SMTL ID : 7sgf.1

Lassa virus glycoprotein construct (Josiah GPC-I53-50A) in complex with LAVA01 antibody

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-3-3-mer

Ligands

9 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: 9 residues within 4Å: Chain A: E.76, T.77, N.79, M.80, N.99, E.228 Chain B: R.282, W.283 Ligands: NAG.28 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.282, B:R.282 NAG-NAG-BMA.5: 6 residues within 4Å: Chain A: S.111, N.114, N.167, S.169, Y.219 Ligands: NAG-NAG-BMA-MAN-MAN.3 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 11 residues within 4Å: Chain A: M.75, G.197, F.233, S.234, S.237 Chain B: N.365, S.367, V.388, G.391, S.392, Y.393 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.393 NAG-NAG-BMA.10: 9 residues within 4Å: Chain E: E.76, T.77, N.79, M.80, N.99, E.228 Chain F: R.282, W.283 Ligands: NAG.30 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.282, F:R.282 NAG-NAG-BMA.14: 6 residues within 4Å: Chain E: S.111, N.114, N.167, S.169, Y.219 Ligands: NAG-NAG-BMA-MAN-MAN.12 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 11 residues within 4Å: Chain E: M.75, G.197, F.233, S.234, S.237 Chain F: N.365, S.367, V.388, G.391, S.392, Y.393 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:Y.393 NAG-NAG-BMA.19: 9 residues within 4Å: Chain I: E.76, T.77, N.79, M.80, N.99, E.228 Chain J: R.282, W.283 Ligands: NAG.32 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:R.282, J:R.282 NAG-NAG-BMA.23: 6 residues within 4Å: Chain I: S.111, N.114, N.167, S.169, Y.219 Ligands: NAG-NAG-BMA-MAN-MAN.21 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 11 residues within 4Å: Chain I: M.75, G.197, F.233, S.234, S.237 Chain J: N.365, S.367, V.388, G.391, S.392, Y.393 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:Y.393

9 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.89, N.90, S.91, H.92 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: F.117, N.119 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 8 residues within 4Å: Chain A: Q.69, L.71 Chain B: E.289, K.291, N.373, T.375, G.378, T.380 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.289, B:K.291 NAG-NAG.11: 4 residues within 4Å: Chain E: N.89, N.90, S.91, H.92 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain E: F.117, N.119 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 8 residues within 4Å: Chain E: Q.69, L.71 Chain F: E.289, K.291, N.373, T.375, G.378, T.380 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:E.289, F:K.291 NAG-NAG.20: 4 residues within 4Å: Chain I: N.89, N.90, S.91, H.92 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 2 residues within 4Å: Chain I: F.117, N.119 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 8 residues within 4Å: Chain I: Q.69, L.71 Chain J: E.289, K.291, N.373, T.375, G.378, T.380 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:E.289, J:K.291

3 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.3: 8 residues within 4Å: Chain A: N.109, N.178, S.216, Y.217, Q.218 Chain D: N.35, S.60 Ligands: NAG-NAG-BMA.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.178 NAG-NAG-BMA-MAN-MAN.12: 8 residues within 4Å: Chain E: N.109, N.178, S.216, Y.217, Q.218 Chain H: N.35, S.60 Ligands: NAG-NAG-BMA.14 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.178 NAG-NAG-BMA-MAN-MAN.21: 8 residues within 4Å: Chain I: N.109, N.178, S.216, Y.217, Q.218 Chain L: N.35, S.60 Ligands: NAG-NAG-BMA.23 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:N.178

3 x NAG- NAG- BMA- FUC: 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-FUC.7: 6 residues within 4Å: Chain B: C.360, P.362, S.389, N.390 Chain C: F.72, F.74 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.72 Hydrogen bonds: C:F.74 NAG-NAG-BMA-FUC.16: 6 residues within 4Å: Chain F: C.360, P.362, S.389, N.390 Chain G: F.72, F.74 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:F.72 Hydrogen bonds: G:F.74 NAG-NAG-BMA-FUC.25: 6 residues within 4Å: Chain J: C.360, P.362, S.389, N.390 Chain K: F.72, F.74 2 PLIP interactions: 2 interactions with chain K Hydrophobic interactions: K:F.72 Hydrogen bonds: K:F.74

3 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.8: 3 residues within 4Å: Chain B: N.395, T.397, H.398 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.17: 3 residues within 4Å: Chain F: N.395, T.397, H.398 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.26: 3 residues within 4Å: Chain J: N.395, T.397, H.398 No protein-ligand interaction detected (PLIP)

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

NAG.28: 4 residues within 4Å: Chain A: M.80, N.99, E.100 Ligands: NAG-NAG-BMA.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.99 NAG.29: 5 residues within 4Å: Chain A: G.159, G.160, N.224, T.225, T.226 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.226 NAG.30: 4 residues within 4Å: Chain E: M.80, N.99, E.100 Ligands: NAG-NAG-BMA.10 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.99 NAG.31: 5 residues within 4Å: Chain E: G.159, G.160, N.224, T.225, T.226 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:T.226 NAG.32: 4 residues within 4Å: Chain I: M.80, N.99, E.100 Ligands: NAG-NAG-BMA.19 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:N.99 NAG.33: 5 residues within 4Å: Chain I: G.159, G.160, N.224, T.225, T.226 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:T.226

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brouwer, P.J.M. et al., Lassa virus glycoprotein nanoparticles elicit neutralizing antibody responses and protection. Cell Host Microbe (2022)

Release Date

2022-10-12

Peptides

GPC-I53-50A: ABEFIJ
LAVA01 mAb - Heavy Chain: CGK
LAVA01 mAb - Light Chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
a

E
B

F
b

I
C

J
c

C
H

G
J

K
M

D
L

H
K

L
N

GPC-I53-50A

LAVA01 mAb - Heavy Chain

LAVA01 mAb - Light Chain

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