SMTL ID : 8tye.1

Lassa GPC (strain Josiah) bound to rabbit polyclonal fusion-peptide-targeting antibody FP-1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-3-3-mer

Ligands

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

NAG-FUC.1: 3 residues within 4Å: Chain C: N.109, S.216, Q.218 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.218

2 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.2: 10 residues within 4Å: Chain B: X.31, X.67, X.68 Chain C: E.76, T.77, N.79, M.80, W.227 Chain F: W.24, I.64 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.16: 11 residues within 4Å: Chain D: C.231, Q.232, F.233, S.234, R.235 Chain G: N.106, S.108, V.129, G.132, S.133, Y.134 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:R.235 Hydrogen bonds: D:R.235

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.3: 4 residues within 4Å: Chain C: F.117, N.119, D.122, N.158 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.7: 5 residues within 4Å: Chain D: H.115, F.117, N.119, D.122, D.156 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.4: 5 residues within 4Å: Chain C: I.113, Q.165, N.167, S.169, Y.219 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain C: K.161, N.224, T.225 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain D: E.76, T.77, N.79 Chain G: W.24, I.64 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain D: K.116, N.167, Y.219 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain D: G.159, G.160, K.161, N.224 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain E: E.76, T.77, N.79 Chain H: W.24, I.64 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:I.64 NAG-NAG.11: 3 residues within 4Å: Chain E: N.109, S.216, Y.217 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain E: I.113, K.116, N.167, S.169, Y.219 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain E: G.159, G.160, N.224, T.225 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 7 residues within 4Å: Chain D: Q.69 Chain G: K.32, Y.112, N.114, H.115, T.116, T.121 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 6 residues within 4Å: Chain E: Q.69 Chain H: L.31, Y.112, N.114, G.119, T.121 No protein-ligand interaction detected (PLIP)

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.14: 8 residues within 4Å: Chain C: Q.232, F.233, S.234, R.235 Chain F: N.106, S.108, G.132, Y.134 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.235, C:Q.232 NAG-NAG-BMA.15: 9 residues within 4Å: Chain A: X.100, X.101, X.102, X.103 Chain C: Q.69 Chain F: Y.112, N.114, H.115, T.116 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 9 residues within 4Å: Chain E: Q.232, F.233, S.234, R.235, S.237 Chain H: N.106, S.108, G.132, Y.134 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain E Hydrophobic interactions: H:Y.134 Hydrogen bonds: E:Q.232

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

NAG.20: 3 residues within 4Å: Chain C: N.89, H.92, H.230 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.89 NAG.21: 3 residues within 4Å: Chain C: M.80, N.99, W.227 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.227 Hydrogen bonds: C:N.99 NAG.22: 4 residues within 4Å: Chain D: N.109, S.216, Y.217, Q.218 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.217 NAG.23: 4 residues within 4Å: Chain D: N.89, S.91, H.92, Y.217 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.89, D:S.91, D:H.92 NAG.24: 2 residues within 4Å: Chain D: N.99, E.100 No protein-ligand interaction detected (PLIP) NAG.25: 5 residues within 4Å: Chain E: K.88, N.89, S.91, H.92, Y.217 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.91, E:S.91 NAG.26: 2 residues within 4Å: Chain E: N.99, E.100 No protein-ligand interaction detected (PLIP) NAG.27: 3 residues within 4Å: Chain E: F.117, N.119, D.122 No protein-ligand interaction detected (PLIP) NAG.28: 1 residues within 4Å: Chain F: N.131 No protein-ligand interaction detected (PLIP) NAG.29: 3 residues within 4Å: Chain F: N.136, T.138, H.139 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.136 NAG.30: 3 residues within 4Å: Chain G: Y.134, N.136, E.137 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.136 NAG.31: 2 residues within 4Å: Chain D: C.207 Chain G: N.131 No protein-ligand interaction detected (PLIP) NAG.32: 1 residues within 4Å: Chain H: N.131 No protein-ligand interaction detected (PLIP) NAG.33: 1 residues within 4Å: Chain H: N.136 No protein-ligand interaction detected (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

2024-09-11

Peptides

Polyclonal Fv heavy chain: A
Polyclonal Fv light chain: B
Glycoprotein GP1: CDE
Glycoprotein GP2: FGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
C

D
A

E
B

F
c

G
a

H
b

Polyclonal Fv heavy chain

Polyclonal Fv light chain

Glycoprotein GP1

Glycoprotein GP2

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