SMTL ID : 9ck7.1

Lineage IV Lassa virus glycoprotein (Josiah) in complex with polyclonal antibody (GPC-A epitope) from rabbit 187

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-3-mer

Ligands

14 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG.1: 4 residues within 4Å: Chain A: N.109, S.216, Y.217, Q.218 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: E.76, T.77, N.79, M.80 Chain F: W.24, I.64 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:I.64 NAG-NAG.4: 4 residues within 4Å: Chain A: Q.165, N.167, S.169, Y.219 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: G.159, G.160, N.224, T.225 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: N.99, E.100 Ligands: NAG-NAG-BMA-MAN.6, NAG-NAG-BMA-MAN.6 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: N.109, S.216, Y.217, Q.218 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: N.167, S.169, Y.219 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 9 residues within 4Å: Chain C: E.76, T.77, L.78, N.79, M.80, T.81 Chain H: W.24, N.60, I.64 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:W.24 NAG-NAG.12: 3 residues within 4Å: Chain C: N.109, S.216, Q.218 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain C: I.113, Q.165, N.167, S.169, Y.219 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 6 residues within 4Å: Chain C: N.158, G.159, G.160, K.161, N.224, T.225 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 10 residues within 4Å: Chain A: F.233, S.234, R.235, S.237 Chain F: N.106, S.108, V.129, G.132, S.133, Y.134 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 7 residues within 4Å: Chain B: Q.69 Chain G: K.32, C.33, Y.112, N.114, G.119, T.121 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 10 residues within 4Å: Chain C: F.233, S.234, R.235, P.236, S.237 Chain H: N.106, S.108, G.132, S.133, Y.134 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:F.233

2 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.2: 3 residues within 4Å: Chain A: F.117, N.119, N.158 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.158, A:N.158 NAG-NAG-FUC.9: 1 residues within 4Å: Chain B: N.119 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-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.6: 11 residues within 4Å: Chain B: E.76, T.77, N.79, M.80, N.99 Chain E: X.55 Chain G: R.23, W.24, N.60, I.64 Ligands: NAG-NAG.7 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:R.23

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.16: 15 residues within 4Å: Chain B: E.72, M.75, R.235, P.236 Chain D: X.105, X.106 Chain E: X.31, X.93, X.94 Chain G: N.106, S.108, V.129, G.132, S.133, Y.134 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain B Hydrophobic interactions: G:Y.134 Hydrogen bonds: B:R.235

15 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose

NAG.19: 5 residues within 4Å: Chain A: K.88, N.89, N.90, S.91, H.92 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: N.99, E.100, W.227 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain B: K.88, N.89, H.92 Chain E: X.97 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: G.159, N.224 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain C: N.99 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain C: N.119 Ligand excluded by PLIP NAG.25: 5 residues within 4Å: Chain C: K.88, N.89, N.90, S.91, H.92 Ligand excluded by PLIP NAG.26: 5 residues within 4Å: Chain F: C.33, F.34, Y.112, N.114, T.121 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain F: N.131 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain F: N.136, T.138 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain G: L.135, N.136, E.137 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain G: N.131 Ligand excluded by PLIP NAG.31: 6 residues within 4Å: Chain C: Q.69 Chain H: K.32, C.33, Y.112, N.114, T.121 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: Y.200 Chain H: N.131 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain H: N.136, E.137, T.138 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brouwer, P.J.M. et al., Defining bottlenecks and opportunities for Lassa virus neutralization by structural profiling of vaccine-induced polyclonal antibody responses. Cell Rep (2024)

Release Date

2024-09-25

Peptides

Glycoprotein GP1: ABC
Rabbit polyclonal Fv heavy chain: D
Rabbit polyclonal Fv light chain: E
Glycoprotein G2: FGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

E
L

F
a

G
b

H
c

Glycoprotein GP1

Rabbit polyclonal Fv heavy chain

Rabbit polyclonal Fv light chain

Glycoprotein G2

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