SMTL ID : 8tyc.1

Lassa GPC (strain Josiah) bound to rabbit polyclonal base-targeting antibody Base-1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-3-mer

Ligands

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

NAG-NAG.1: 2 residues within 4Å: Chain A: N.119, D.156 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: K.88, N.89, N.90, S.91, H.92 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.99 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.109, S.216, Y.217 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 7 residues within 4Å: Chain A: S.111, N.114, Q.165, N.167, S.169, H.170, Y.219 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 6 residues within 4Å: Chain A: N.158, G.159, G.160, N.224, T.225, T.226 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: M.80, N.99, E.100 Ligands: NAG-NAG-BMA.14 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain B: F.117, C.118, N.119, C.155 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.117 NAG-NAG.13: 4 residues within 4Å: Chain B: K.88, N.89, S.91, H.92 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain C: F.117, N.119 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 5 residues within 4Å: Chain C: K.88, N.89, N.90, S.91, H.92 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 5 residues within 4Å: Chain C: N.158, G.159, N.224, T.225, T.226 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 7 residues within 4Å: Chain A: Q.69 Chain F: K.32, C.33, F.34, Y.112, N.114, T.121 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 1 residues within 4Å: Chain G: N.136 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 7 residues within 4Å: Chain C: Q.69 Chain H: K.32, C.33, F.34, Y.112, N.114, T.121 No protein-ligand interaction detected (PLIP)

7 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.2: 6 residues within 4Å: Chain A: E.76, T.77, N.79, N.99, W.227 Chain F: W.24 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 4 residues within 4Å: Chain B: D.130, G.160, K.161, N.224 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 7 residues within 4Å: Chain B: S.111, I.113, N.114, Q.165, N.167, S.169, Y.219 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 9 residues within 4Å: Chain B: E.76, T.77, N.79, M.80, N.99, W.227 Chain G: R.23, W.24 Ligands: NAG-NAG.8 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:R.23, G:W.24 NAG-NAG-BMA.16: 8 residues within 4Å: Chain C: E.76, T.77, N.79, M.80, N.99, W.227 Chain H: W.24 Ligands: NAG.28 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 8 residues within 4Å: Chain C: S.111, I.113, Q.165, N.167, S.169, H.170, Y.172, Y.219 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 8 residues within 4Å: Chain B: Q.69 Chain G: K.32, C.33, F.34, Y.112, N.114, G.119, T.121 No protein-ligand interaction detected (PLIP)

1 x NAG- FUC: alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-FUC.12: 3 residues within 4Å: Chain B: N.109, S.216, Q.218 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.109, B:S.216

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.18: 4 residues within 4Å: Chain C: N.109, S.216, Y.217, Q.218 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.21: 13 residues within 4Å: Chain A: G.197, D.229, C.231, Q.232, F.233, S.234, R.235, S.237 Chain F: N.106, S.108, V.129, G.132, Y.134 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain A Hydrophobic interactions: F:Y.134 Hydrogen bonds: A:Q.232 NAG-NAG-BMA-MAN-MAN-MAN.24: 14 residues within 4Å: Chain B: G.197, D.229, C.231, Q.232, F.233, S.234, R.235, S.237 Chain G: N.106, S.108, V.129, G.132, S.133, Y.134 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:C.231, B:Q.232 NAG-NAG-BMA-MAN-MAN-MAN.26: 15 residues within 4Å: Chain C: M.75, G.197, D.229, C.231, Q.232, F.233, S.234, R.235, S.237 Chain H: N.106, S.108, V.129, G.132, S.133, Y.134 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain C Hydrophobic interactions: H:Y.134 Hydrogen bonds: C:Q.232

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

NAG.28: 4 residues within 4Å: Chain C: M.80, N.99, E.100 Ligands: NAG-NAG-BMA.16 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:E.100 NAG.29: 2 residues within 4Å: Chain F: N.136, H.139 No protein-ligand interaction detected (PLIP) NAG.30: 2 residues within 4Å: Chain A: C.207 Chain F: N.131 No protein-ligand interaction detected (PLIP) NAG.31: 4 residues within 4Å: Chain G: C.101, I.102, S.130, N.131 No protein-ligand interaction detected (PLIP) NAG.32: 1 residues within 4Å: Chain H: N.136 No protein-ligand interaction detected (PLIP) NAG.33: 3 residues within 4Å: Chain C: Y.200 Chain H: N.131, G.132 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brouwer, P.J.M. et al., Mapping of vaccine-induced humoral responses to the Lassa virus glycoprotein reveals off-target and immunodominant responses. To Be Published

Release Date

2024-09-11

Peptides

Glycoprotein G1: ABC
Polyclonal antibody Base-1 heavy chain: D
Polyclonal antibody Base-1 light chain: E
Glycoprotein G2, 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase fusion protein: 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 G1

Polyclonal antibody Base-1 heavy chain

Polyclonal antibody Base-1 light chain

Glycoprotein G2, 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase fusion protein

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