SMTL ID : 7kel.1 (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

1 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.166

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

ACT.2: 2 residues within 4Å: Chain A: G.112, D.114 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.114 ACT.3: 7 residues within 4Å: Chain A: L.211, G.214, G.215, K.216, A.237, L.238, Y.242 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.242 Water bridges: A:Y.242, A:Y.242 Salt bridges: A:K.216 ACT.11: 3 residues within 4Å: Chain B: S.212, G.214, Y.242 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.212 ACT.12: 3 residues within 4Å: Chain B: P.195, G.214, K.216 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.195 Salt bridges: B:K.216 ACT.13: 5 residues within 4Å: Chain B: D.250, E.251, Y.253, N.254, K.304 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.253, B:N.254, B:Y.305 Salt bridges: B:K.304

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 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.1

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

EDO.5: 6 residues within 4Å: Chain A: R.154, F.260, S.263, N.264 Chain B: K.125 Ligands: EDO.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.154, A:E.262, A:N.264 EDO.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.7: 3 residues within 4Å: Chain A: T.127, Q.128 Chain B: E.262 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.262, A:Q.128 Water bridges: B:S.263, B:S.291, A:Q.129 EDO.8: 5 residues within 4Å: Chain A: F.168, C.171, E.172, I.174, Y.175 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.168 EDO.9: 10 residues within 4Å: Chain A: T.59, Y.149, V.151, R.154, K.178, A.180, G.202, F.260, N.264 Ligands: EDO.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.154, A:G.202, A:N.264 EDO.10: 2 residues within 4Å: Chain A: P.290, F.295 No protein-ligand interaction detected (PLIP) EDO.14: 5 residues within 4Å: Chain B: Q.128, Q.129, Y.132, T.163, K.166 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.129 Water bridges: B:S.160, B:S.160, B:K.166 EDO.15: 10 residues within 4Å: Chain B: E.179, A.180, S.181, G.182, N.183, I.184, C.187, E.203, I.206, I.210 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.179, B:S.181, B:G.182, B:N.183, B:N.183 EDO.16: 9 residues within 4Å: Chain A: Y.123 Chain B: G.58, T.59, S.63, A.93, G.94, L.117, S.118, V.119 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.59, B:T.59, B:S.63, B:A.93, B:G.94, B:V.119 EDO.17: 6 residues within 4Å: Chain B: T.59, Y.149, R.154, K.178, F.260, N.264 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.154, B:N.264 EDO.18: 3 residues within 4Å: Chain B: T.161, D.162, D.189 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.189 Water bridges: B:D.162 EDO.19: 3 residues within 4Å: Chain B: G.112, A.113, D.114 No protein-ligand interaction detected (PLIP) EDO.20: 5 residues within 4Å: Chain B: K.109, Q.140, S.141, V.142, D.143 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.140, B:D.143

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
A

B
B

4-hydroxy-tetrahydrodipicolinate synthase

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