SMTL ID : 7mxp.1

Cryo-EM structure of NTD-directed neutralizing antibody LP5 Fab in complex with SARS-CoV-2 S2P spike

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

3 x NAG- NAG- BMA- MAN- NAG- NAG- BMA- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)][beta-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-NAG-NAG-BMA-FUC.1: 11 residues within 4Å: Chain B: C.15, N.17, R.21 Chain D: D.54, G.55, S.56, N.57, T.69, Q.82, T.84, S.85 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.82, D:Q.82, D:T.84, D:Q.82 NAG-NAG-BMA-MAN-NAG-NAG-BMA-FUC.3: 10 residues within 4Å: Chain A: N.17 Chain F: S.56, N.57, K.58, F.59, F.68, T.69, Q.82, T.84, S.85 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:K.58, F:F.68, F:Q.82, F:Q.82 NAG-NAG-BMA-MAN-NAG-NAG-BMA-FUC.6: 12 residues within 4Å: Chain C: N.17 Chain H: S.56, N.57, K.58, F.59, G.66, R.67, F.68, T.69, Q.82, T.84, S.85 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain H Hydrophobic interactions: C:N.17 Hydrogen bonds: H:F.68, H:Q.82, H:T.84

3 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: 3 residues within 4Å: Chain B: N.149, S.151, W.152 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.152 NAG-NAG.4: 3 residues within 4Å: Chain A: N.149, S.151, W.152 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.152 NAG-NAG.7: 3 residues within 4Å: Chain C: N.149, S.151, W.152 No protein-ligand interaction detected (PLIP)

1 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.5: 6 residues within 4Å: Chain C: N.122, T.124, N.125, V.127, F.157, V.171 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.171 Hydrogen bonds: C:N.125

28 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.8: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain A: N.331, P.579, Q.580, L.582 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: E.340, N.343, A.344 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.122, T.124, N.125 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.164, N.165 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: S.60 Ligands: NAG.25 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: N.616, Q.644 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: N.709, N.710 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain B: N.1074 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: S.112, K.113, E.132 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain B: N.122, T.124, N.125, S.155, F.157 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: Y.28, N.61 Ligands: NAG.17 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.164, N.165 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: K.558 Chain C: G.283, T.284 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain C: N.331, Q.580, L.582 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain C: F.338, G.339, F.342, N.343 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: N.709, N.710 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: A.713, K.1073, N.1074 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.164, N.165 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Madan, B. et al., Antibody screening at reduced pH enables preferential selection of potently neutralizing antibodies targeting SARS-CoV-2. Aiche J (2021)

Release Date

2022-05-25

Peptides

Spike glycoprotein: ABC
LP5 Fab Heavy Chain: DFH
LP5 Fab Light Chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
G

F
I

H
H

E
J

G
K

I
L

Spike glycoprotein

LP5 Fab Heavy Chain

LP5 Fab Light Chain