SMTL ID : 7kh4.2 (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: 18 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 Ligands: EDO.6, PEG.11 13 PLIP interactions: 7 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:W.68, A:W.68 Hydrogen bonds: B:H.71, B:N.96, B:N.96, B:N.96, A:H.71, A:N.96, A:N.96, A:E.100, A:Y.122 Water bridges: B:Y.122, B:Y.122

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

MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.3: 2 residues within 4Å: Chain A: K.83, G.84 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Chain A: H.99 No protein-ligand interaction detected (PLIP) MG.17: 1 residues within 4Å: Chain B: E.76 No protein-ligand interaction detected (PLIP) MG.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

PG4.5: 4 residues within 4Å: Chain A: Q.129, D.162, T.163, K.166 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.129, A:K.166 Water bridges: A:Q.129, A:K.166 PG4.19: 6 residues within 4Å: Chain B: Q.128, Q.129, Y.132, D.162, T.163, K.166 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.166 Water bridges: B:Q.129

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

EDO.6: 7 residues within 4Å: Chain A: V.57, S.63, H.71, G.92, A.93, G.94 Ligands: 3VN.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.92, A:G.94 Water bridges: A:S.63, A:S.63, A:S.63, A:A.93 EDO.7: 4 residues within 4Å: Chain A: A.180, S.181, G.182, E.203 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.182 Water bridges: A:G.202 EDO.8: 5 residues within 4Å: Chain A: S.212, G.214, E.240, Y.242 Ligands: PGE.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.212, A:E.240, A:Y.242 EDO.9: 3 residues within 4Å: Chain A: K.44, I.47, E.48 No protein-ligand interaction detected (PLIP) EDO.10: 4 residues within 4Å: Chain A: K.125, P.126, T.127, Q.128 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.125, A:Q.128 Water bridges: A:Q.128 EDO.20: 3 residues within 4Å: Chain B: K.308, G.309, F.310 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.309, B:F.310 EDO.21: 7 residues within 4Å: Chain B: L.211, G.214, G.215, K.216, A.237, L.238, Y.242 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.215, B:K.216, B:L.238 EDO.22: 4 residues within 4Å: Chain B: A.180, S.181, G.182, E.203 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.182 EDO.23: 3 residues within 4Å: Chain B: Y.253, N.254, K.257 No protein-ligand interaction detected (PLIP) EDO.24: 3 residues within 4Å: Chain B: K.303, Y.305, K.306 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.306 Water bridges: B:I.307 EDO.25: 4 residues within 4Å: Chain B: K.15, F.168, R.169, R.196 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.15, B:K.15

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

PEG.11: 5 residues within 4Å: Chain A: W.68, E.100 Chain B: W.68, E.100 Ligands: 3VN.1 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.100 PEG.12: 7 residues within 4Å: Chain A: W.68, R.72, H.99, E.100, G.103, L.104, F.107 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.72 PEG.13: 6 residues within 4Å: Chain A: E.262, S.289, P.290, S.291, N.294 Chain B: Q.129 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:N.294 Water bridges: B:T.127, B:T.127, B:Q.129, B:Q.129 PEG.26: 5 residues within 4Å: Chain B: W.68, R.72, G.103, L.104, F.107 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.72 Water bridges: B:F.107

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

ACT.14: 4 residues within 4Å: Chain A: I.17, M.198, K.216 Ligands: PGE.16 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.216 ACT.15: 5 residues within 4Å: Chain A: P.152, G.153, G.156 Chain B: P.152, G.153 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.153

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

PGE.16: 10 residues within 4Å: Chain A: L.211, G.214, G.215, K.216, A.237, L.238, E.240, Y.242 Ligands: EDO.8, ACT.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.215, A:K.216

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.27: 3 residues within 4Å: Chain B: E.36, T.73, E.76 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.36, B:T.73, B:E.76

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
B

B
C

4-hydroxy-tetrahydrodipicolinate synthase

Related Entries With Identical Sequence