SMTL ID : 8dmi.1

Lymphocytic choriomeningitis virus glycoprotein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

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

NAG-NAG.1: 6 residues within 4Å: Chain A: S.42, H.43, N.45, N.197, Y.201 Chain B: L.64 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.64 NAG-NAG.2: 4 residues within 4Å: Chain A: A.54, N.55, H.58, Y.60 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: N.74, R.148, S.184, Y.185, Q.186 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.148, A:R.148 NAG-NAG.4: 7 residues within 4Å: Chain A: S.76, I.78, N.81, Q.129, N.131, T.133, Y.187 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.124, G.125, N.192, T.194 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 7 residues within 4Å: Chain A: T.200, A.202 Chain B: N.106, S.108, V.129, G.132, Y.134 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.200 NAG-NAG.7: 6 residues within 4Å: Chain C: S.42, H.43, N.45, N.197, Y.201 Chain D: L.64 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.64 NAG-NAG.8: 4 residues within 4Å: Chain C: A.54, N.55, H.58, Y.60 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain C: N.74, R.148, S.184, Y.185, Q.186 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.148, C:R.148 NAG-NAG.10: 7 residues within 4Å: Chain C: S.76, I.78, N.81, Q.129, N.131, T.133, Y.187 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain C: N.124, G.125, N.192, T.194 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 7 residues within 4Å: Chain C: T.200, A.202 Chain D: N.106, S.108, V.129, G.132, Y.134 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.200 NAG-NAG.13: 6 residues within 4Å: Chain E: S.42, H.43, N.45, N.197, Y.201 Chain F: L.64 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain E: A.54, N.55, H.58, Y.60 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain E: N.74, R.148, S.184, Y.185, Q.186 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.148, E:R.148 NAG-NAG.16: 7 residues within 4Å: Chain E: S.76, I.78, N.81, Q.129, N.131, T.133, Y.187 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain E: N.124, G.125, N.192, T.194 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 7 residues within 4Å: Chain E: T.200, A.202 Chain F: N.106, S.108, V.129, G.132, Y.134 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.200

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

NAG.19: 1 residues within 4Å: Chain A: N.84 No protein-ligand interaction detected (PLIP) NAG.20: 2 residues within 4Å: Chain B: N.136, T.138 No protein-ligand interaction detected (PLIP) NAG.21: 1 residues within 4Å: Chain C: N.84 No protein-ligand interaction detected (PLIP) NAG.22: 2 residues within 4Å: Chain D: N.136, T.138 No protein-ligand interaction detected (PLIP) NAG.23: 1 residues within 4Å: Chain E: N.84 No protein-ligand interaction detected (PLIP) NAG.24: 2 residues within 4Å: Chain F: N.136, T.138 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moon-Walker, A. et al., Structural basis for antibody-mediated neutralization of lymphocytic choriomeningitis virus. Cell Chem Biol (2023)

Release Date

2023-04-12

Peptides

Glycoprotein G1: ACE
Glycoprotein G2,Cobalamin adenosyltransferase-like domain-containing protein trimerization tag: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

E
C

B
a

D
b

F
c

Glycoprotein G1

Glycoprotein G2,Cobalamin adenosyltransferase-like domain-containing protein trimerization tag

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