SMTL ID : 7pqz.1

Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with FI-3A and FD-11A Fabs

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-1-1-1-1-1-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: 2 residues within 4Å: Chain A: G.16, N.20 No protein-ligand interaction detected (PLIP)

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 7 residues within 4Å: Chain A: K.94, Y.130, Q.170 Chain B: V.100 Chain C: Y.32, Y.91 Ligands: PO4.3 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:Y.130, A:Y.130, A:Q.170, C:Y.91, C:Y.91 Salt bridges: A:K.94 PO4.3: 5 residues within 4Å: Chain A: K.94 Chain B: Y.33, D.98 Chain C: Y.91 Ligands: PO4.2 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.98 Salt bridges: A:K.94

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
FI-3A Fab heavy chain: B
FI-3A Fab light chain: C
FD-11A Fab heavy chain: D
FD-11A Fab light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
H

C
L

D
A

E
B

Spike protein S1

FI-3A Fab heavy chain

FI-3A Fab light chain

FD-11A Fab heavy chain

FD-11A Fab light chain

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