SMTL ID : 8bsf.1

CRYSTAL STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN (RBD-beta variant) in complex with 3D2 Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: G.21, N.25 Chain B: Y.104 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.104

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 1 residues within 4Å: Chain B: T.128 No protein-ligand interaction detected (PLIP) GOL.3: 7 residues within 4Å: Chain C: Q.38, K.46, I.59, P.60, F.63, G.82, D.83 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.38, C:K.46, C:K.46, C:D.83 GOL.4: 6 residues within 4Å: Chain C: A.115, A.116, P.117, H.201, E.202, S.204 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.201, C:S.204 Water bridges: C:H.201 GOL.5: 9 residues within 4Å: Chain B: H.176, F.178, V.193 Chain C: S.118, V.119, T.120, L.139, I.140, S.141 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.118, C:T.120, C:T.120, C:L.139, C:S.141, C:S.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Boonkrai, C. et al., Efficacy of the combination of monoclonal antibodies against the SARS-CoV-2 Beta and Delta variants. Plos One (2023)

Release Date

2023-05-17

Peptides

Spike protein S1: A
3D2 FAB HEAVY CHAIN: B
3D2 FAB LIGHT CHAIN: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

Spike protein S1

3D2 FAB HEAVY CHAIN

3D2 FAB LIGHT CHAIN

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