SMTL ID : 8fhy.2 (2 other biounits)

Crystal structure of the SARS-CoV-2 receptor binding domain in complex with neutralizing antibody WRAIR-5021

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

hetero-1-1-1-mer

Ligands

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: R.73, Y.175 Chain C: Q.1, V.2, R.99, V.106 Ligands: GOL.2 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:R.73, A:R.73, C:V.2, C:R.99 GOL.2: 10 residues within 4Å: Chain A: R.73, S.164, Y.165, G.166 Chain C: Q.1, V.2, Y.27, Y.33, R.99 Ligands: GOL.1 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain C Hydrogen bonds: A:R.73, A:G.166, C:Q.1, C:Q.1, C:V.2, C:Y.33, C:R.99, C:R.99 GOL.3: 5 residues within 4Å: Chain A: A.22, W.23, N.24, R.136, I.138 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.24, A:R.136 GOL.4: 1 residues within 4Å: Chain A: S.199 No protein-ligand interaction detected (PLIP) GOL.6: 8 residues within 4Å: Chain B: P.119, Y.186, F.209, N.210, R.211, G.212, E.213 Chain C: K.218 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.186, B:N.210, B:G.212, B:E.213 GOL.7: 10 residues within 4Å: Chain B: Q.160, S.162, S.176, T.178 Chain C: F.170, P.171, V.173, S.181, L.182, S.183 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:F.170, C:S.181, C:S.183, B:S.176, B:T.178 GOL.8: 3 residues within 4Å: Chain C: D.212, K.213, R.214 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.214

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

NAG.5: 3 residues within 4Å: Chain A: N.13, A.14, T.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sankhala, R.S. et al., Diverse array of neutralizing antibodies elicited upon Spike Ferritin Nanoparticle vaccination in rhesus macaques. Nat Commun (2024)

Release Date

2024-01-17

Peptides

Spike protein S1: A
WRAIR-5021 Fab Light chain: B
WRAIR-5021 Fab Heavy chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike protein S1

WRAIR-5021 Fab Light chain

WRAIR-5021 Fab Heavy chain

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