SMTL ID : 5f1v.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

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

3VN.1: 10 residues within 4Å: Chain A: V.66, C.69, K.70, G.71, T.72, K.73, V.74, K.75, G.99, D.101 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.71, A:T.72, A:T.72, A:G.99, A:D.101 Water bridges: A:V.76 Salt bridges: A:K.70, A:K.75 3VN.4: 17 residues within 4Å: Chain A: S.50, A.51, L.53, H.55, H.58, N.83, E.87, Y.109 Chain C: S.50, A.51, L.53, T.54, H.55, H.58, N.83, E.87, Y.109 13 PLIP interactions: 8 interactions with chain C, 5 interactions with chain A Hydrogen bonds: C:H.58, C:N.83, C:N.83, C:N.83, C:Y.109, A:H.58, A:N.83, A:E.87 Water bridges: C:E.87, C:Y.109, C:Y.109, A:S.50, A:Y.109 3VN.9: 18 residues within 4Å: Chain B: S.50, A.51, L.53, T.54, H.55, H.58, N.83, E.87, Y.109 Chain D: S.50, A.51, L.53, T.54, H.55, H.58, N.83, E.87, Y.109 12 PLIP interactions: 8 interactions with chain D, 4 interactions with chain B Hydrogen bonds: D:H.58, D:N.83, D:N.83, D:N.83, B:H.58, B:N.83, B:E.87, B:Y.109 Water bridges: D:E.87, D:E.87, D:Y.109, D:Y.109 3VN.17: 11 residues within 4Å: Chain D: V.66, C.69, K.70, T.72, K.73, V.74, K.75, G.99, A.100, D.101, I.131 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.72, D:V.74, D:G.99 Salt bridges: D:K.70, D:K.75

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

PGE.2: 6 residues within 4Å: Chain A: Q.115, Q.116, Y.119, D.149, T.150, K.153 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.116, A:D.149, A:K.153 PGE.5: 6 residues within 4Å: Chain B: Q.115, Q.116, Y.119, D.149, T.150, K.153 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.153 Water bridges: B:K.153 PGE.13: 6 residues within 4Å: Chain D: Q.115, Q.116, Y.119, D.149, T.150, K.153 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.153

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

EDO.3: 2 residues within 4Å: Chain A: I.6, K.203 No protein-ligand interaction detected (PLIP) EDO.6: 5 residues within 4Å: Chain B: A.262, G.263, I.294, K.295, G.296 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.294 EDO.7: 3 residues within 4Å: Chain B: H.222, F.223, D.226 No protein-ligand interaction detected (PLIP) EDO.8: 2 residues within 4Å: Chain B: K.93, S.128 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.93 EDO.10: 1 residues within 4Å: Chain C: K.291 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.291 EDO.11: 3 residues within 4Å: Chain C: A.262, I.294, G.296 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:I.294 EDO.14: 4 residues within 4Å: Chain D: E.145, S.147, T.148, K.173 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.145, D:T.148 Water bridges: D:N.170 EDO.15: 3 residues within 4Å: Chain D: K.31, I.34, T.68 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.68 EDO.16: 3 residues within 4Å: Chain D: A.219, H.222, F.223 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 4 residues within 4Å: Chain A: R.271, L.272 Chain C: T.85, H.86 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:T.85, C:H.86, A:L.272, A:L.272

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