SMTL ID : 6tit.1

VSV G_440

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

monomer

Ligands

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-functional Binders)

NAG.1: 4 residues within 4Å: Chain A: N.20, T.86, N.163 Ligands: NAG.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.163 NAG.2: 2 residues within 4Å: Chain A: F.425 Ligands: NAG.1 No protein-ligand interaction detected (PLIP) NAG.3: 1 residues within 4Å: Chain A: N.320 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.320

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

ACT.4: 5 residues within 4Å: Chain A: D.365, V.366, T.376, S.377, D.395 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.377, A:S.377 Water bridges: A:S.378

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 7 residues within 4Å: Chain A: G.38, T.39, A.40, D.185, I.186, T.187, F.189 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.38

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 9 residues within 4Å: Chain A: M.45, P.46, K.47, K.50, E.138, Y.139, M.184, Y.209, P.262 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.46, A:K.50, A:E.138, A:E.138 Water bridges: A:R.329 GOL.7: 6 residues within 4Å: Chain A: Y.139, T.140, L.176, C.177, Y.223, C.224 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.139, A:C.224 Water bridges: A:K.225 GOL.8: 10 residues within 4Å: Chain A: F.6, S.303, A.306, P.370, N.371, V.373, F.382, P.383, L.384, Y.385 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.371, A:L.384 GOL.9: 2 residues within 4Å: Chain A: F.2, Y.385 No protein-ligand interaction detected (PLIP)

4 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.10: 8 residues within 4Å: Chain A: I.37, G.38, T.39, F.188, F.189, S.190, G.193, E.194 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.190 CA.11: 4 residues within 4Å: Chain A: H.8, K.47, K.50, Y.209 No protein-ligand interaction detected (PLIP) CA.12: 1 residues within 4Å: Chain A: E.286 No protein-ligand interaction detected (PLIP) CA.13: 6 residues within 4Å: Chain A: W.227, G.228, E.238, M.239, K.242, F.245 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Beilstein, F. et al., Identification of a pH-Sensitive Switch in VSV-G and a Crystal Structure of the G Pre-fusion State Highlight the VSV-G Structural Transition Pathway. Cell Rep (2020)

Release Date

2020-09-02

Peptides

Glycoprotein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glycoprotein