SMTL ID : 2pmb.1

Crystal structure of predicted nucleotide-binding protein from Vibrio cholerae

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-tetramer

Ligands

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

PO4.1: 7 residues within 4Å: Chain A: G.155, H.156, G.256, G.257, P.258, G.259, T.260 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:H.156, A:G.257, A:G.257, A:G.259, A:T.260, A:T.260 Water bridges: A:S.157 Salt bridges: A:H.156 PO4.2: 4 residues within 4Å: Chain A: R.336, K.340, Y.346 Chain D: R.72 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:E.71, A:Y.346 Water bridges: D:R.72 Salt bridges: D:R.72, A:R.336, A:K.340 PO4.3: 7 residues within 4Å: Chain B: G.155, H.156, G.256, G.257, P.258, G.259, T.260 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:H.156, B:G.257, B:G.259, B:T.260, B:T.260 Water bridges: B:H.156, B:S.157 Salt bridges: B:H.156 PO4.4: 6 residues within 4Å: Chain B: P.282, I.283, K.312, H.313, Y.314, S.315 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.283, B:I.283, B:S.315 PO4.5: 5 residues within 4Å: Chain B: R.336, K.340, Y.346 Chain C: E.71, R.72 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:E.71, B:Y.346 Salt bridges: C:R.72, B:R.336, B:K.340 PO4.6: 4 residues within 4Å: Chain B: E.190, K.194, N.225 Chain D: K.202 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:N.225 Salt bridges: B:K.194, D:K.202 PO4.8: 8 residues within 4Å: Chain C: G.154, G.155, H.156, G.256, G.257, P.258, G.259, T.260 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:H.156, C:G.257, C:G.259, C:T.260 Water bridges: C:H.156, C:S.157 Salt bridges: C:H.156 PO4.9: 4 residues within 4Å: Chain A: K.202 Chain C: E.190, K.194, N.225 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Water bridges: A:K.202 Salt bridges: A:K.202, C:K.194 Hydrogen bonds: C:N.225 PO4.10: 4 residues within 4Å: Chain B: R.72 Chain C: R.336, K.340, Y.346 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Y.346, C:Y.346 Salt bridges: C:R.336, C:K.340, B:R.72 PO4.12: 7 residues within 4Å: Chain D: G.155, H.156, G.256, G.257, P.258, G.259, T.260 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:H.156, D:G.257, D:G.257, D:G.259, D:T.260, D:T.260 Water bridges: D:G.154, D:S.157, D:E.222 Salt bridges: D:H.156 PO4.13: 4 residues within 4Å: Chain B: K.202 Chain D: E.190, K.194, N.225 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:N.225 Salt bridges: D:K.194, B:K.202 Water bridges: B:K.202, B:K.202 PO4.14: 5 residues within 4Å: Chain A: E.71, R.72 Chain D: R.336, K.340, Y.346 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:Y.346, A:E.71, A:E.71 Salt bridges: D:R.336, D:K.340, A:R.72

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain B: M.13, D.14, L.16, R.104, Y.108, N.137 Chain C: R.136 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.14, B:D.14, B:Y.108, B:N.137 Water bridges: B:D.14, B:D.14 GOL.11: 7 residues within 4Å: Chain C: A.124, T.128, R.246, W.350, L.352, K.353, I.354 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.128, C:L.352, C:I.354

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Patskovsky, Y. et al., Crystal Structure of Predicted Nucleotide-Binding Protein from Vibrio Cholerae. To be Published

Release Date

2007-05-08

Peptides

Uncharacterized protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Uncharacterized protein

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