SMTL ID : 6tzu.1 (1 other biounit)

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, N84A mutant with pyruvate bound in the active site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 1 residues within 4Å: Chain A: D.239 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.239, H2O.5 MG.2: 4 residues within 4Å: Chain A: S.212, Y.242 Chain B: Y.208, K.246 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Chain B: D.239 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.239, H2O.13, H2O.14 MG.27: 1 residues within 4Å: Chain D: D.52 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.52, H2O.26, H2O.31, H2O.31

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

EDO.3: 8 residues within 4Å: Chain A: L.211, G.214, G.215, K.216, A.237, L.238, E.240, Y.242 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.215, A:K.216 EDO.4: 6 residues within 4Å: Chain A: D.250, E.251, Y.253, N.254, Y.305 Chain B: H.193 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.253, A:N.254, A:Y.305 EDO.5: 5 residues within 4Å: Chain A: T.59, V.151, R.154, F.260, N.264 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.154, A:N.264 EDO.6: 7 residues within 4Å: Chain A: A.24, G.58, T.59, T.60, L.117, Y.149, K.178 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.59, A:T.59, A:T.60, A:T.60, A:T.60, A:K.178 EDO.10: 7 residues within 4Å: Chain B: A.24, G.58, T.59, T.60, L.117, Y.149, K.178 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.59, B:T.59, B:T.60, B:K.178 EDO.11: 4 residues within 4Å: Chain B: I.17, I.19, M.198, K.216 No protein-ligand interaction detected (PLIP) EDO.12: 4 residues within 4Å: Chain B: Q.129, Y.132, E.133, K.136 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.129, B:K.136, B:K.136 EDO.13: 3 residues within 4Å: Chain B: D.162, I.165, K.166 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.169 EDO.14: 9 residues within 4Å: Chain A: Y.208, Y.242, K.243, K.246 Chain B: L.211, S.212, G.214, Y.242 Ligands: EDO.15 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.211, A:Y.242 EDO.15: 8 residues within 4Å: Chain B: L.211, G.214, G.215, K.216, A.237, L.238, Y.242 Ligands: EDO.14 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.214, B:G.215, B:K.216 EDO.28: 5 residues within 4Å: Chain D: I.19, G.20, D.52, L.238 Ligands: ACT.32 No protein-ligand interaction detected (PLIP) EDO.29: 4 residues within 4Å: Chain D: L.274, A.275, M.302, I.307 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.274 Water bridges: D:M.302 EDO.30: 6 residues within 4Å: Chain D: Y.149, R.154, K.178, G.202, F.260, N.264 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.154, D:R.154, D:G.202, D:N.264

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

ACT.7: 4 residues within 4Å: Chain A: K.303, K.304, Y.305, K.306 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.303 Salt bridges: A:K.306 ACT.16: 2 residues within 4Å: Chain B: R.169, R.196 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.169, B:R.196 Salt bridges: B:R.196 ACT.17: 5 residues within 4Å: Chain B: V.34, E.36, E.69, E.70, T.73 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.34, B:E.70, B:T.73 Hydrogen bonds: B:E.36, B:E.69, B:T.73 ACT.20: 3 residues within 4Å: Chain C: K.15, F.168, R.196 3 PLIP interactions: 3 interactions with chain C Water bridges: C:K.15 Salt bridges: C:K.15, C:R.196 ACT.21: 3 residues within 4Å: Chain B: T.67, R.284 Chain C: H.99 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:T.67 Water bridges: B:R.284 Salt bridges: B:R.284, C:H.99 ACT.22: 6 residues within 4Å: Chain C: Y.149, V.151, R.154, F.260, N.264 Ligands: PEG.26 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.151 Hydrogen bonds: C:N.264 Salt bridges: C:R.154 ACT.23: 6 residues within 4Å: Chain C: S.212, G.214, Y.242 Chain D: Y.208, K.243, K.246 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:K.246 Hydrogen bonds: D:Y.208 ACT.24: 2 residues within 4Å: Chain B: H.99 Chain C: R.284 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Salt bridges: C:R.284, B:H.99 ACT.31: 3 residues within 4Å: Chain A: H.99 Chain D: T.67, R.284 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Salt bridges: A:H.99, D:R.284 Water bridges: D:R.284 ACT.32: 5 residues within 4Å: Chain D: I.17, I.18, I.19, K.88 Ligands: EDO.28 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:I.19 Water bridges: D:D.52 Salt bridges: D:K.88 ACT.33: 2 residues within 4Å: Chain D: I.17, I.19 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.19 ACT.34: 3 residues within 4Å: Chain D: K.44, I.47, E.48 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:E.48 Salt bridges: D:K.44

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

PGE.8: 5 residues within 4Å: Chain A: Q.129, Y.132, D.162, T.163, K.166 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.162, A:D.162, A:K.166 Water bridges: A:Q.129 PGE.19: 6 residues within 4Å: Chain B: Q.128, Q.129, Y.132, D.162, T.163, K.166 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.166 Water bridges: B:Q.129, B:Y.132 PGE.35: 6 residues within 4Å: Chain D: Q.128, Q.129, Y.132, D.162, T.163, K.166 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.129, D:K.166 Water bridges: D:Q.129

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

PEG.18: 3 residues within 4Å: Chain B: I.47, E.48, G.50 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.50 PEG.25: 5 residues within 4Å: Chain C: Q.128, Q.129, Y.132, T.163, K.166 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.166 Water bridges: C:K.166 PEG.26: 11 residues within 4Å: Chain C: A.24, G.58, T.59, T.60, L.117, Y.149, K.178, G.202, I.219, V.221 Ligands: ACT.22 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:Y.123, C:T.59, C:T.60, C:T.60, C:K.178, C:G.202

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
A

B
B

C
C

D
F

4-hydroxy-tetrahydrodipicolinate synthase

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