SMTL ID : 9cj8.1

Lineage IV Lassa virus glycoprotein (Josiah) in complex with rabbit polyclonal antibody (LAVA01-like epitope)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-3-3-mer

Ligands

5 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: 3 residues within 4Å: Chain C: H.115, F.117, N.119 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain D: E.76, T.77, N.79, W.227 Chain F: W.24, I.64 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain E: E.76, T.77, N.79, M.80, N.99 Chain G: W.24 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 7 residues within 4Å: Chain F: L.31, K.32, C.33, F.34, Y.112, N.114, T.121 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:L.31 NAG-NAG.7: 3 residues within 4Å: Chain G: S.130, N.131, H.139 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-MAN-FUC.4: 4 residues within 4Å: Chain E: N.109, S.216, Y.217, Q.218 No protein-ligand interaction detected (PLIP)

1 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.5: 3 residues within 4Å: Chain E: F.117, N.119, D.122 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:D.122

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[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-MAN.8: 7 residues within 4Å: Chain E: F.233, R.235, S.237 Chain G: N.106, S.108, G.132, Y.134 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:F.233

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

NAG.9: 2 residues within 4Å: Chain C: N.99, E.100 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain C: N.109, S.216, Y.217 Ligand excluded by PLIP NAG.11: 6 residues within 4Å: Chain C: K.88, N.89, N.90, S.91, H.92, Y.217 Ligand excluded by PLIP NAG.12: 5 residues within 4Å: Chain C: S.111, Q.165, N.167, S.169, Y.219 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain C: E.76, N.79, M.80 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain C: G.159, N.224 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain D: N.89, H.92 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain D: N.99, W.227 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain D: N.109, S.216, Y.217, Q.218 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain D: H.115, N.119 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain D: K.116, N.167, S.169, Y.219 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain D: G.159, N.224 Ligand excluded by PLIP NAG.21: 7 residues within 4Å: Chain E: S.111, I.113, K.116, Q.165, N.167, S.169, Y.219 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain E: K.88, N.89, H.92 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain E: M.80, N.99 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain E: G.159, G.160, K.161, N.224 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain F: N.131 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain F: N.136, T.138 Ligand excluded by PLIP NAG.27: 7 residues within 4Å: Chain D: W.196, G.197 Chain F: Y.104, N.106, S.108, V.129, Y.134 Ligand excluded by PLIP NAG.28: 6 residues within 4Å: Chain E: Q.69 Chain G: K.32, C.33, Y.112, N.114, T.116 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain G: N.136, T.138 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain H: 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: 8 residues within 4Å: Chain C: S.234, R.235, S.237 Chain H: N.106, S.108, V.129, G.132, Y.134 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain H: N.136, 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

Rabbit polyclonal Fv heavy chain: A
Rabbit polyclonal Fv light chain: B
Glycoprotein G1: CDE
Glycoprotein G2: FGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
C

D
A

E
B

F
a

G
b

H
c

Rabbit polyclonal Fv heavy chain

Rabbit polyclonal Fv light chain

Glycoprotein G1

Glycoprotein G2

Related Entries With Identical Sequence