SMTL ID : 7m06.1

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, Y110F mutant with R,R-bislysine bound at the allosteric site at 2.7 Angstrom

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

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

MG.1: 4 residues within 4Å: Chain A: R.154, F.260, S.263, N.264 No protein-ligand interaction detected (PLIP) MG.2: 2 residues within 4Å: Chain A: R.154, N.264 No protein-ligand interaction detected (PLIP) MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain C: G.94, V.119 No protein-ligand interaction detected (PLIP) MG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.11: 5 residues within 4Å: Chain C: R.154, F.260, S.263, N.264 Chain D: K.125 No protein-ligand interaction detected (PLIP) MG.12: 4 residues within 4Å: Chain C: A.139, C.171, E.172, N.173 No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain D: R.154, F.260, S.263, N.264 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain D: R.154, N.264 No protein-ligand interaction detected (PLIP)

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

PGE.3: 8 residues within 4Å: Chain A: S.63, A.64, G.94, L.117, V.119, F.122 Chain B: N.96 Ligands: 3VN.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.64, A:F.122 Hydrogen bonds: A:S.63, A:L.117, A:V.119 PGE.6: 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:T.163, B:K.166 PGE.13: 5 residues within 4Å: Chain C: Q.129, Y.132, D.162, T.163, K.166 1 PLIP interactions: 1 interactions with chain C Water bridges: C:S.160 PGE.16: 5 residues within 4Å: Chain D: Q.129, Y.132, D.162, T.163, K.166 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.166

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

3VN.4: 10 residues within 4Å: Chain A: E.100 Chain B: S.63, H.68, H.71, G.94, E.100, L.104, F.122 Ligands: PGE.3, PEG.7 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.104 Hydrogen bonds: B:S.63, B:H.71, B:N.96, B:E.100, A:E.100 3VN.8: 15 residues within 4Å: Chain C: S.63, A.64, H.71, G.94, N.96, E.100, L.104 Chain D: S.63, A.64, L.66, H.68, N.96, E.100, F.122 Ligands: PEG.17 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:S.63, C:E.100, D:A.64, D:L.66, D:N.96

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

PEG.7: 8 residues within 4Å: Chain A: Y.123 Chain B: S.63, G.92, A.93, G.94, L.117, V.119 Ligands: 3VN.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.63, B:L.117, B:V.119 PEG.17: 8 residues within 4Å: Chain D: S.63, A.64, A.93, G.94, L.117, V.119, F.122 Ligands: 3VN.8 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.63, D:A.93, D:G.94, D:L.117, D:V.119

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

EDO.18: 5 residues within 4Å: Chain D: D.250, E.251, Y.253, N.254, Y.305 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.253, D:N.254, D:N.254

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saran, S. et al., B-FACTOR ANALYSIS SUGGEST THAT L-LYSINE AND R, R-BISLYSINE ALLOSTERICALLY INHIBIT Cj.DHDPS ENZYME BY DECREASING PROTEIN DYNAMICS. To Be Published

Release Date

2022-03-16

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

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