SMTL ID : 8bse.1

CRYSTAL STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN (RBD) in complex with 1D1 Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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, L.50 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.50 Hydrogen bonds: A:N.25

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: R.85, E.88, K.99, I.100, Y.135, Y.177, Y.187 Chain C: Y.32, D.92 6 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: C:Y.32, C:D.92, A:R.85, A:K.99, A:Y.177 Water bridges: B:Y.100 GOL.3: 4 residues within 4Å: Chain B: S.17, L.18, R.19, Q.81 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.81 Water bridges: B:S.17, B:S.17 GOL.4: 3 residues within 4Å: Chain A: Y.171 Chain B: Y.100, G.101 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.101 GOL.5: 6 residues within 4Å: Chain B: V.165, H.166 Chain C: T.164, E.165, Q.166, D.167 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:E.165, C:D.167, B:V.165, B:H.166 Water bridges: C:T.164, C:D.167, B:T.167 GOL.7: 8 residues within 4Å: Chain C: Q.37, K.39, K.45, P.59, R.61, F.62, E.81, D.82 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:Q.37, C:K.39, C:K.45, C:G.57, C:R.61, C:E.81, C:E.81, C:D.82 Water bridges: C:Q.37

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.6: 8 residues within 4Å: Chain B: Y.147, E.150, P.151, V.152, F.168, P.169, A.170, L.180 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.150, B:V.152, B:V.152, B:F.168, B:A.170 Water bridges: B:V.152

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 glycoprotein: A
1D1 FAB HEAVY CHAIN: B
1D1 FAB LIGHT CHAIN: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

Spike glycoprotein

1D1 FAB HEAVY CHAIN

1D1 FAB LIGHT CHAIN

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