SMTL ID : 7pr0.1 (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 Compare

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: 2 residues within 4Å: Chain A: N.20, S.50 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.20

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: W.30, F.141, R.143 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.32, A:R.143 SO4.4: 4 residues within 4Å: Chain B: K.44, Q.50, L.52, P.64 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.50, B:Q.50 Salt bridges: B:K.44 SO4.7: 2 residues within 4Å: Chain B: K.214 Chain C: K.145 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Salt bridges: C:K.145, B:K.214

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

NO3.3: 5 residues within 4Å: Chain B: Y.37, L.97, T.99 Chain C: V.109, L.110 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.110 NO3.6: 5 residues within 4Å: Chain C: S.52, S.53, S.54, S.56, T.103 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.52, C:S.52, C:S.54, C:T.103

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 3 residues within 4Å: Chain B: Y.35, N.36, L.55 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: G.123 Chain C: G.112 Ligand excluded by PLIP

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
E

B
L

C
H

Spike protein S1

FD-5D Fab light chain

FD-5D Fab heavy chain

Related Entries With Identical Sequence