SMTL ID : 7kh4.3 (2 other biounits)

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H56W mutant with pyruvate bound in the active site and R,R-bislysine bound at the allosteric site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

1 x 3VN: (2R,5R)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid(Non-covalent)

3VN.1: 16 residues within 4Å: Chain A: S.63, A.64, L.66, W.68, H.71, N.96, E.100, Y.122 Chain B: S.63, A.64, L.66, W.68, H.71, N.96, E.100, Y.122 12 PLIP interactions: 6 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:W.68 Hydrogen bonds: B:H.71, B:N.96, B:N.96, B:E.100, B:Y.122, A:S.63, A:H.71, A:N.96, A:N.96, A:N.96 Water bridges: A:Y.122

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

MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.15: 4 residues within 4Å: Chain B: R.154, F.260, S.263, N.264 No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Chain B: E.282, F.283 No protein-ligand interaction detected (PLIP) MG.17: 4 residues within 4Å: Chain B: L.211, G.214, G.215, K.216 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:G.215, H2O.15 MG.18: 3 residues within 4Å: Chain B: H.235, F.236, D.239 No protein-ligand interaction detected (PLIP) MG.19: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 7 residues within 4Å: Chain A: Q.128, Q.129, Y.132, D.162, T.163, K.166 Ligands: EDO.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.166 PG4.20: 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:K.166 Water bridges: B:Q.129, B:S.160

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

EDO.4: 5 residues within 4Å: Chain A: R.41, K.44, R.45, E.48, F.310 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.48, A:F.310 EDO.5: 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:T.161, A:N.183, A:N.183, A:D.189, A:D.189 EDO.6: 4 residues within 4Å: Chain A: L.274, E.299, M.302, K.303 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.299, A:K.303 EDO.7: 4 residues within 4Å: Chain A: D.162, I.165, K.166 Ligands: PG4.3 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.169 EDO.21: 3 residues within 4Å: Chain A: H.99 Chain B: T.67, R.284 No protein-ligand interaction detected (PLIP) EDO.22: 5 residues within 4Å: Chain B: K.15, F.168, R.169, D.170, E.172 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.15, B:K.15 EDO.23: 4 residues within 4Å: Chain B: H.99, E.100, G.103 Ligands: EDO.24 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.99 Water bridges: B:G.103 EDO.24: 6 residues within 4Å: Chain B: W.68, R.72, E.100, L.104, F.107 Ligands: EDO.23 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.72 EDO.25: 5 residues within 4Å: Chain B: K.136, 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.26: 3 residues within 4Å: Chain B: I.19, M.198, K.216 No protein-ligand interaction detected (PLIP)

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

PEG.8: 4 residues within 4Å: Chain A: Q.37, A.40, R.41, K.44 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.44 PEG.27: 5 residues within 4Å: Chain B: A.139, Q.140, V.142, D.143, N.173 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.173

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

ACT.9: 5 residues within 4Å: Chain A: I.17, I.18, K.88, D.114, P.145 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.114 Salt bridges: A:K.88 ACT.10: 3 residues within 4Å: Chain A: S.212, G.214, Y.242 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.212, A:Y.242 ACT.11: 5 residues within 4Å: Chain A: T.59, Y.149, R.154, K.178, N.264 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.149, A:N.264 Salt bridges: A:R.154 ACT.12: 1 residues within 4Å: Chain A: K.306 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.306, A:K.306 Salt bridges: A:K.306 ACT.28: 4 residues within 4Å: Chain B: P.152, G.156, C.157, E.158 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.152

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

PGE.13: 4 residues within 4Å: Chain A: P.152, G.153, G.156, S.181 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.181 Water bridges: A:K.125, A:K.125, A:G.153 PGE.14: 5 residues within 4Å: Chain A: R.169, H.193, E.194, P.195, R.196 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.169, A:R.196, A:R.196 PGE.29: 4 residues within 4Å: Chain B: K.303, K.304, Y.305, K.306 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.304, B:K.306

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Majdi Yazd, M. et al., Fluorescence-based Assay Development for Screening Novel Inhibitors of Dihydrodipicolinate Synthase from Campylobacter jejuni. To Be Published

Release Date

2021-10-27

Peptides

4-hydroxy-tetrahydrodipicolinate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

4-hydroxy-tetrahydrodipicolinate synthase

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