SMTL ID : 9pcs.1 (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

4 x PYR: PYRUVIC ACID(Covalent)

PYR.1: 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:T.55, A:Y.143 Salt bridges: A:K.171 PYR.8: 9 residues within 4Å: Chain B: A.18, G.53, T.54, T.55, L.111, 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.17: 8 residues within 4Å: Chain C: A.18, G.53, T.54, T.55, Y.143, K.171, I.211, V.213 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:A.18, C:K.171, C:V.213 Hydrogen bonds: C:T.54, C:T.55 Salt bridges: C:K.171 PYR.23: 9 residues within 4Å: Chain D: A.18, G.53, T.54, T.55, L.111, Y.143, K.171, I.211, V.213 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:A.18, D:K.171, D:V.213 Hydrogen bonds: D:T.54, D:T.55, D:T.55 Water bridges: D:Y.143 Salt bridges: D:K.171

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: E.137, P.165, N.166 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.166, A:N.166 Water bridges: A:D.134, A:E.137, A:E.137, A:N.166 GOL.4: 11 residues within 4Å: Chain A: S.52, G.53, T.54, S.58, G.86, A.87, G.88, L.111, V.112, V.113 Chain B: Y.117 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.58, A:S.58, A:A.87, A:G.88, A:L.111, A:V.113, B:Y.117, B:Y.117 GOL.5: 5 residues within 4Å: Chain A: Q.126, T.130, A.160, S.163, H.164 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.126 GOL.13: 3 residues within 4Å: Chain B: D.176, H.178 Chain C: A.197 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.176, B:S.179 Water bridges: B:H.178 GOL.14: 11 residues within 4Å: Chain A: Y.117 Chain B: S.52, G.53, T.54, S.58, G.86, A.87, G.88, L.111, V.112, V.113 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:Y.117, A:Y.117, B:S.58, B:A.87, B:G.88, B:L.111, B:V.113 GOL.20: 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 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.58, C:S.58, C:A.87, C:G.88, C:L.111, C:V.113, D:Y.117 GOL.21: 7 residues within 4Å: Chain C: K.119, P.121 Chain D: S.252, R.253, L.254, G.255 Ligands: EDO.16 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.119 Water bridges: C:Q.122

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

MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.7: 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.23, H2O.23 MG.11: 1 residues within 4Å: Chain B: N.166 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain B: T.61 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain C: A.162, H.164, I.167 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:A.162, C:H.164, C:I.167, H2O.33, H2O.36 MG.18: 1 residues within 4Å: Chain C: T.61 No protein-ligand interaction detected (PLIP) MG.19: 2 residues within 4Å: Chain C: E.137, N.166 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:E.137, H2O.28, H2O.28, H2O.29, H2O.31, H2O.36 MG.22: 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.51, H2O.51 MG.25: 1 residues within 4Å: Chain D: T.61 No protein-ligand interaction detected (PLIP)

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

EDO.6: 3 residues within 4Å: Chain A: I.145, G.147 Chain B: K.119 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:G.147, A:R.148 Hydrogen bonds: B:K.119 EDO.9: 5 residues within 4Å: Chain A: L.254, G.255 Chain B: K.119, P.121 Ligands: EDO.10 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:S.118, B:K.119, A:R.148 EDO.10: 6 residues within 4Å: Chain B: K.119, P.120, P.121, Q.122, V.151 Ligands: EDO.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.119, B:Q.122 Water bridges: B:Q.122 EDO.16: 6 residues within 4Å: Chain C: P.120, P.121, Q.122, V.151, E.154 Ligands: GOL.21 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.119, C:Q.122, C:E.154, C:E.154 EDO.24: 5 residues within 4Å: Chain A: R.238, I.242 Chain D: A.181, A.185, M.205 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:M.205

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
A

B
B

C
C

D
D

4-hydroxy-tetrahydrodipicolinate synthase

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