SMTL ID : 6xgs.1

Crystal Structure of Dihydrodipicolinate synthase (DHDPS) from Brucella suis 1330

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x CIT: CITRIC ACID(Non-functional Binders)

CIT.1: 9 residues within 4Å: Chain A: Y.154, I.156, R.159, K.183, G.208, E.209, V.227, F.266, N.270 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.156, A:F.266 Hydrogen bonds: A:R.159, A:R.159, A:E.209, A:E.209, A:N.270 Salt bridges: A:R.159, A:R.159, A:K.183, B:K.130 CIT.4: 9 residues within 4Å: Chain B: T.66, Y.154, I.156, R.159, G.208, E.209, V.227, F.266, N.270 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.266 Hydrogen bonds: B:T.66, B:R.159, B:E.209, B:E.209, B:N.270 Water bridges: B:Y.154, B:G.158, B:K.183, B:K.183, B:K.183 Salt bridges: B:R.159, B:R.159, B:K.183, A:K.130 CIT.6: 9 residues within 4Å: Chain C: Y.154, I.156, R.159, K.183, G.208, E.209, V.227, F.266, N.270 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:F.266 Hydrogen bonds: C:Y.154, C:Y.154, C:R.159, C:E.209, C:N.270 Water bridges: C:K.183, C:K.183, C:K.183, C:K.183 Salt bridges: C:R.159, C:R.159, C:K.183, D:K.130 CIT.9: 10 residues within 4Å: Chain D: T.65, Y.154, I.156, R.159, K.183, G.208, E.209, V.227, F.266, N.270 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:I.156, D:F.266 Hydrogen bonds: D:Y.154, D:Y.154, D:R.159, D:R.159, D:N.270 Water bridges: D:K.183, D:K.183, D:K.183 Salt bridges: D:R.159, D:R.159, D:K.183

5 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 4 residues within 4Å: Chain A: R.289, S.290 Chain B: V.104, R.142 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.142 Hydrogen bonds: A:S.290 PO4.3: 4 residues within 4Å: Chain A: V.104, R.142 Chain B: R.289, S.290 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.290 Water bridges: B:R.289, B:R.289, B:S.290, A:V.104 Salt bridges: A:R.142 PO4.5: 3 residues within 4Å: Chain B: R.280, I.313, N.314 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.314 Salt bridges: B:R.280 PO4.7: 4 residues within 4Å: Chain C: R.289, S.290 Chain D: V.104, R.142 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.290 Salt bridges: D:R.142 PO4.8: 4 residues within 4Å: Chain C: V.104, R.142 Chain D: R.289, S.290 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.290 Water bridges: D:S.290 Salt bridges: C:R.142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., Crystal Structure of Dihydrodipicolinate synthase (DHDPS) from Brucella suis 1330. to be published

Release Date

2020-07-08

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