SMTL ID : 3mko.1

Crystal Structure of the Lymphocytic Choriomeningitis Virus Membrane Fusion Glycoprotein GP2 in its Postfusion Conformation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

9 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 5 residues within 4Å: Chain A: N.100, E.101, T.102 Chain B: A.38, V.41 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:A.38, A:T.102 Water bridges: B:A.38, A:N.100 Hydrogen bonds: A:N.100 MPD.2: 9 residues within 4Å: Chain A: Y.71, S.72, K.73, Y.76, L.92, S.97 Chain B: T.44, T.45, S.48 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.92, B:T.44 Hydrogen bonds: A:S.72, A:S.97 Water bridges: A:Y.71 MPD.3: 4 residues within 4Å: Chain A: N.70, Y.71, S.72, W.75 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.75, A:W.75 Hydrogen bonds: A:S.72, A:S.72 MPD.6: 5 residues within 4Å: Chain B: N.100, E.101, T.102 Chain C: A.38, V.41 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:A.38, B:T.102 Water bridges: C:A.38, B:N.100 Hydrogen bonds: B:N.100 MPD.7: 9 residues within 4Å: Chain B: Y.71, S.72, K.73, Y.76, L.92, S.97 Chain C: T.44, T.45, S.48 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.92, C:T.44 Hydrogen bonds: B:S.72, B:S.97 Water bridges: B:Y.71 MPD.8: 4 residues within 4Å: Chain B: N.70, Y.71, S.72, W.75 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.75, B:W.75 Hydrogen bonds: B:S.72, B:S.72 MPD.11: 5 residues within 4Å: Chain A: A.38, V.41 Chain C: N.100, E.101, T.102 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:A.38, C:T.102 Water bridges: A:A.38, C:N.100 Hydrogen bonds: C:N.100 MPD.12: 9 residues within 4Å: Chain A: T.44, T.45, S.48 Chain C: Y.71, S.72, K.73, Y.76, L.92, S.97 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.92, A:T.44 Hydrogen bonds: C:S.72, C:S.97 Water bridges: C:Y.71 MPD.13: 4 residues within 4Å: Chain C: N.70, Y.71, S.72, W.75 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:W.75, C:W.75 Hydrogen bonds: C:S.72, C:S.72

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

CL.4: 5 residues within 4Å: Chain A: N.24 Chain B: N.24 Chain C: N.24 Ligands: CL.9, CL.14 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain A: N.24 Chain B: N.24 Chain C: N.24 Ligands: CL.4, CL.14 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain A: N.24 Chain B: N.24 Chain C: N.24 Ligands: CL.4, CL.9 Ligand excluded by PLIP

3 x IUM: URANYL (VI) ION(Non-covalent)

IUM.5: 5 residues within 4Å: Chain A: R.61 Chain B: R.61 Chain C: R.61 Ligands: IUM.10, IUM.15 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: C:R.61, A:R.61 Water bridges: B:R.61, B:R.61 IUM.10: 5 residues within 4Å: Chain A: R.61 Chain B: R.61 Chain C: R.61 Ligands: IUM.5, IUM.15 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Water bridges: C:R.61, C:R.61 Hydrogen bonds: B:R.61, A:R.61 IUM.15: 5 residues within 4Å: Chain A: R.61 Chain B: R.61 Chain C: R.61 Ligands: IUM.5, IUM.10 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: C:R.61, B:R.61 Water bridges: A:R.61, A:R.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Igonet, S. et al., X-ray structure of the arenavirus glycoprotein GP2 in its postfusion hairpin conformation. Proc.Natl.Acad.Sci.USA (2011)

Release Date

2011-04-20

Peptides

Glycoprotein C: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Glycoprotein C