SMTL ID : 4mlr.1 (1 other biounit)

dihydrodipicolinate synthase from C. jejuni, Y110F mutation with pyruvate and Lysine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x LYS: LYSINE(Non-covalent)

LYS.1: 8 residues within 4Å: Chain A: S.59, A.60, L.62, H.67, F.118 Chain D: N.92, E.96 Ligands: LYS.2 5 PLIP interactions: 2 interactions with chain D, 2 Ligand-Ligand interactions, 1 interactions with chain A Hydrogen bonds: D:N.92, D:N.92, K.2, A:H.67 Salt bridges: K.1 LYS.2: 9 residues within 4Å: Chain A: N.92, E.96 Chain D: S.59, A.60, L.62, H.64, H.67, F.118 Ligands: LYS.1 4 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain D, 2 interactions with chain A Hydrogen bonds: K.1, D:H.67, A:N.92, A:N.92 LYS.7: 9 residues within 4Å: Chain B: S.59, A.60, L.62, H.64, H.67, F.118 Chain C: N.92, E.96 Ligands: LYS.10 6 PLIP interactions: 3 Ligand-Ligand interactions, 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: K.10, K.10, B:H.67, C:N.92, C:E.96 Salt bridges: K.7 LYS.10: 8 residues within 4Å: Chain B: N.92, E.96 Chain C: S.59, A.60, L.62, H.67, F.118 Ligands: LYS.7 7 PLIP interactions: 4 Ligand-Ligand interactions, 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: K.7, K.7, K.7, B:N.92, B:N.92, C:H.67 Salt bridges: K.10

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

EDO.3: 1 residues within 4Å: Chain A: Y.269 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.269 EDO.5: 1 residues within 4Å: Chain A: K.212 No protein-ligand interaction detected (PLIP) EDO.6: 3 residues within 4Å: Chain A: H.231, F.232, D.235 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.235, A:D.235 EDO.14: 1 residues within 4Å: Chain D: R.280 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.280

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

ACT.4: 3 residues within 4Å: Chain A: T.157, D.185, H.189 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.189

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

PG4.8: 5 residues within 4Å: Chain B: Q.125, Y.128, D.158, T.159, K.162 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.162 PG4.11: 6 residues within 4Å: Chain C: Q.124, Q.125, Y.128, D.158, T.159, K.162 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.162

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

PGE.9: 5 residues within 4Å: Chain B: I.15, P.191, M.194, G.210, K.212 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.210 Water bridges: B:K.212, B:K.212 PGE.12: 5 residues within 4Å: Chain C: I.15, P.191, M.194, K.212, L.234 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.212

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 3 residues within 4Å: Chain C: P.148, G.152, C.153 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Conly, C.J. et al., Tyrosine 110 Plays a Critical Role in Regulating the Allosteric Inhibition of Campylobacter jejuni Dihydrodipicolinate Synthase by Lysine. Biochemistry (2014)

Release Date

2015-01-14

Peptides

dihydrodipicolinate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

dihydrodipicolinate synthase

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