SMTL ID : 6o04.1

M.tb MenD IntII bound with Inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

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

DNA.1: 9 residues within 4Å: Chain A: N.114, Y.115, R.117, G.296, R.297, R.323, W.324, P.325 Chain B: G.135 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.115, A:R.297, A:R.297, A:R.323 Hydrogen bonds: A:Y.115, A:G.296, A:R.323 Water bridges: A:R.117, A:R.117 Salt bridges: A:R.117 pi-Cation interactions: A:R.297 DNA.7: 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 Hydrogen bonds: B:Y.115, B:R.323 Water bridges: B:R.117, B:R.297, B:G.321 Salt bridges: B:R.117 DNA.8: 8 residues within 4Å: Chain C: N.114, Y.115, R.117, H.252, R.297, R.323, W.324, P.325 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:Y.115, C:R.297, C:R.297, C:R.323 Hydrogen bonds: C:Y.115, C:G.296, C:R.323 Water bridges: C:R.117, C:R.117 Salt bridges: C:R.117 pi-Cation interactions: C:R.297 DNA.13: 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 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:R.323 Hydrogen bonds: D:Y.115, D:R.323 Water bridges: D:G.321, D:G.321, D:G.321, D:G.321 Salt bridges: D:R.117

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

ACT.2: 4 residues within 4Å: Chain A: E.130, L.158 Chain C: E.130, L.158 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.130, A:L.158, A:L.158 ACT.9: 2 residues within 4Å: Chain B: W.324 Chain C: R.179 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:R.179 Salt bridges: C:R.179

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

FMT.3: 6 residues within 4Å: Chain A: T.270, I.413, R.414, V.415, R.416 Ligands: FMT.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.415, A:R.416 FMT.4: 5 residues within 4Å: Chain A: P.272, R.273, T.410, I.413 Ligands: FMT.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.273

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 5 residues within 4Å: Chain B: D.460, D.489, G.491, G.493 Ligands: TOI.6 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 MG.12: 5 residues within 4Å: Chain D: D.460, D.489, G.491, G.493 Ligands: TOI.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.14

2 x TOI: (1~{R},2~{S},5~{S},6~{S})-2-[(1~{S})-1-[3-[(4-azanylidene-2-methyl-1~{H}-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl (phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-3-ium-2-yl]-1,4-bis(oxidanyl)-4-oxidanylidene-butyl]-6-oxidanyl-5-(3-oxid anyl-3-oxidanylidene-prop-1-en-2-yl)oxy-cyclohex-3-ene-1-carboxylic acid(Non-covalent)

TOI.6: 35 residues within 4Å: Chain A: P.47, G.48, S.49, R.50, E.75, T.98, T.101, A.102, R.127, N.137, Q.138 Chain B: R.302, 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, L.498 Ligands: MG.5 41 PLIP interactions: 24 interactions with chain B, 17 interactions with chain A Hydrophobic interactions: B:A.422, B:I.424, B:I.424, B:L.461, B:I.494, B:F.495, B:F.495, B:L.498, A:P.47, A:T.98 Hydrogen bonds: B:S.397, B:S.397, B:N.398, B:N.398, B:I.424, B:D.460, B:L.461, B:T.462, B:G.493, B:I.494, A:S.49, A:R.50, A:E.75, A:T.98, A:R.127, A:R.127, A:N.137, A:Q.138, A:Q.138, A:Q.138 Water bridges: B:R.302, B:T.462, A:S.49, A:S.49, A:R.50, A:A.102 Salt bridges: B:R.302, B:R.401, B:R.419, A:R.127 pi-Stacking: B:F.495 TOI.11: 35 residues within 4Å: Chain C: P.47, G.48, S.49, R.50, E.75, T.98, T.101, A.102, R.127, N.137, Q.138 Chain D: R.302, 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, L.498 Ligands: MG.12 42 PLIP interactions: 16 interactions with chain C, 26 interactions with chain D Hydrophobic interactions: C:P.47, C:T.98, D:I.424, D:I.424, D:D.425, D:I.494, D:F.495, D:F.495, D:L.498 Hydrogen bonds: C:S.49, C:R.50, C:E.75, C:R.127, C:R.127, C:N.137, C:Q.138, C:Q.138, C:Q.138, D:S.397, D:S.397, D:S.397, D:N.398, D:N.398, D:I.424, D:G.459, D:D.460, D:L.461, D:T.462, D:T.462, D:G.493, D:I.494 Water bridges: C:S.49, C:R.50, C:A.102, C:A.102, D:R.401, D:R.401, D:D.489 Salt bridges: C:R.127, D:R.302, D:R.401, D:R.419

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

CL.10: 4 residues within 4Å: Chain C: L.287, R.288, W.348, R.351 Ligand excluded by PLIP

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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