SMTL ID : 7urs.1

Crystal Structure of SARS-CoV-2 S delta variant receptor-binding domain (RBD) in complex CoV11 Fab crystal form 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 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.20, G.21, N.25 No protein-ligand interaction detected (PLIP)

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

PO4.2: 5 residues within 4Å: Chain A: R.28, S.31, Y.33, N.132, R.134 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.31, A:Y.33 Water bridges: A:S.31 Salt bridges: A:R.28, A:R.134 PO4.3: 4 residues within 4Å: Chain A: S.57, G.86, V.185, Y.190 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.57, A:Y.190 Water bridges: A:V.89

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 3 residues within 4Å: Chain A: R.139, K.144, E.147 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.144 MPD.5: 9 residues within 4Å: Chain A: K.99 Chain B: V.50, Y.52, F.58 Chain C: G.93, S.94, S.95, P.96, G.97 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tolbert, W.D. et al., The molecular basis of the neutralization breadth of the RBD-specific antibody CoV11. Front Immunol (2023)

Release Date

2022-05-04

Peptides

Spike protein S1: A
COV11 Fab HEAVY CHAIN: B
COV11 Fab HEAVY CHAIN: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

Spike protein S1

COV11 Fab HEAVY CHAIN

COV11 Fab HEAVY CHAIN

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