SMTL ID : 7k8x.1

Structure of the SARS-CoV-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, C121 (State 1)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.90 Å

Oligo State

hetero-3-2-2-mer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: F.59, N.61 Ligand excluded by PLIP NAG.2: 4 residues within 4Å: Chain A: N.122, T.124, N.125, V.127 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain A: N.282 Chain C: K.558 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: N.331, Q.580, T.581 Ligand excluded by PLIP NAG.5: 4 residues within 4Å: Chain A: F.338, G.339, N.343, V.367 Ligand excluded by PLIP NAG.6: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: N.717, F.718, L.922, Q.926 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: A.706, A.713, N.1074 Chain B: Q.895 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: I.1132, N.1134 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain B: T.108, N.234, T.236, R.237 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain B: N.280, E.281, N.282, T.286 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain B: N.616, T.618 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain B: N.709 Chain C: I.794, D.796 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.19: 5 residues within 4Å: Chain B: N.331, P.579, Q.580, T.581, L.582 Ligand excluded by PLIP NAG.20: 5 residues within 4Å: Chain C: N.122, T.124, N.125, V.127, K.129 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain C: T.108, N.234 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain C: E.281, N.282 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain C: E.132, N.165 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain C: N.331, I.332, Q.580 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain C: D.614, N.616 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: D.796 Chain C: N.709 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain C: N.717, N.919, L.922, Q.926, Q.1071 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 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: DE
C121 Fab Light chain: FG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

Spike glycoprotein

C121 Fab Heavy chain

C121 Fab Light chain

Related Entries With Identical Sequence