SMTL ID : 7k8v.1

Structure of the SARS-CoV-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, C110

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-mer

Ligands

10 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: 3 residues within 4Å: Chain A: N.234, T.236, R.237 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.1098, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain B: N.801 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain C: N.717 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain C: N.1098, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain C: N.343 No protein-ligand interaction detected (PLIP)

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

NAG.11: 4 residues within 4Å: Chain A: Y.28, T.29, N.30, N.61 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.122, T.124, V.127 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: N.343, V.367, L.368, S.373 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.616, Q.644, T.645 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: N.709, N.710, G.1131 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.801 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain B: N.122 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: T.108, N.234, T.236 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: N.343, V.367 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.709 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.717 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: K.1073, N.1074 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.1098 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain C: T.114, N.234 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain A: D.796 Chain C: N.709 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: E.1072, N.1074 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barnes, C.O. et al., SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies. Nature (2020)

Release Date

2020-10-21

Peptides

Spike glycoprotein: ABC
C110 Fab Heavy Chain: DF
C110 Fab Light Chain: EG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

F
M

E
L

G
N

Spike glycoprotein

C110 Fab Heavy Chain

C110 Fab Light Chain

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