SMTL ID : 4mlr.2 (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: 10 residues within 4Å: Chain A: S.59, A.60, L.62, T.63, H.64, H.67, F.118 Chain B: N.92, E.96 Ligands: LYS.5 6 PLIP interactions: 1 interactions with chain A, 3 Ligand-Ligand interactions, 2 interactions with chain B Hydrogen bonds: A:H.67, B:N.92, B:N.92 Water bridges: K.1, K.1 Salt bridges: K.1 LYS.5: 9 residues within 4Å: Chain A: N.92, E.96 Chain B: S.59, A.60, L.62, H.64, H.67, F.118 Ligands: LYS.1 5 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain A, 2 interactions with chain B Salt bridges: K.5 Hydrogen bonds: A:N.92, A:N.92, B:H.67, B:N.92 LYS.8: 11 residues within 4Å: Chain C: S.59, A.60, L.62, T.63, H.64, H.67, N.92, F.118 Chain D: N.92, E.96 Ligands: LYS.12 8 PLIP interactions: 4 Ligand-Ligand interactions, 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: K.8, K.12, K.12, C:A.60, C:H.67, D:N.92, D:N.92 Salt bridges: K.8 LYS.12: 8 residues within 4Å: Chain C: N.92, E.96 Chain D: S.59, A.60, L.62, H.67, F.118 Ligands: LYS.8 5 PLIP interactions: 2 Ligand-Ligand interactions, 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: K.8, C:N.92, C:E.96, D:H.67 Salt bridges: K.12

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

PGE.2: 6 residues within 4Å: Chain A: P.148, G.149, G.152, C.153, E.154, S.177 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.149, A:E.154, A:S.177 PGE.6: 4 residues within 4Å: Chain B: Q.125, Y.128, D.158, K.162 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.125, B:K.162 PGE.13: 3 residues within 4Å: Chain D: Q.125, Y.128, K.162 No protein-ligand interaction detected (PLIP)

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

EDO.3: 3 residues within 4Å: Chain A: A.271, I.303, G.305 No protein-ligand interaction detected (PLIP) EDO.4: 4 residues within 4Å: Chain A: Q.125, Y.128, T.159, K.162 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.125, A:K.162 EDO.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.10: 2 residues within 4Å: Chain C: E.295, K.299 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.295, C:K.299 EDO.11: 1 residues within 4Å: Chain C: Y.269 No protein-ligand interaction detected (PLIP)

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

ACT.7: 3 residues within 4Å: Chain A: H.64, E.96 Chain B: H.64 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:H.64 Salt bridges: A:H.64

Links

RCSB   PDBe   PDBe-KB   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
E

B
F

C
G

D
H

dihydrodipicolinate synthase

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