SMTL ID : 2p5m.1

C-terminal domain hexamer of AhrC bound with L-arginine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-hexamer

Ligands

10 x ARG: ARGININE(Non-covalent)

ARG.1: 15 residues within 4Å: Chain A: G.58, D.59, D.60, T.61 Chain B: Q.38, G.41, A.42, D.45, T.55, I.56, C.57 Chain D: P.34, G.35, D.59 Ligands: ARG.6 22 PLIP interactions: 8 interactions with chain A, 6 interactions with chain B, 2 interactions with chain D, 6 Ligand-Ligand interactions Hydrogen bonds: A:D.59, A:D.60, A:D.60, A:D.60, A:T.61, A:T.61, B:Q.38, B:Q.38, B:D.45, B:C.57, R.1, R.6 Water bridges: A:G.35, B:D.45, B:T.55, D:G.35, R.1, R.1, R.1, R.6 Salt bridges: A:D.59, D:D.59 ARG.2: 15 residues within 4Å: Chain B: G.58, D.59, D.60, T.61 Chain C: Q.38, G.41, A.42, D.45, T.55, I.56, C.57 Chain F: P.34, G.35, D.59 Ligands: ARG.8 21 PLIP interactions: 9 interactions with chain B, 6 Ligand-Ligand interactions, 5 interactions with chain C, 1 interactions with chain F Hydrogen bonds: B:D.59, B:D.60, B:D.60, B:D.60, B:T.61, B:T.61, R.2, R.8, C:Q.38, C:Q.38, C:D.45, C:C.57 Water bridges: B:D.59, R.2, R.2, R.2, R.8, C:T.55 Salt bridges: B:D.59, B:D.60, F:D.59 ARG.3: 15 residues within 4Å: Chain A: Q.38, G.41, A.42, D.45, T.55, I.56, C.57 Chain C: G.58, D.59, D.60, T.61 Chain E: P.34, G.35, D.59 Ligands: ARG.7 24 PLIP interactions: 8 interactions with chain C, 6 interactions with chain A, 8 Ligand-Ligand interactions, 2 interactions with chain E Hydrogen bonds: C:D.59, C:D.60, C:D.60, C:T.61, C:T.61, A:Q.38, A:Q.38, A:D.45, A:T.55, A:C.57, R.3, R.7 Water bridges: C:D.59, C:D.60, A:T.55, R.3, R.3, R.3, R.3, R.7, R.7, E:D.59 Salt bridges: C:D.59, E:D.59 ARG.4: 2 residues within 4Å: Chain B: D.48, D.50 8 PLIP interactions: 2 Ligand-Ligand interactions, 4 interactions with chain B, 2 interactions with chain A Water bridges: R.4, R.4, B:M.53, A:K.20, A:K.20 Hydrogen bonds: B:D.48, B:D.48, B:D.50 ARG.5: 1 residues within 4Å: Chain B: D.71 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:E.51, B:D.71 ARG.6: 15 residues within 4Å: Chain A: P.34, G.35, D.59 Chain D: G.58, D.59, D.60, T.61 Chain E: Q.38, G.41, A.42, D.45, T.55, I.56, C.57 Ligands: ARG.1 22 PLIP interactions: 9 interactions with chain D, 6 interactions with chain E, 2 interactions with chain A, 5 Ligand-Ligand interactions Hydrogen bonds: D:D.59, D:D.60, D:D.60, D:T.61, D:T.61, E:Q.38, E:Q.38, E:D.45, E:T.55, E:C.57, R.1, R.6 Water bridges: D:K.31, D:G.35, D:D.60, E:T.55, A:G.35, R.1, R.6, R.6 Salt bridges: D:D.59, A:D.59 ARG.7: 15 residues within 4Å: Chain C: P.34, G.35, D.59 Chain E: G.58, D.59, D.60, T.61 Chain F: Q.38, G.41, A.42, D.45, T.55, I.56, C.57 Ligands: ARG.3 23 PLIP interactions: 2 interactions with chain C, 7 interactions with chain F, 5 Ligand-Ligand interactions, 9 interactions with chain E Water bridges: C:D.59, F:D.45, F:T.55, R.3, R.7, R.7, E:D.59, E:D.60 Salt bridges: C:D.59, E:D.59, E:D.60 Hydrogen bonds: F:Q.38, F:Q.38, F:D.45, F:T.55, F:C.57, R.3, R.7, E:D.59, E:D.60, E:D.60, E:T.61, E:T.61 ARG.8: 15 residues within 4Å: Chain B: P.34, G.35, D.59 Chain D: Q.38, G.41, A.42, D.45, T.55, I.56, C.57 Chain F: G.58, D.59, D.60, T.61 Ligands: ARG.2 23 PLIP interactions: 5 interactions with chain D, 7 interactions with chain F, 10 Ligand-Ligand interactions, 1 interactions with chain B Hydrogen bonds: D:Q.38, D:Q.38, D:D.45, D:C.57, F:D.59, F:D.60, F:D.60, F:D.60, F:T.61, F:T.61, R.2, R.8 Water bridges: D:T.55, R.2, R.2, R.8, R.8, R.8, R.8, R.8, R.8 Salt bridges: F:D.59, B:D.59 ARG.9: 2 residues within 4Å: Chain E: D.48, D.50 8 PLIP interactions: 2 interactions with chain D, 4 interactions with chain E, 2 Ligand-Ligand interactions Water bridges: D:K.20, D:K.20, E:M.53, R.9, R.9 Hydrogen bonds: E:D.48, E:D.50, E:D.50 ARG.10: 1 residues within 4Å: Chain E: D.71 2 PLIP interactions: 2 interactions with chain E Salt bridges: E:E.51, E:D.71

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garnett, J.A. et al., Structure of the C-terminal effector-binding domain of AhrC bound to its corepressor L-arginine. Acta Crystallogr.,Sect.F (2007)

Release Date

2007-10-30

Peptides

Arginine repressor: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Arginine repressor