SMTL ID : 8bec.2 (1 other biounit)

Crystal structure of the SARS-CoV-2 S RBD in complex with pT1375 scFV

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-MAN-FUC.1: 9 residues within 4Å: Chain B: F.5, G.6, F.9, N.10, V.34, L.35, N.37, S.38, A.39 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.37, B:S.38, B:A.39

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

SO4.2: 3 residues within 4Å: Chain B: R.13, K.111, N.117 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.117 Water bridges: B:R.13, B:R.13 Salt bridges: B:R.13, B:K.111

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stein, C.S. et al., Activity of broadly neutralizing antibodies against sarbecoviruses: a trade-off between SARS-CoV-2 variants and distant coronaviruses?. To be published

Release Date

2023-11-01

Peptides

pT1375 single-chain Fv: A
Spike protein S1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

pT1375 single-chain Fv

Spike protein S1

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