SMTL ID : 7k8o.1

Crystal structure of an anti-SARS-CoV-2 human neutralizing antibody Fab fragment, C002

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-1-1-mer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: F.27, T.28, I.31, Y.32 Ligands: GOL.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.28, A:T.28, A:Y.32, A:Y.32 GOL.2: 4 residues within 4Å: Chain A: S.143, G.144, G.145, T.146 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.145 GOL.3: 5 residues within 4Å: Chain A: Y.32, G.100, R.101, P.102 Ligands: GOL.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.32, A:R.101, A:R.101 GOL.5: 3 residues within 4Å: Chain B: S.91, Y.92, R.96 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.91, B:R.96, B:R.96 GOL.6: 3 residues within 4Å: Chain B: Q.37, K.45, P.59 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.37 Water bridges: B:R.61 GOL.7: 5 residues within 4Å: Chain A: P.134, K.225 Chain B: S.121, D.122, E.123 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.122, B:D.122, B:E.123, B:E.123, B:E.123, A:K.225, A:K.225 GOL.8: 3 residues within 4Å: Chain B: P.8, S.9, S.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.9, B:S.10, B:S.10 GOL.9: 2 residues within 4Å: Chain B: P.59, S.60 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.60, B:S.60

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 1 residues within 4Å: Chain B: R.211 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.211

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

C002 Fab Heavy Chain: A
C002 Fab Light Chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C002 Fab Heavy Chain

C002 Fab Light Chain

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