SMTL ID : 6zcz.1

Crystal structure of receptor binding domain of SARS-CoV-2 Spike glycoprotein in ternary complex with EY6A Fab and a nanobody.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: G.16, N.20, V.44 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.44

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

CL.2: 2 residues within 4Å: Chain A: R.34, Y.73 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain B: S.17, N.84 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain C: A.26, N.77 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain C: N.74 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain D: Q.38, G.41 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 3 residues within 4Å: Chain C: S.187 Chain D: S.177, T.179 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, D. et al., Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient. Nat.Struct.Mol.Biol. (2020)

Release Date

2020-06-24

Peptides

Spike protein S1: A
Nanobody: B
EY6A heavy chain: C
EY6A light chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
H

D
L

Spike protein S1

Nanobody

EY6A heavy chain

EY6A light chain

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