SMTL ID : 8dmh.1

Lymphocytic choriomeningitis virus glycoprotein in complex with neutralizing antibody M28

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

3 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.1: 5 residues within 4Å: Chain A: S.42, H.43, N.45, L.46, N.197 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 7 residues within 4Å: Chain E: S.42, H.43, N.45, L.46, N.197, Y.201 Chain H: L.64 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 6 residues within 4Å: Chain I: S.42, H.43, N.45, L.46, N.197 Chain L: L.64 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 4 residues within 4Å: Chain A: N.55, H.58, Y.60, R.193 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.74, S.184, Y.185, Q.186 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.131, T.133, S.135, Y.187 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain A: T.93, N.123, N.124, G.125, N.192 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain B: Q.27, I.30, Y.91, S.94 Chain D: Y.134, N.136 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.27 NAG-NAG.8: 4 residues within 4Å: Chain E: A.54, N.55, H.58, Y.60 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain E: N.74, S.184, Y.185, Q.186 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 7 residues within 4Å: Chain E: S.76, I.78, Q.129, N.131, T.133, S.135, Y.187 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain E: N.124, G.125, N.192 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:N.124 NAG-NAG.12: 6 residues within 4Å: Chain F: Q.27, I.30, Y.91, S.94, S.95 Chain H: N.136 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 6 residues within 4Å: Chain I: A.54, N.55, H.58, Y.60, E.69, H.198 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain I: N.74, S.184, Y.185, Q.186 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 7 residues within 4Å: Chain I: S.76, I.78, Q.129, N.131, T.133, S.135, Y.187 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain I: N.124, N.192, R.193, T.194 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:N.124 NAG-NAG.18: 5 residues within 4Å: Chain J: D.1, Q.27, Y.91, S.94 Chain L: N.136 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:Q.27

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

NAG.19: 3 residues within 4Å: Chain A: F.82, N.84, N.123 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.123 NAG.20: 8 residues within 4Å: Chain A: Y.201, A.202 Chain D: N.106, S.108, V.129, G.132, A.133, Y.134 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.132, D:Y.134 NAG.21: 3 residues within 4Å: Chain E: F.82, N.84, N.123 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.121 NAG.22: 9 residues within 4Å: Chain E: M.41, K.162, T.200, Y.201, A.202 Chain H: N.106, S.108, G.132, Y.134 6 PLIP interactions: 2 interactions with chain E, 4 interactions with chain H Hydrogen bonds: E:K.162, E:T.200, H:N.106, H:S.108, H:S.108, H:G.132 NAG.23: 3 residues within 4Å: Chain I: N.84, C.120, D.121 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:D.121, I:D.121 NAG.24: 8 residues within 4Å: Chain I: M.41, T.200, Y.201, A.202 Chain L: N.106, S.108, G.132, Y.134 4 PLIP interactions: 3 interactions with chain L, 1 interactions with chain I Hydrogen bonds: L:S.108, L:S.108, L:G.132, I:T.200

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: AEI
18.5C-M28 Fab Light Chain: BFJ
18.5C-M28 Fab Heavy Chain: CGK
Glycoprotein G2,Cobalamin adenosyltransferase-like domain-containing protein trimerization tag: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
B

I
C

B
E

F
G

J
I

C
F

G
H

K
J

D
a

H
b

L
c

Glycoprotein G1

18.5C-M28 Fab Light Chain

18.5C-M28 Fab Heavy Chain

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

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