SMTL ID : 5ine.1

Crystal structure of the prefusion glycoprotein of LCMV

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

homo-dimer

Ligands

5 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.1: 4 residues within 4Å: Chain A: N.95, S.97, H.98, R.233 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.233, A:R.233 NAG-NAG-BMA-MAN.2: 4 residues within 4Å: Chain A: N.114, S.224, Y.225, Q.226 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.8: 4 residues within 4Å: Chain B: N.95, S.97, H.98, R.233 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.233, B:R.233 NAG-NAG-BMA-MAN.11: 6 residues within 4Å: Chain B: N.163, N.164, G.165, N.232, R.233, T.234 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.12: 9 residues within 4Å: Chain B: M.81, A.94, R.240, A.242, N.371, S.373, V.394, G.397, Y.399 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.94, B:Y.399 Hydrophobic interactions: B:Y.399

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 6 residues within 4Å: Chain A: L.118, N.121, Q.169, N.171, S.173, Y.227 No protein-ligand interaction detected (PLIP)

6 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.4: 6 residues within 4Å: Chain A: N.163, N.164, G.165, N.232, R.233, T.234 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 9 residues within 4Å: Chain A: M.81, K.202, R.240, A.242, N.371, S.373, V.394, G.397, Y.399 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.399 NAG-NAG-BMA.6: 8 residues within 4Å: Chain A: S.82, N.85, L.86, G.104, S.105, W.235, Y.241, W.289 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 7 residues within 4Å: Chain B: S.82, N.85, G.104, S.105, W.235, Y.241, W.289 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 4 residues within 4Å: Chain B: N.114, S.224, Y.225, Q.226 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 6 residues within 4Å: Chain B: L.118, N.121, Q.169, N.171, S.173, Y.227 No protein-ligand interaction detected (PLIP)

5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.13: 3 residues within 4Å: Chain A: F.122, N.124 Chain B: T.271 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.124 NAG.14: 2 residues within 4Å: Chain A: N.396, G.397 No protein-ligand interaction detected (PLIP) NAG.15: 2 residues within 4Å: Chain A: N.401, E.402 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.401 NAG.16: 5 residues within 4Å: Chain A: T.271, E.279, N.308 Chain B: F.122, N.124 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.279, A:N.308, B:N.124 NAG.17: 2 residues within 4Å: Chain B: N.401, E.402 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.401

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hastie, K.M. et al., Crystal structure of the prefusion surface glycoprotein of the prototypic arenavirus LCMV. Nat.Struct.Mol.Biol. (2016)

Release Date

2016-04-20

Peptides

Pre-glycoprotein polyprotein GP complex: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pre-glycoprotein polyprotein GP complex