SMTL ID : 9pcs.2 (1 other biounit)

Crystal structure of Dihydrodipicolinate Synthase from Mycobacterium tuberculosis in complex with pyruvate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

10 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 3 residues within 4Å: Chain A: A.162, H.164, I.167 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.162, A:H.164, A:I.167, H2O.6, H2O.9 MG.5: 1 residues within 4Å: Chain A: T.61 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain B: A.162, H.164, I.167 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.164, B:I.167, H2O.19, H2O.21, H2O.21 MG.10: 2 residues within 4Å: Chain B: E.137, N.166 No protein-ligand interaction detected (PLIP) MG.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain C: A.162, H.164, I.167 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:H.164, C:I.167, H2O.29, H2O.33, H2O.33 MG.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.19: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.20: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.23: 3 residues within 4Å: Chain D: A.162, H.164, I.167 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:A.162, D:H.164, D:I.167, H2O.48, H2O.48

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

CL.2: 4 residues within 4Å: Chain A: P.155, K.174, S.179, I.183 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain B: P.155, K.174, S.179, I.183 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain B: G.232, D.233, I.234, A.235 Ligand excluded by PLIP

4 x PYR: PYRUVIC ACID(Covalent)

PYR.3: 8 residues within 4Å: Chain A: A.18, G.53, T.54, T.55, Y.143, K.171, I.211, V.213 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.18, A:K.171, A:V.213 Hydrogen bonds: A:T.54, A:T.54, A:T.55, A:Y.143 Water bridges: A:R.148 Salt bridges: A:K.171 PYR.9: 8 residues within 4Å: Chain B: A.18, G.53, T.54, T.55, Y.143, K.171, I.211, V.213 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:A.18, B:K.171, B:V.213 Hydrogen bonds: B:T.54, B:T.54, B:T.55, B:T.55, B:Y.143 Salt bridges: B:K.171 PYR.15: 8 residues within 4Å: Chain C: A.18, G.53, T.54, T.55, Y.143, K.171, I.211, V.213 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:A.18, C:K.171, C:V.213 Hydrogen bonds: C:T.54, C:T.55, C:T.55 Water bridges: C:Y.143 Salt bridges: C:K.171 PYR.25: 8 residues within 4Å: Chain D: A.18, G.53, T.54, T.55, Y.143, K.171, I.211, V.213 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:A.18, D:K.171, D:V.213 Hydrogen bonds: D:T.54, D:T.55 Water bridges: D:Y.143 Salt bridges: D:K.171

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

EDO.4: 3 residues within 4Å: Chain A: K.119 Chain B: I.145, G.147 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:G.147, B:R.148 Hydrogen bonds: A:K.119

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 3 residues within 4Å: Chain B: T.130, D.134, H.164 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.130 Water bridges: B:T.130, B:D.134 GOL.13: 7 residues within 4Å: Chain A: K.119, P.121 Chain B: M.251, S.252, R.253, L.254, G.255 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:S.118, A:Q.122, B:R.148 Hydrogen bonds: B:S.252 GOL.17: 7 residues within 4Å: Chain C: M.251, S.252, R.253, L.254, G.255 Chain D: K.119, P.121 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.252 Water bridges: C:R.148, D:S.118 GOL.21: 3 residues within 4Å: Chain C: V.42, D.43, R.80 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.42 Hydrogen bonds: C:D.43, C:D.43, C:R.80 GOL.22: 11 residues within 4Å: Chain C: S.52, G.53, T.54, S.58, G.86, A.87, G.88, L.111, V.112, V.113 Chain D: Y.117 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.58, C:A.87, C:G.88, C:L.111, C:V.113, D:Y.117 GOL.24: 3 residues within 4Å: Chain D: E.137, P.165, N.166 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.166, D:N.166

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.16: 4 residues within 4Å: Chain C: P.146, A.150, P.152, K.174 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rosa, L.V.S. et al., Crystal structure of dihydrodipicolinate synthase from Mycobacterium tuberculosis in complex with pyruvate and insights into allosteric regulation. Int.J.Biol.Macromol. (2025)

Release Date

2025-10-08

Peptides

4-hydroxy-tetrahydrodipicolinate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

4-hydroxy-tetrahydrodipicolinate synthase

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