SMTL ID : 7kel.2 (5 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

PGE.1: 6 residues within 4Å: Chain A: Q.128, Q.129, Y.132, D.162, T.163, K.166 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.166 Water bridges: A:Q.129 PGE.2: 5 residues within 4Å: Chain A: T.161, N.183, D.185, K.186, D.189 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.183, A:D.189 Water bridges: A:T.161, A:N.183, A:D.185 PGE.17: 6 residues within 4Å: Chain B: Q.128, Q.129, Y.132, D.162, T.163, K.166 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.162, B:K.166 Water bridges: B:K.166, B:D.170

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

ACT.3: 7 residues within 4Å: Chain A: T.59, Y.149, R.154, K.178, G.202, F.260, N.264 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.59, A:N.264 Hydrogen bonds: A:Y.149 Water bridges: A:R.154 Salt bridges: A:R.154 ACT.18: 4 residues within 4Å: Chain B: H.68, K.71, E.100, L.104 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.71 Salt bridges: B:H.68, B:K.71

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 1 residues within 4Å: Chain A: D.239 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.239, H2O.1, H2O.2 MG.5: 1 residues within 4Å: Chain A: D.189 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.189

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

EDO.6: 9 residues within 4Å: Chain A: G.58, T.59, S.63, A.93, G.94, L.117, S.118, V.119 Chain B: Y.123 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.63, A:S.63, A:A.93, A:G.94, A:L.117, A:V.119 EDO.7: 5 residues within 4Å: Chain A: D.250, E.251, Y.253, N.254, Y.305 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.253, A:N.254 EDO.8: 8 residues within 4Å: Chain A: T.59, E.62, S.63, A.64, P.265, L.287 Chain B: Y.123, N.124 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.62, A:S.63, A:S.63, A:A.64 EDO.9: 3 residues within 4Å: Chain A: G.112, D.114 Ligands: EDO.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.112, A:D.114 EDO.10: 8 residues within 4Å: Chain A: L.211, G.214, G.215, K.216, A.237, L.238, E.240, Y.242 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.214, A:G.215, A:K.216 EDO.11: 10 residues within 4Å: Chain A: E.179, A.180, S.181, G.182, N.183, I.184, C.187, E.203, I.206, I.210 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.179, A:S.181, A:G.182, A:N.183, A:N.183, A:E.203 EDO.12: 6 residues within 4Å: Chain A: L.25, I.26, L.42, Q.46, N.224, M.272 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.26, A:I.26, A:Q.46, A:N.224 EDO.13: 3 residues within 4Å: Chain A: Y.132, E.133, K.136 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.136 EDO.14: 3 residues within 4Å: Chain A: P.152, G.156, C.157 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.156 EDO.15: 8 residues within 4Å: Chain A: V.79, C.82, K.83, V.89, G.112, A.113, D.114 Ligands: EDO.9 2 PLIP interactions: 2 interactions with chain A Water bridges: A:C.82, A:V.87 EDO.16: 4 residues within 4Å: Chain A: E.76, V.79, E.80, H.111 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.76 EDO.19: 10 residues within 4Å: Chain A: Y.123 Chain B: G.58, T.59, S.63, G.92, A.93, G.94, L.117, S.118, V.119 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.63, B:A.93, B:G.94, B:V.119, A:Y.123, A:Y.123 EDO.20: 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.21: 4 residues within 4Å: Chain B: P.152, G.156, C.157, E.158 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.152 Water bridges: B:E.158

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

PEG.22: 4 residues within 4Å: Chain B: K.44, I.47, E.48, T.81 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.44, B:E.48

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

2021-10-13

Peptides

4-hydroxy-tetrahydrodipicolinate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
F

4-hydroxy-tetrahydrodipicolinate synthase

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