SMTL ID : 2y7i.1

Structural basis for high arginine specificity in Salmonella typhimurium periplasmic binding protein STM4351.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x ARG: ARGININE(Non-covalent)

ARG.1: 15 residues within 4Å: Chain A: S.13, T.15, Y.16, E.20, F.54, A.71, G.72, M.73, D.74, R.79, E.118, T.121, T.122, H.123, D.160 16 PLIP interactions: 15 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.16, A:F.54, A:T.121 Hydrogen bonds: A:S.13, A:S.13, A:T.15, A:T.15, A:D.74, A:D.74, A:T.122, A:D.160, R.1 Water bridges: A:T.122 Salt bridges: A:E.20, A:R.79, A:E.118 ARG.7: 15 residues within 4Å: Chain B: S.13, T.15, Y.16, E.20, F.54, A.71, G.72, M.73, D.74, R.79, E.118, T.121, T.122, H.123, D.160 15 PLIP interactions: 14 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:Y.16, B:F.54, B:T.121 Hydrogen bonds: B:S.13, B:S.13, B:T.15, B:D.74, B:D.74, B:D.74, B:T.122, B:D.160, R.7 Salt bridges: B:E.20, B:R.79, B:E.118

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain A: S.53, D.55, D.140 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.55, A:D.55, A:D.140, A:D.140 ZN.3: 3 residues within 4Å: Chain A: T.7, H.9, D.67 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.9, A:D.67, A:D.67, H2O.6 ZN.4: 3 residues within 4Å: Chain A: D.23, D.25, K.27 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.23, A:D.25 ZN.8: 2 residues within 4Å: Chain B: D.55, D.140 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.55, B:D.55, B:D.140, H2O.9 ZN.9: 2 residues within 4Å: Chain B: H.9, D.67 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.9, B:D.67, B:D.67, H2O.9 ZN.12: 2 residues within 4Å: Chain A: D.211 Chain B: D.211 No protein-ligand interaction detected (PLIP)

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

ACT.5: 6 residues within 4Å: Chain A: T.76, K.78, R.79, T.121, T.122, R.125 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.78, A:R.125 Salt bridges: A:R.79, A:R.125 ACT.10: 6 residues within 4Å: Chain B: T.76, K.78, R.79, T.121, T.122, R.125 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:R.125 Hydrogen bonds: B:T.76 Water bridges: B:R.79, B:G.120 Salt bridges: B:K.78, B:R.79, B:R.125

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: K.101, G.102, Y.104, H.105, A.175, I.176, M.177, D.178 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.99, A:G.102, A:D.178, A:D.178 GOL.11: 8 residues within 4Å: Chain B: K.101, G.102, Y.104, H.105, A.175, I.176, M.177, D.178 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.102, B:Y.104, B:D.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stamp, A.L. et al., Crystallographic and Microcalorimetric Analyses Reveal the Structural Basis for High Arginine Specificity in the Salmonella Enterica Serovar Typhimurium Periplasmic Binding Protein Stm4351. Proteins (2011)

Release Date

2011-05-11

Peptides

STM4351: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

STM4351