SMTL ID : 8gb5.2 (3 other biounits)

Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody 25F9

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.35 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 6 residues within 4Å: Chain A: F.6, F.10, N.11, L.36, N.38, S.39 No protein-ligand interaction detected (PLIP)

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

SO4.2: 4 residues within 4Å: Chain A: N.169, G.170, Y.173 Chain B: R.68 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.170, B:R.68 SO4.3: 7 residues within 4Å: Chain B: E.85, R.106, T.108, Y.144, P.145, G.146, Y.176 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.85, B:E.85, B:Y.144, B:G.146 Salt bridges: B:R.106 SO4.4: 3 residues within 4Å: Chain B: S.61, R.63, Q.81 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.61, B:S.61, B:Q.81 Salt bridges: B:R.63

1 x BCN: BICINE(Covalent)

BCN.5: 5 residues within 4Å: Chain B: R.106, P.168, S.169, K.170, Y.176 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.176, B:Y.176 Salt bridges: B:K.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feng, Y. et al., Broadly neutralizing antibodies against sarbecoviruses generated by immunization of macaques with an AS03-adjuvanted COVID-19 vaccine. Sci Transl Med (2023)

Release Date

2023-05-24

Peptides

Spike protein S1: A
25F9 Light chain: B
25F9 Heavy chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

Spike protein S1

25F9 Light chain

25F9 Heavy chain

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