SMTL ID : 8sgu.1

Crystal structure of the SARS-CoV-2 receptor binding domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

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

NAG-NAG-FUC.1: 9 residues within 4Å: Chain A: F.8, G.9, N.13, V.37, L.38 Ligands: NAG.2, NAG.3, FUC.4, GOL.9 No protein-ligand interaction detected (PLIP)

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

NAG.2: 10 residues within 4Å: Chain A: F.8, G.9, N.13, V.37, L.38 Ligands: NAG-NAG-FUC.1, NAG-NAG-FUC.1, NAG-NAG-FUC.1, NAG.3, FUC.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.13 NAG.3: 6 residues within 4Å: Ligands: NAG-NAG-FUC.1, NAG-NAG-FUC.1, NAG-NAG-FUC.1, NAG.2, FUC.4, GOL.9 No protein-ligand interaction detected (PLIP)

1 x FUC: alpha-L-fucopyranose(Non-functional Binders)

FUC.4: 5 residues within 4Å: Ligands: NAG-NAG-FUC.1, NAG-NAG-FUC.1, NAG-NAG-FUC.1, NAG.2, NAG.3 No protein-ligand interaction detected (PLIP)

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: F.12, N.13, S.43, W.106 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.43 Water bridges: A:N.13, A:W.106 GOL.6: 4 residues within 4Å: Chain A: F.17, S.19, N.120, Y.121 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.19, A:Y.121 Water bridges: A:S.19, A:S.19, A:Y.121 GOL.7: 3 residues within 4Å: Chain A: R.25, F.134, R.136 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.136, A:R.136 Water bridges: A:R.25, A:R.136 GOL.8: 7 residues within 4Å: Chain A: N.30, C.31, A.192, T.193, V.194, C.195, H.202 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.192, A:C.195, A:C.195 GOL.9: 2 residues within 4Å: Ligands: NAG-NAG-FUC.1, NAG.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sankhala, R.S. et al., Antibody targeting of conserved sites of vulnerability on the SARS-CoV-2 spike receptor-binding domain. Structure (2024)

Release Date

2023-12-13

Peptides

Spike protein S1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Spike protein S1

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