SMTL ID : 7k8y.1

Structure of the SARS-CoV-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, C121 (State 2)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 4.40 Å

Oligo State

hetero-3-1-1-mer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: N.282 Chain C: K.558 Ligand excluded by PLIP NAG.2: 3 residues within 4Å: Chain A: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: N.717, N.919, L.922 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.6: 4 residues within 4Å: Chain A: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: I.1132, N.1134 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain B: N.282 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain B: N.331, P.579, Q.580, L.582 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain B: N.603, T.604 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain B: N.616, T.618 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain B: N.709, N.710 Chain C: D.796 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain B: N.717, L.922, Q.926 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain B: I.1132, N.1134 Ligand excluded by PLIP NAG.16: 5 residues within 4Å: Chain C: N.122, T.124, N.125, V.127, V.171 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain B: K.558 Chain C: E.281, N.282 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain C: N.331, T.333, Q.580 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: D.796 Chain C: N.709, I.1130 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain C: T.716, N.717, F.718, L.922 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain C: A.706, E.1072, K.1073, 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
C121 Fab Heavy chain: D
C121 Fab Light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
E

D
G

E
I

Spike glycoprotein

C121 Fab Heavy chain

C121 Fab Light chain

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