SMTL ID : 3m5v.1

Crystal Structure of Dihydrodipicolinate Synthase from Campylobacter jejuni

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

9 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: N.87, Y.113 Chain C: N.87, Y.113 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:Y.113, A:N.87, A:Y.113 Water bridges: C:N.87, C:N.87, C:Y.113, A:Y.113 SO4.2: 5 residues within 4Å: Chain A: R.145, F.251, S.254, N.255 Chain C: K.116 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:N.255 Salt bridges: A:R.145, C:K.116 SO4.3: 4 residues within 4Å: Chain A: N.232, Y.233, K.234, E.235 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.232, A:K.234, A:E.235 SO4.5: 2 residues within 4Å: Chain A: T.118, Q.119 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.119 Water bridges: A:P.117, A:Q.119, A:Q.120 SO4.6: 5 residues within 4Å: Chain B: R.145, F.251, S.254, N.255 Chain D: K.116 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:N.255 Water bridges: B:R.145, B:R.145, D:K.116 Salt bridges: B:R.145, D:K.116 SO4.15: 5 residues within 4Å: Chain A: K.116 Chain C: R.145, F.251, S.254, N.255 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:N.255 Water bridges: C:R.145, C:R.145 Salt bridges: C:R.145, A:K.116 SO4.17: 4 residues within 4Å: Chain B: N.87, Y.113 Chain D: N.87, Y.113 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:N.87, B:Y.113 Water bridges: B:N.87, D:N.87, D:E.91, D:E.91 SO4.18: 4 residues within 4Å: Chain D: N.232, Y.233, K.234, E.235 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.232, D:K.234, D:E.235 Water bridges: D:Y.233 Salt bridges: D:K.234 SO4.22: 5 residues within 4Å: Chain B: K.116 Chain D: R.145, F.251, S.254, N.255 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:N.255 Water bridges: D:R.145 Salt bridges: D:R.145, B:K.116

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

CL.4: 2 residues within 4Å: Chain A: S.282, K.283 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain B: T.118, Q.119 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain B: R.160, H.184 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain B: N.245 Chain C: H.184 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain C: S.282, K.283 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain C: T.118, Q.119 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain C: S.280 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain D: S.282, K.283 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain D: H.59, R.63, F.98 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain D: T.118, Q.119 Ligand excluded by PLIP

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

PEG.9: 11 residues within 4Å: Chain B: A.15, G.49, T.50, A.84, G.85, L.108, S.109, V.110, Y.140, K.169, I.210 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:T.50, B:A.84, B:G.85, B:V.110 Water bridges: B:T.51, B:T.51, B:T.51, B:S.54, B:S.54, B:G.83, B:K.169, D:Y.114 PEG.16: 11 residues within 4Å: Chain C: A.15, G.49, T.50, G.83, A.84, G.85, L.108, S.109, V.110, Y.140, K.169 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:T.50, C:A.84, C:G.85, C:L.108, C:V.110, C:K.169 Water bridges: C:T.51, C:T.51, C:S.54 PEG.23: 11 residues within 4Å: Chain B: Y.114 Chain D: A.15, G.49, T.50, A.84, G.85, L.108, S.109, V.110, Y.140, K.169 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:T.50, D:T.50, D:A.84, D:G.85, D:V.110, D:K.169 Water bridges: D:T.51, D:T.51, D:S.54, D:K.169

1 x FMT: FORMIC ACID(Non-functional Binders)

FMT.11: 3 residues within 4Å: Chain B: H.90 Chain D: T.58, R.275 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.275 Water bridges: D:R.275

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal Structure of Dihydrodipicolinate Synthase from Campylobacter jejuni. To be Published

Release Date

2010-04-28

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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