.323 Salt bridges: B:R.117 DNA.15: 11 residues within 4Å: Chain C: N.114, Y.115, R.117, G.296, R.297, R.323, W.324, P.325 Chain D: T.134, G.135 Ligands: PGE.20 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:Y.115, C:R.323 Hydrogen bonds: C:Y.115, C:R.323 Water bridges: C:R.117, C:R.117, C:R.297, C:T.319, C:R.323 Salt bridges: C:R.117 pi-Cation interactions: C:R.297 DNA.24: 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 Hydrogen bonds: D:Y.115 Water bridges: D:R.117, D:R.117, D:T.319, D:G.321 Salt bridges: D:R.117

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

ACT.2: 6 residues within 4Å: Chain A: P.23, E.160, A.162, P.163, T.166, L.169 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.23 Hydrogen bonds: A:A.162 ACT.3: 4 residues within 4Å: Chain A: E.130, L.158 Chain C: E.130, L.158 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Water bridges: A:E.130, A:E.130, A:L.158, A:L.158 Hydrogen bonds: C:E.130 ACT.4: 5 residues within 4Å: Chain A: T.265, V.266, A.267, P.278, L.279 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.267 Salt bridges: A:R.273 ACT.5: 5 residues within 4Å: Chain A: R.50, P.128, L.131, R.202, E.203 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.128, A:L.131, A:R.202 Hydrogen bonds: A:E.203 Salt bridges: A:R.50, A:R.127

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

FMT.6: 7 residues within 4Å: Chain A: G.48, S.49, R.50, T.98, Q.138 Ligands: AKG.8, TOG.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.49, A:R.50, A:T.98, A:Q.138 FMT.7: 4 residues within 4Å: Chain A: Y.129, L.143 Chain C: Y.129, L.143 No protein-ligand interaction detected (PLIP) FMT.12: 8 residues within 4Å: Chain B: C.46, E.75, V.95, A.96, M.97, T.98, A.102, L.106 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.98, B:T.98 FMT.13: 4 residues within 4Å: Chain B: T.270, I.413, V.415, R.416 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.415, B:R.416 FMT.16: 7 residues within 4Å: Chain C: G.48, S.49, R.50, T.98, R.127, Q.138 Ligands: TOG.22 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.49, C:R.50, C:R.127, C:Q.138 FMT.17: 3 residues within 4Å: Chain C: T.299, R.419, G.420 No protein-ligand interaction detected (PLIP) FMT.18: 5 residues within 4Å: Chain A: Y.129, L.132 Chain C: S.153, I.154, S.155 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.155 FMT.19: 4 residues within 4Å: Chain C: R.50, P.128, L.131, E.203 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.50, C:E.203, C:E.203

1 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.8: 8 residues within 4Å: Chain A: S.49, R.50, S.99, R.127, N.137 Chain B: L.498 Ligands: FMT.6, TOG.9 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.99, A:S.99, A:R.127, A:N.137 Water bridges: A:E.203 Salt bridges: A:R.50, A:R.127, B:R.401

2 x TOG: 4-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-3 -ium-2-yl]-4-oxidanyl-butanoic acid(Non-covalent)

TOG.9: 32 residues within 4Å: Chain A: P.47, G.48, E.75, T.98, T.101, A.102, N.137, Q.138 Chain B: A.396, S.397, N.398, P.399, R.401, R.419, 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: FMT.6, AKG.8, MG.10 24 PLIP interactions: 4 interactions with chain A, 20 interactions with chain B Hydrophobic interactions: A:P.47, A:T.98, B:I.424, B:I.424, B:L.461, B:F.495 Hydrogen bonds: A:N.137, B:S.397, B:S.397, B:N.398, B:N.398, B:A.422, B:I.424, B:G.459, B:D.460, B:L.461, B:T.462, B:G.493, B:I.494 Water bridges: A:A.102, B:T.462 Salt bridges: B:R.401, B:R.419 pi-Stacking: B:F.495 TOG.22: 31 residues within 4Å: Chain C: P.47, G.48, E.75, T.98, T.101, A.102, N.137, Q.138 Chain D: A.396, S.397, N.398, P.399, R.401, R.419, 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: FMT.16, MG.23 26 PLIP interactions: 5 interactions with chain C, 21 interactions with chain D Hydrophobic interactions: C:P.47, C:T.98, D:I.424, D:I.424, D:L.461 Hydrogen bonds: C:N.137, D:S.397, D:S.397, D:N.398, D:A.422, D:I.424, D:D.460, D:D.460, D:L.461, D:T.462, D:T.462, D:G.493, D:I.494 Water bridges: C:A.102, C:A.102, D:N.398, D:N.398, D:D.460 Salt bridges: D:R.401, D:R.419 pi-Stacking: D:F.495

2 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 5 residues within 4Å: Chain B: D.460, D.489, G.491, G.493 Ligands: TOG.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.5 MG.23: 4 residues within 4Å: Chain D: D.460, D.489, G.491 Ligands: TOG.22 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

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

CL.14: 1 residues within 4Å: Chain B: R.288 Ligand excluded by PLIP

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.20: 7 residues within 4Å: Chain B: R.179 Chain C: N.114, Y.115, T.148, R.323, W.324 Ligands: DNA.15 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:R.179, C:N.114, C:Y.115, C:T.148, C:W.324 Water bridges: C:R.323

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.21: 6 residues within 4Å: Chain A: G.133 Chain B: R.323, W.324 Chain C: R.179, A.182, A.183 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:W.324, C:R.179, C:R.179, C:A.183

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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