SMTL ID : 7q3q.1

Crystal structure of SARS-CoV-2 RBD in complex with the neutralizing nanobody VHH-12

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain B: F.8, G.9, N.13, F.37 No protein-ligand interaction detected (PLIP)

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 6 residues within 4Å: Chain A: T.36, R.55, W.56, K.57, F.58, I.107 Ligand excluded by PLIP CL.3: 6 residues within 4Å: Chain A: Y.97, Y.98, C.99, G.121, Q.122, G.123 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain B: G.166 Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain B: F.12, N.13, S.43, F.44, W.106 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.13, B:S.43, B:S.43 GOL.5: 5 residues within 4Å: Chain B: F.17, A.18, S.19, N.120, Y.121 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.17 Water bridges: B:S.19, B:N.120 GOL.6: 5 residues within 4Å: Chain B: R.25, F.134, S.184, F.185, E.186 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.25, B:S.184, B:S.184, B:F.185

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

SO4.8: 2 residues within 4Å: Chain B: T.15, R.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.15 Salt bridges: B:R.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fernandez, I. et al., NANOBODIES AGAINST SARS-COV-2 NEUTRALIZE VARIANTS OF CONCERN AND EXPLORE CONFORMATIONAL DIFFERENCES ON THE SPIKE PROTEIN. To Be Published

Release Date

2022-11-16

Peptides

VHH-12: A
Spike glycoprotein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

VHH-12

Spike glycoprotein

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