SMTL ID : 2od0.1

The crystal structure of gene product VP1028 from Vibrio parahaemolyticus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: R.48, D.50, Q.51 No protein-ligand interaction detected (PLIP) MG.5: 6 residues within 4Å: Chain A: P.4, L.6, K.7 Chain B: P.4, L.6, K.7 No protein-ligand interaction detected (PLIP)

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

SO4.2: 3 residues within 4Å: Chain A: K.68, K.69, R.70 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.70 Water bridges: A:G.71, A:G.71, A:G.71, A:G.71 Salt bridges: A:K.69 SO4.3: 5 residues within 4Å: Chain A: N.42, Q.44, H.46, Y.65, A.80 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.42, A:A.80 Water bridges: A:K.63, A:K.63, A:P.64 Salt bridges: A:H.46 SO4.4: 5 residues within 4Å: Chain A: K.7, K.11 Chain B: V.41, N.42, N.43 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:N.42, B:N.42, B:N.43 Water bridges: A:K.7, A:K.7 Salt bridges: A:K.7, A:K.11 SO4.6: 5 residues within 4Å: Chain B: N.42, Q.44, H.46, Y.65, A.80 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.44 Water bridges: B:Q.44, B:P.64, B:A.80 Salt bridges: B:H.46 SO4.7: 5 residues within 4Å: Chain B: R.48, D.50, Q.51, K.77, N.102 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.51 Water bridges: B:D.50, B:D.50, B:Q.51, B:N.102 Salt bridges: B:R.48, B:K.77 SO4.8: 3 residues within 4Å: Chain B: K.68, K.69, R.70 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.70 Water bridges: B:G.71 Salt bridges: B:K.69 SO4.9: 1 residues within 4Å: Chain B: T.59 2 PLIP interactions: 2 interactions with chain B Water bridges: B:T.59, B:T.59 SO4.10: 2 residues within 4Å: Chain B: K.68, G.71 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.71 Salt bridges: B:K.68 SO4.11: 4 residues within 4Å: Chain B: F.25, R.48, K.77, Y.78 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.48, B:K.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, R. et al., The crystal structure of gene product VP1028 from Vibrio parahaemolyticus. To be Published

Release Date

2007-01-23

Peptides

Hypothetical protein VP1028: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Hypothetical protein VP1028