SMTL ID : 3igq.2 (1 other biounit)

Crystal structure of the extracellular domain of a bacterial pentameric ligand-gated ion channel

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-hexamer

Ligands

6 x ACY: ACETIC ACID(Non-functional Binders)

ACY.1: 7 residues within 4Å: Chain A: I.73, P.74, E.75, I.76, R.77, R.85, Y.102 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.76, A:I.76, A:R.77 Salt bridges: A:R.85 ACY.5: 6 residues within 4Å: Chain B: P.74, E.75, I.76, R.77, R.85, Y.102 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.76, B:R.77 Salt bridges: B:R.85 ACY.9: 7 residues within 4Å: Chain C: L.45, P.74, E.75, I.76, R.77, R.85, Y.102 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:I.76, C:R.77 Water bridges: C:E.75, C:R.77, C:Y.102 Salt bridges: C:R.85 ACY.13: 7 residues within 4Å: Chain D: I.73, P.74, E.75, I.76, R.77, R.85, Y.102 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:I.76, D:I.76, D:R.77 Salt bridges: D:R.85 ACY.17: 6 residues within 4Å: Chain E: P.74, E.75, I.76, R.77, R.85, Y.102 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:I.76, E:R.77 Salt bridges: E:R.85 ACY.21: 7 residues within 4Å: Chain F: L.45, P.74, E.75, I.76, R.77, R.85, Y.102 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:I.76, F:R.77 Water bridges: F:E.75, F:R.77, F:Y.102 Salt bridges: F:R.85

6 x NA: SODIUM ION(Non-functional Binders)

NA.2: 3 residues within 4Å: Chain A: V.5, P.68, I.71 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.71 NA.6: 2 residues within 4Å: Chain B: P.68, I.71 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.68 NA.10: 2 residues within 4Å: Chain C: P.68, I.71 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.71, C:I.73 NA.14: 3 residues within 4Å: Chain D: V.5, P.68, I.71 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:I.71 NA.18: 2 residues within 4Å: Chain E: P.68, I.71 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:I.71 NA.22: 2 residues within 4Å: Chain F: P.68, I.71 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:P.68, F:I.73

6 x HG: MERCURY (II) ION(Non-covalent)

HG.3: 3 residues within 4Å: Chain A: L.24, E.26, C.27 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.27, H2O.2 HG.7: 4 residues within 4Å: Chain B: L.24, E.26, C.27, F.156 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.27, H2O.5 HG.11: 3 residues within 4Å: Chain C: L.24, E.26, C.27 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:C.27 HG.15: 3 residues within 4Å: Chain D: L.24, E.26, C.27 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.27, H2O.10 HG.19: 4 residues within 4Å: Chain E: L.24, E.26, C.27, F.156 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:C.27, H2O.13 HG.23: 3 residues within 4Å: Chain F: L.24, E.26, C.27 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:C.27

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 5 residues within 4Å: Chain A: R.77, F.78, A.84, R.85 Chain F: R.105 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: R.105 Chain B: F.78, A.84, R.85 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain B: R.105 Chain C: R.77, F.78, A.84, R.85 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain C: R.105 Chain D: R.77, F.78, A.84, R.85 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain D: R.105 Chain E: F.78, A.84, R.85 Ligand excluded by PLIP CL.24: 5 residues within 4Å: Chain E: R.105 Chain F: R.77, F.78, A.84, R.85 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nury, H. et al., Crystal structure of the extracellular domain of a bacterial ligand-gated ion channel. J.Mol.Biol. (2010)

Release Date

2009-12-08

Peptides

Glr4197 protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

D
D

E
E

F
F

Glr4197 protein

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