SMTL ID : 4ly8.1

dihydrodipicolinate synthase from C. jejuni with pyruvate bound to the active site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 2 residues within 4Å: Chain A: H.231, F.232 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: A.135, Q.136, V.138, D.139, N.169 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: D.246, E.247, Y.249, N.250 Chain B: H.189 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain A: S.208, G.210, Y.238 Chain B: Y.204, Y.238, K.239, K.242 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain A: P.286, F.291 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: P.148, G.152, C.153 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain B: I.15, G.16, D.48, L.234 Ligands: PGE.18 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain B: T.157, D.158, D.185, H.189 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain B: R.37, K.40, R.41, F.306 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain C: V.98, K.102, S.137 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain C: H.64, G.99, L.100 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain C: A.271, I.303, G.305 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain C: A.228, H.231, F.232 Ligand excluded by PLIP EDO.31: 4 residues within 4Å: Chain C: T.157, D.158, D.185, H.189 Ligand excluded by PLIP EDO.36: 2 residues within 4Å: Chain D: Y.269, L.270 Ligand excluded by PLIP EDO.37: 5 residues within 4Å: Chain C: K.239, K.242 Chain D: S.208, G.210, Y.238 Ligand excluded by PLIP EDO.38: 2 residues within 4Å: Chain D: G.178, E.199 Ligand excluded by PLIP EDO.39: 3 residues within 4Å: Chain D: H.64, E.96, G.99 Ligand excluded by PLIP EDO.40: 3 residues within 4Å: Chain B: L.281 Chain D: T.94, H.95 Ligand excluded by PLIP EDO.41: 3 residues within 4Å: Chain D: I.15, H.231, L.234 Ligand excluded by PLIP EDO.42: 4 residues within 4Å: Chain D: D.10, K.11, F.164, R.192 Ligand excluded by PLIP

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

PGE.2: 3 residues within 4Å: Chain A: G.28, R.280 Ligands: PGE.4 No protein-ligand interaction detected (PLIP) PGE.4: 4 residues within 4Å: Chain A: F.279, R.280, L.281 Ligands: PGE.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.281 Water bridges: A:F.279, A:F.279, A:F.279 PGE.5: 4 residues within 4Å: Chain A: I.15, M.194, K.212, L.234 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.212, A:L.234 Water bridges: A:P.191 PGE.7: 5 residues within 4Å: Chain A: L.270, A.271, G.272, I.303, G.305 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.272 Water bridges: A:F.306 PGE.16: 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 PGE.18: 4 residues within 4Å: Chain B: M.194, K.212, L.234 Ligands: EDO.19 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.234 Water bridges: B:K.212, B:K.212 PGE.20: 3 residues within 4Å: Chain B: Y.269, L.270, G.272 No protein-ligand interaction detected (PLIP) PGE.21: 3 residues within 4Å: Chain B: H.231, F.232, D.235 No protein-ligand interaction detected (PLIP) PGE.28: 4 residues within 4Å: Chain C: I.15, M.194, K.212, L.234 No protein-ligand interaction detected (PLIP) PGE.32: 3 residues within 4Å: Chain C: P.148, G.149, S.177 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.177 Water bridges: C:S.177 PGE.34: 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

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

ACT.8: 3 residues within 4Å: Chain A: K.40, E.44, T.81 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.81 Hydrogen bonds: A:E.44 ACT.12: 4 residues within 4Å: Chain A: D.158, R.165, H.189 Ligands: GOL.10 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.165 ACT.33: 6 residues within 4Å: Chain A: K.121 Chain C: R.150, F.256, E.258, S.259, N.260 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.256 Hydrogen bonds: C:N.260 Salt bridges: C:R.150

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 5 residues within 4Å: Chain A: T.157, D.158, D.185, H.189 Ligands: ACT.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.185 Water bridges: A:D.158 GOL.14: 6 residues within 4Å: Chain A: S.59, L.62, H.64, H.67, G.90, L.100 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.67, A:G.90 Water bridges: A:A.60, A:L.62, A:Y.118 GOL.17: 7 residues within 4Å: Chain B: T.55, Y.145, R.150, K.174, G.198, F.256, N.260 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.145, B:R.150, B:R.150, B:G.198, B:N.260 GOL.22: 4 residues within 4Å: Chain B: S.59, L.62, H.64, H.67 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.67 Water bridges: B:S.59, B:S.59 GOL.35: 4 residues within 4Å: Chain D: L.62, H.64, H.67, L.100 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.64, D:H.67 Water bridges: D:G.90

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

PG4.13: 5 residues within 4Å: Chain A: Q.125, Y.128, D.158, T.159, K.162 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.162 Water bridges: A:S.156 PG4.25: 5 residues within 4Å: Chain C: Q.125, Y.128, D.158, T.159, K.162 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.162 Water bridges: C:S.156, C: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

2015-01-14

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