SMTL ID : 7lm8.1

Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with two cross-neutralizing antibodies CV38-142 and COVA1-16 Fabs isolated from COVID-19 patients

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

hetero-1-1-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.1: 13 residues within 4Å: Chain A: F.20, G.21, F.24, N.25, V.49, L.50 Chain D: R.100, Y.103 Chain E: S.31, Y.49, A.50, S.53 Ligands: EDO.5 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:R.100, E:Y.49, E:S.53, E:S.53 Water bridges: E:S.31

16 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 7 residues within 4Å: Chain A: K.60, Y.62, A.93 Chain B: P.100, R.101, Y.103, Y.115 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: F.111, T.112, S.196, F.197, E.198 Ligand excluded by PLIP EDO.4: 8 residues within 4Å: Chain A: C.61, Y.62, G.63 Chain B: R.101, N.102, Y.103, Y.104, Y.110 Ligand excluded by PLIP EDO.5: 7 residues within 4Å: Chain A: F.24, N.25, S.53, S.55, F.56 Chain D: S.104 Ligands: NAG-NAG-BMA-FUC.1 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: R.28, F.29, S.31, N.132, Y.133 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: R.85, D.87, E.88, Q.91, K.99 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain B: Q.111, R.112 Chain C: Y.32, Y.91, D.92 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain C: Q.37, R.39, K.45, R.61, F.62, E.81, D.82 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain C: K.45, T.56, G.57, V.58 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain D: Y.112 Chain E: S.56 Ligands: EDO.12 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain D: V.2, Y.27, Y.32, R.98 Ligands: EDO.11 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: K.126, V.127 Chain D: T.58, R.59, Y.60, Q.65 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain D: G.8, A.9, P.159, T.161, K.211 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain E: Q.37, K.39, K.45, R.61, F.62, E.81, D.82 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain D: L.151, V.179, S.187, L.188, S.189 Chain E: T.180 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain E: T.5, Q.6, S.7, R.24 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, H. et al., A combination of cross-neutralizing antibodies synergizes to prevent SARS-CoV-2 and SARS-CoV pseudovirus infection. Cell Host Microbe (2021)

Release Date

2021-03-31

Peptides

Spike protein S1: A
COVA1-16 Fab heavy chain: B
COVA1-16 Fab light chain: C
CV38-142 Fab heavy chain: D
CV38-142 Fab light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

D
M

E
N

Spike protein S1

COVA1-16 Fab heavy chain

COVA1-16 Fab light chain

CV38-142 Fab heavy chain

CV38-142 Fab light chain

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