SMTL ID : 7pr0.2 (2 other biounits)

Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with FD-5D Fab

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.92 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: F.19, N.20, S.50 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain B: K.44, Q.50, L.52, P.64, D.87 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.44, B:K.44, B:D.87

1 x NO3: NITRATE ION(Non-functional Binders)

NO3.3: 6 residues within 4Å: Chain C: S.52, S.53, S.54, S.56, T.57, T.103 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.52, C:S.52, C:S.54, C:S.56, C:T.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, K.A. et al., Structures and therapeutic potential of anti-RBD human monoclonal antibodies against SARS-CoV-2. Theranostics (2022)

Release Date

2022-02-02

Peptides

Spike protein S1: A
FD-5D Fab light chain: B
FD-5D Fab heavy chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike protein S1

FD-5D Fab light chain

FD-5D Fab heavy chain

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