SMTL ID : 6xcm.1

Structure of the SARS-CoV-2 spike glycoprotein in complex with the C105 neutralizing antibody Fab fragment (state 1)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-mer

Ligands

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.1: 2 residues within 4Å: Chain A: N.280, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.717, L.922 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.922 NAG-NAG.4: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain B: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.717, L.922, N.925 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.922, B:N.925 NAG-NAG.8: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain C: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain C: G.339, N.343, L.368, S.371 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP)

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

NAG-FUC.3: 2 residues within 4Å: Chain A: N.801, S.803 No protein-ligand interaction detected (PLIP)

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.6: 2 residues within 4Å: Chain B: H.1083, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.13: 1 residues within 4Å: Chain C: N.1134 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.11: 4 residues within 4Å: Chain C: N.717, L.922, N.925, Q.926 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.922, C:N.925

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

NAG.14: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: N.122, T.124, N.125, V.127 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.234 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: G.339, N.343 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: N.616, Q.644 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain A: N.1074 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.709, G.1131 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.26: 5 residues within 4Å: Chain B: N.122, A.123, T.124, V.127, K.129 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: T.108, N.234, T.236 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain B: F.338, G.339, F.342, N.343, L.368 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.616, T.618 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: A.706, N.1074 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain C: N.122, T.124, V.127, K.129 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.165 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: N.234, T.236 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barnes, C.O. et al., Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies. Cell (2020)

Release Date

2020-07-01

Peptides

Spike glycoprotein: ABC
C105 Fab Heavy Chain: DE
C105 Fab Light Chain: FG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

E
N

F
L

G
S

Spike glycoprotein

C105 Fab Heavy Chain

C105 Fab Light Chain

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