SMTL ID : 4r53.1

dihydrodipicolinate synthase from C. jejuni with vacant active site and vacant allosteric site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: E.44, N.45, D.224 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.44 Water bridges: A:S.227 EDO.4: 2 residues within 4Å: Chain B: N.12, E.168 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.168 EDO.5: 6 residues within 4Å: Chain B: D.246, E.247, Y.249, N.250, Y.301 Chain D: H.189 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.249, B:N.250, B:Y.301 EDO.8: 4 residues within 4Å: Chain C: C.78, T.81, V.83, D.110 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.81, C:D.110 EDO.9: 4 residues within 4Å: Chain C: H.64, G.99, L.100, F.103 No protein-ligand interaction detected (PLIP)

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

PEG.2: 6 residues within 4Å: Chain A: A.271, G.272, L.273, I.303, K.304, G.305 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.303 PEG.10: 6 residues within 4Å: Chain A: A.188, H.189 Chain C: D.246, E.247, Y.249, N.250 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.249, C:N.250, C:N.250

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

CL.3: 5 residues within 4Å: Chain B: A.20, G.54, T.55, T.56, K.174 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain D: A.20, T.55, T.56, Y.145, K.174 Ligand excluded by PLIP

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

PGE.6: 6 residues within 4Å: Chain B: Q.124, Q.125, Y.128, D.158, T.159, K.162 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.125, B:S.156, B:T.159, B:K.162 Water bridges: B:S.156, B:D.158 PGE.13: 3 residues within 4Å: Chain D: H.231, F.232, D.235 No protein-ligand interaction detected (PLIP) PGE.14: 2 residues within 4Å: Chain B: E.236 Chain D: K.239 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:K.239 Water bridges: B:K.212

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

PG4.7: 6 residues within 4Å: Chain C: Q.124, Q.125, Y.128, D.158, T.159, K.162 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.162 Water bridges: C:K.162 PG4.11: 6 residues within 4Å: Chain D: Q.124, Q.125, Y.128, D.158, T.159, K.162 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.162

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

2015-10-07

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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