SMTL ID : 7lbd.1 (1 other biounit)

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H59K mutant with pyruvate bound in the active site in C2221 space group

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-tetramer

Ligands

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

MG.1: 1 residues within 4Å: Chain A: D.239 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.239 MG.2: 1 residues within 4Å: Chain A: K.88 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain B: D.162, D.189 No protein-ligand interaction detected (PLIP) MG.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.18: 2 residues within 4Å: Chain C: D.189, H.193 No protein-ligand interaction detected (PLIP)

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

EDO.3: 9 residues within 4Å: Chain A: G.58, T.59, S.63, A.93, G.94, L.117, S.118, V.119 Chain D: Y.123 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:S.63, A:S.63, A:A.93, A:G.94, A:L.117, A:V.119, D:Y.123 EDO.4: 7 residues within 4Å: Chain A: L.211, G.214, G.215, K.216, A.237, L.238, Y.242 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.215, A:K.216 Water bridges: A:K.216 EDO.5: 7 residues within 4Å: Chain A: D.250, E.251, Y.253, N.254, Y.305 Chain B: A.192, H.193 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.253, A:N.254, A:N.254 Water bridges: A:N.254 EDO.6: 4 residues within 4Å: Chain A: H.68, H.99, E.100, G.103 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.68 EDO.13: 8 residues within 4Å: Chain A: A.192, H.193 Chain B: D.250, E.251, Y.253, N.254, K.304, Y.305 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.253, B:N.254, B:K.304, B:Y.305, B:Y.305 Water bridges: B:N.254 EDO.14: 3 residues within 4Å: Chain B: P.152, G.156, C.157 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.152 EDO.15: 7 residues within 4Å: Chain B: L.211, G.214, G.215, K.216, A.237, L.238, Y.242 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.215, B:K.216 EDO.19: 6 residues within 4Å: Chain C: I.17, I.18, I.19, D.52, A.53, K.88 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.19, C:D.52 EDO.20: 7 residues within 4Å: Chain C: D.250, E.251, Y.253, N.254, Y.305 Chain D: A.192, H.193 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.253, C:N.254, C:N.254 EDO.21: 2 residues within 4Å: Chain C: K.83, G.112 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.83, C:K.83 EDO.28: 2 residues within 4Å: Chain D: P.152, G.156 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:P.152

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

PGE.7: 5 residues within 4Å: Chain A: Q.129, Y.132, D.162, T.163, K.166 No protein-ligand interaction detected (PLIP) PGE.16: 5 residues within 4Å: Chain B: Q.129, Y.132, D.162, T.163, K.166 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.163, B:K.166 Water bridges: B:S.160 PGE.22: 5 residues within 4Å: Chain C: Q.129, Y.132, D.162, T.163, K.166 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.162, C:K.166 Water bridges: C:S.160 PGE.29: 2 residues within 4Å: Chain D: H.235, F.236 2 PLIP interactions: 2 interactions with chain D Water bridges: D:H.235, D:H.235 PGE.30: 5 residues within 4Å: Chain D: Q.129, Y.132, D.162, T.163, K.166 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.166 Water bridges: D:S.160

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

ACT.8: 6 residues within 4Å: Chain A: Y.149, V.151, R.154, K.178, G.202, N.264 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.264 Salt bridges: A:R.154 ACT.23: 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 ACT.24: 3 residues within 4Å: Chain C: K.15, F.168, R.196 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:K.15, C:R.196 ACT.25: 7 residues within 4Å: Chain C: L.211, G.214, G.215, K.216, A.237, L.238, Y.242 3 PLIP interactions: 3 interactions with chain C Water bridges: C:K.216, C:K.216 Salt bridges: C:K.216 ACT.31: 6 residues within 4Å: Chain C: Y.208, K.243, K.246 Chain D: S.212, G.214, Y.242 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Salt bridges: C:K.246 Hydrogen bonds: D:Y.242, D:Y.242 Water bridges: D:K.216 ACT.32: 6 residues within 4Å: Chain A: K.125 Chain D: R.154, F.260, E.262, S.263, N.264 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:K.125 Hydrogen bonds: D:N.264 Water bridges: D:S.263 Salt bridges: D:R.154

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

PEG.9: 6 residues within 4Å: Chain A: R.169, A.192, H.193, E.194, P.195, R.196 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.196, A:R.196 PEG.10: 6 residues within 4Å: Chain A: A.97, T.98, H.99 Chain D: F.283, R.284, L.285 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:L.285, D:L.285, A:H.99 Water bridges: D:F.283 PEG.17: 3 residues within 4Å: Chain B: I.19, M.198, K.216 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.216 PEG.26: 5 residues within 4Å: Chain B: T.127, Q.128 Chain C: E.262, S.291, N.294 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:S.291, C:S.291, C:N.294, B:Q.128 Water bridges: B:Q.129 PEG.27: 11 residues within 4Å: Chain B: Y.123 Chain C: V.57, G.58, T.59, S.63, G.92, A.93, G.94, L.117, S.118, V.119 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:V.119 Hydrogen bonds: C:S.63, B:Y.123, B:Y.123 PEG.33: 4 residues within 4Å: Chain D: I.17, I.19, M.198, K.216 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yazdi, M.M. et al., Reversing the roles of a crucial hydrogen-bonding pair: a lysine-insensitive mutant of Campylobacter jejuni dihydrodipicolinate synthase, H59K, binds histidine in its allosteric site. To Be Published

Release Date

2022-01-12

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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