SMTL ID : 7uds.1

Structure of lineage I (Pinneo) Lassa virus glycoprotein bound to Fab 25.10C

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

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.1: 11 residues within 4Å: Chain B: R.101, R.102, A.103, S.104 Chain E: V.51, N.52 Chain G: E.75, T.76, N.78, M.79 Chain J: W.24 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.52, E:N.52 NAG-NAG-BMA-MAN-MAN.6: 11 residues within 4Å: Chain C: V.51, N.52 Chain D: R.101, R.102, A.103, S.104 Chain H: E.75, T.76, N.78, M.79 Chain K: W.24 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.52, C:N.52 NAG-NAG-BMA-MAN-MAN.11: 11 residues within 4Å: Chain A: R.101, R.102, A.103, S.104 Chain F: V.51, N.52 Chain I: E.75, T.76, N.78, M.79 Chain L: W.24 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.52

8 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 G: K.87, N.88, S.90, H.91 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain G: N.108, S.215, Q.217 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:S.215, G:S.215 NAG-NAG.5: 5 residues within 4Å: Chain G: G.159, K.160, N.223, T.224, T.225 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain H: K.87, N.88, S.90, H.91 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain H: N.108, S.215 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain H: G.159, K.160, N.223, T.224, T.225 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain I: K.87, N.88, S.90, H.91 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain I: G.159, K.160, N.223, T.224 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN: 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.3: 9 residues within 4Å: Chain B: K.31, Y.32, R.98, I.100, D.109 Chain E: E.54, T.55 Chain G: N.98, E.99 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.109, B:R.98 NAG-NAG-BMA-MAN.8: 8 residues within 4Å: Chain C: E.54, T.55 Chain D: K.31, Y.32, R.98, I.100 Chain H: N.98, E.99 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:E.54, C:E.54, C:T.55, D:R.98 NAG-NAG-BMA-MAN.13: 7 residues within 4Å: Chain A: K.31, Y.32, R.98, I.100 Chain F: T.55 Chain I: N.98, E.99 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain A Hydrogen bonds: F:T.55, F:T.55, A:R.98, A:R.98

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

NAG.15: 6 residues within 4Å: Chain G: N.113, H.114, K.115, S.153, N.166, Y.218 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:K.115 Hydrogen bonds: G:S.153, G:N.166 NAG.16: 2 residues within 4Å: Chain G: F.116, N.118 No protein-ligand interaction detected (PLIP) NAG.17: 6 residues within 4Å: Chain H: H.114, K.115, S.153, Q.164, N.166, Y.218 2 PLIP interactions: 2 interactions with chain H Hydrophobic interactions: H:K.115 Hydrogen bonds: H:N.166 NAG.18: 3 residues within 4Å: Chain H: F.116, C.117, N.118 No protein-ligand interaction detected (PLIP) NAG.19: 2 residues within 4Å: Chain I: N.108, S.215 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:N.108, I:N.108, I:S.215 NAG.20: 7 residues within 4Å: Chain I: N.113, H.114, K.115, S.153, Q.164, N.166, Y.218 4 PLIP interactions: 4 interactions with chain I Hydrophobic interactions: I:K.115 Hydrogen bonds: I:S.153, I:Q.164, I:N.166 NAG.21: 3 residues within 4Å: Chain I: F.116, C.117, N.118 No protein-ligand interaction detected (PLIP) NAG.22: 5 residues within 4Å: Chain J: K.32, C.33, F.34, Y.112, N.114 6 PLIP interactions: 6 interactions with chain J Hydrophobic interactions: J:K.32, J:F.34, J:Y.112 Hydrogen bonds: J:K.32, J:Y.112, J:N.114 NAG.23: 5 residues within 4Å: Chain K: K.32, C.33, F.34, Y.112, N.114 6 PLIP interactions: 6 interactions with chain K Hydrophobic interactions: K:K.32, K:F.34, K:Y.112 Hydrogen bonds: K:K.32, K:Y.112, K:N.114 NAG.24: 5 residues within 4Å: Chain L: K.32, C.33, F.34, Y.112, N.114 6 PLIP interactions: 6 interactions with chain L Hydrophobic interactions: L:K.32, L:F.34, L:Y.112 Hydrogen bonds: L:K.32, L:Y.112, L:N.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Buck, T.K. et al., Neutralizing Antibodies against Lassa Virus Lineage I. Mbio (2022)

Release Date

2022-06-15

Peptides

25.10C Fab Heavy Chain: ABD
25.10C Fab Light Chain: CEF
Glycoprotein G1: GHI
Glycoprotein G2: JKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
F

D
H

C
L

E
G

F
E

G
A

H
C

I
B

J
a

K
c

L
b

25.10C Fab Heavy Chain

25.10C Fab Light Chain

Glycoprotein G1

Glycoprotein G2

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