SMTL ID : 5f1u.1

biomimetic design results in a potent allosteric inhibitor of dihydrodipicolinate synthase from Campylobacter jejuni

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-tetramer

Ligands

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

3VN.1: 17 residues within 4Å: Chain A: S.50, A.51, L.53, H.55, H.58, N.83, E.87, F.109 Chain B: S.50, A.51, L.53, H.55, H.58, N.83, E.87, F.109 Ligands: EDO.10 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.50, A:H.58, A:N.83, A:N.83, A:E.87, B:H.58, B:N.83, B:N.83 Water bridges: A:E.87 3VN.13: 16 residues within 4Å: Chain C: S.50, A.51, L.53, H.55, H.58, N.83, E.87, F.109 Chain D: S.50, A.51, L.53, H.55, H.58, N.83, E.87, F.109 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:H.58, C:N.83, C:N.83, D:H.58, D:N.83, D:N.83, D:E.87 Water bridges: D:S.82

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

PG4.2: 6 residues within 4Å: Chain A: Q.115, Q.116, Y.119, D.149, T.150, K.153 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.153 Water bridges: A:S.147

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

EDO.3: 3 residues within 4Å: Chain A: A.262, G.263, G.296 No protein-ligand interaction detected (PLIP) EDO.4: 2 residues within 4Å: Chain A: G.143, C.144 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.145 EDO.5: 3 residues within 4Å: Chain A: T.68, K.70, T.72 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.70 EDO.8: 3 residues within 4Å: Chain B: G.263, L.264, E.266 1 PLIP interactions: 1 interactions with chain B Water bridges: B:L.264 EDO.9: 3 residues within 4Å: Chain B: K.31, E.35, T.68 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.35, B:E.35, B:T.68 EDO.10: 7 residues within 4Å: Chain A: A.51, T.52, L.53, T.54 Chain B: H.86, E.87 Ligands: 3VN.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.51 Water bridges: A:H.55 EDO.11: 6 residues within 4Å: Chain C: C.69, K.70, G.71, T.72, V.74, D.101 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:C.69, C:G.71, C:T.72, C:D.101 Water bridges: C:V.76 EDO.12: 2 residues within 4Å: Chain C: Y.260, L.261 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.261 EDO.14: 3 residues within 4Å: Chain D: Y.260, L.261, G.263 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.260, D:L.261 EDO.15: 5 residues within 4Å: Chain D: Q.115, Q.116, D.149, T.150, K.153 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.116

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 5 residues within 4Å: Chain B: A.11, G.45, T.46, T.47, K.165 Ligand excluded by PLIP

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

PGE.7: 6 residues within 4Å: Chain B: Q.115, Q.116, Y.119, D.149, T.150, K.153 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.153

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Skovpen, Y.V. et al., Biomimetic Design Results in a Potent Allosteric Inhibitor of Dihydrodipicolinate Synthase from Campylobacter jejuni. J.Am.Chem.Soc. (2016)

Release Date

2016-02-17

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