› 7pqz

X-ray diffraction
3.2Å resolution

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

Released:
DOI: 10.2210/pdb7pqz/pdb
Model geometry
Fit model/data
PDB entry 7pqz coloured by chain, front view.
PDB entry 7pqz coloured by chain, side view.
PDB entry 7pqz coloured by chain, top view.
Source organisms:
Primary publication:
Structures and therapeutic potential of anti-RBD human monoclonal antibodies against SARS-CoV-2.
Huang KA, Zhou D, Tan TK, Chen C, Duyvesteyn HME, Zhao Y, Ginn HM, Qin L, Rijal P, Schimanski L, Donat R, Harding A, Gilbert-Jaramillo J, James W, Tree JA, Buttigieg K, Carroll M, Charlton S, Lien CE, Lin MY, Chen CP, Cheng SH, Chen X, Lin TY, Fry EE, Ren J, Ma C, Townsend AR, Stuart DI
OpenAccess logo Theranostics 12 1-17 (2022)
PMID: 34987630

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-209880 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (6 distinct):
Spike protein S1 Chain: E
Molecule details ›
Chain: E
Length: 205 amino acids
Theoretical weight: 23.15 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTC2 (Residues: 333-526; Coverage: 15%)
Gene names: 2, S
Sequence domains: Betacoronavirus spike glycoprotein S1, receptor binding
FI-3A Fab heavy chain Chain: H
Molecule details ›
Chain: H
Length: 222 amino acids
Theoretical weight: 23.52 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
FI-3A Fab light chain Chain: L
FD-11A Fab heavy chain Chain: A
FD-11A Fab light chain Chain: B

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
1 bound ligand:
Ligand PO4 2 x PO4
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P3121
Unit cell:
a: 115.813Å b: 115.813Å c: 237.778Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.203 0.201 0.24
Expression system: Homo sapiens

Quick links

Citations

1 review citation

State of the art in epitope mapping and opportunities in COVID-19.
Hamed et al. (2023)
5 other articles

3 mentions without citation

Broadly neutralizing aptamers to SARS-CoV-2: A diverse panel of modified DNA antiviral agents.
Gelinas et al. (2023)
2 more