SMTL ID : 6u01.2 (1 other biounit)

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, N84D mutant with pyruvate bound in the active site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 7 residues within 4Å: Chain A: D.250, E.251, Y.253, N.254, Y.305 Chain D: H.193 Ligands: EDO.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.253, A:N.254 EDO.2: 5 residues within 4Å: Chain A: E.251, N.254, K.304, Y.305 Ligands: EDO.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.254, A:Y.305 EDO.8: 4 residues within 4Å: Chain B: Q.140, D.170, C.171, E.172 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.140, B:E.172 Water bridges: B:A.139 EDO.9: 7 residues within 4Å: Chain B: T.59, Y.149, R.154, K.178, G.202, F.260, N.264 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.154, B:G.202, B:N.264 EDO.10: 3 residues within 4Å: Chain B: S.291, E.293, N.294 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.291 Water bridges: B:N.294 EDO.11: 4 residues within 4Å: Chain B: K.15, R.169, C.171, E.172 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.15, B:D.170 EDO.13: 7 residues within 4Å: Chain B: H.193 Chain C: D.250, E.251, Y.253, N.254, Y.305 Ligands: EDO.14 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.253, C:N.254, C:Y.305 EDO.14: 5 residues within 4Å: Chain C: E.251, N.254, K.304, Y.305 Ligands: EDO.13 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.254 EDO.20: 4 residues within 4Å: Chain D: Q.140, D.170, C.171, E.172 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.140, D:E.172 Water bridges: D:A.139 EDO.21: 7 residues within 4Å: Chain D: T.59, Y.149, R.154, K.178, G.202, F.260, N.264 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.154, D:G.202, D:N.264 EDO.22: 3 residues within 4Å: Chain D: S.291, E.293, N.294 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.291 Water bridges: D:N.294 EDO.23: 4 residues within 4Å: Chain D: K.15, R.169, C.171, E.172 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.15, D:D.170

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

PGE.3: 6 residues within 4Å: Chain A: Q.128, Q.129, Y.132, D.162, T.163, K.166 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.166 PGE.15: 6 residues within 4Å: Chain C: Q.128, Q.129, Y.132, D.162, T.163, K.166 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.162, C:K.166

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: L.274, E.299, M.302, K.303 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.274, A:E.299, A:K.303, A:K.303 GOL.16: 4 residues within 4Å: Chain C: L.274, E.299, M.302, K.303 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:L.274, C:K.303, C:K.303

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

ACT.5: 7 residues within 4Å: Chain A: Y.149, V.151, R.154, K.178, G.202, F.260, N.264 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.264 Salt bridges: A:R.154 ACT.17: 7 residues within 4Å: Chain C: Y.149, V.151, R.154, K.178, G.202, F.260, N.264 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.264 Salt bridges: C:R.154

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

MG.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain B: D.170 No protein-ligand interaction detected (PLIP) MG.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.19: 1 residues within 4Å: Chain D: D.170 No protein-ligand interaction detected (PLIP)

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

PEG.12: 5 residues within 4Å: Chain B: Q.128, Q.129, Y.132, T.163, K.166 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.166 Water bridges: B:Y.132, B:S.160, B:S.160, B:D.170 PEG.24: 5 residues within 4Å: Chain D: Q.128, Q.129, Y.132, T.163, K.166 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.166 Water bridges: D:Y.132, D:S.160, D:S.160, D:D.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Majdi Yazdi, M. et al., Asparagine-84, a regulatory allosteric site residue, helps maintain the quaternary structure of Campylobacter jejuni dihydrodipicolinate synthase. J.Struct.Biol. (2020)

Release Date

2019-12-04

Peptides

4-hydroxy-tetrahydrodipicolinate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
E

D
F

4-hydroxy-tetrahydrodipicolinate synthase

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