SMTL ID : 7l7d.1

Crystal structure of SARS-CoV-2 spike RBD in complex with human monoclonal antibody AZD8895

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-1-mer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: V.93, Q.115, G.116 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.116 GOL.2: 5 residues within 4Å: Chain A: M.2, Y.100, N.107, D.111 Chain B: T.57 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.57, A:N.107 Water bridges: B:T.57, B:T.57 GOL.3: 4 residues within 4Å: Chain B: N.160, L.183, S.184, D.187 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.160, B:S.184, B:D.187, B:D.187 GOL.4: 5 residues within 4Å: Chain A: H.174 Chain B: T.166, E.167, Q.168, D.169 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.169, B:D.169, A:H.174 Water bridges: B:T.166, A:T.175 GOL.6: 8 residues within 4Å: Chain C: T.47, K.49, Y.51, V.78, R.79, I.81, A.82, V.104 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.51 Water bridges: C:K.49 GOL.7: 6 residues within 4Å: Chain C: F.13, N.14, S.44, F.45, W.107 Ligands: NAG.5 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.14

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.5: 3 residues within 4Å: Chain C: G.10, N.14 Ligands: GOL.7 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, J. et al., Genetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail. Nat Microbiol (2021)

Release Date

2021-09-01

Peptides

heavy chain of human monoclonal antibody Fab AZD8895: A
light chain of human monoclonal antibody Fab AZD8895: B
Spike protein S1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
E

heavy chain of human monoclonal antibody Fab AZD8895

light chain of human monoclonal antibody Fab AZD8895

Spike protein S1

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