› 2qsc

X-ray diffraction
2.8Å resolution

Crystal structure analysis of anti-HIV-1 V3-Fab F425-B4e8 in complex with a V3-peptide

Released:
DOI: 10.2210/pdb2qsc/pdb
PDB entry 2qsc coloured by chain, front view.
PDB entry 2qsc coloured by chain, side view.
PDB entry 2qsc coloured by chain, top view.
Source organisms:
Primary publication:
Structure of antibody F425-B4e8 in complex with a V3 peptide reveals a new binding mode for HIV-1 neutralization.
Bell CH, Pantophlet R, Schiefner A, Cavacini LA, Stanfield RL, Burton DR, Wilson IA
J Mol Biol 375 969-78 (2008)
PMID: 18068724

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-209254 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (4 distinct):
Fab F425-B4e8, Light chain Chain: L
Molecule details ›
Chain: L
Length: 215 amino acids
Theoretical weight: 23.33 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
Fab F425-B4e8, Heavy chain Chain: H
Molecule details ›
Chain: H
Length: 222 amino acids
Theoretical weight: 23.73 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
Surface protein gp120 Chain: P
Molecule details ›
Chain: P
Length: 15 amino acids
Theoretical weight: 1.78 KDa
Source organism: HIV-1 M:B_MN
Expression system: Not provided
UniProt:
  • Canonical: P05877 (Residues: 309-323; Coverage: 2%)
Gene name: env

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
2 bound ligands:
Ligand ZN 4 x ZN
Ligand CL 4 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL11-1
Spacegroup: P2
Unit cell:
a: 82.912Å b: 39.858Å c: 97.96Å
α: 90° β: 108.5° γ: 90°
R-values:
R R work R free
0.222 0.219 0.264
Expression systems:
  • Homo sapiens
  • Not provided

Quick links

Citations

4 review citations

Human antibodies that neutralize HIV-1: identification, structures, and B cell ontogenies.
Kwong et al. (2012)
3 more

10 mentions without citation

Max Bergmann lecture protein epitope mimetics in the age of structural vaccinology.
Robinson JA. (2013)
9 more