› 3idi

X-ray diffraction
2.1Å resolution

Crystal structure of the HIV-1 Cross Neutralizing Monoclonal Antibody 2F5 Fab' fragment in complex with gp41 Peptide ALDKWNQ

Released:
DOI: 10.2210/pdb3idi/pdb
PDB entry 3idi coloured by chain, front view.
PDB entry 3idi coloured by chain, side view.
PDB entry 3idi coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystallographic definition of the epitope promiscuity of the broadly neutralizing anti-human immunodeficiency virus type 1 antibody 2F5: vaccine design implications.
Bryson S, Julien JP, Hynes RC, Pai EF
J Virol 83 11862-75 (2009)
PMID: 19740978

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-211629 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
2F5 Fab light chain Chain: A
Molecule details ›
Chain: A
Length: 214 amino acids
Theoretical weight: 23.36 KDa
Source organism: Homo sapiens
Structure domains: Immunoglobulins
2F5 Fab heavy chain Chain: B
Molecule details ›
Chain: B
Length: 237 amino acids
Theoretical weight: 25.25 KDa
Source organism: Homo sapiens
Structure domains: Immunoglobulins
gp41 MPER peptide Chain: C
Molecule details ›
Chain: C
Length: 7 amino acids
Theoretical weight: 875 Da

Ligands and Environments

2 bound ligands:
Ligand SO4 2 x SO4
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P212121
Unit cell:
a: 63.5Å b: 76.5Å c: 94.2Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.212 0.212 0.23

Quick links

Citations

8 review citations

Broadly neutralizing antibodies present new prospects to counter highly antigenically diverse viruses.
Burton et al. (2012)
7 more

3 mentions without citation

AbDesign: An algorithm for combinatorial backbone design guided by natural conformations and sequences.
Lapidoth et al. (2015)
2 more