› 5kjr

X-ray diffraction
2.98Å resolution

Crystal structure of the ADCC-potent antibody N60-i3 Fab in complex with HIV-1 Clade A/E gp120 W69A/S115W mutant and M48U1.

Released:
DOI: 10.2210/pdb5kjr/pdb
PDB entry 5kjr coloured by chain, front view.
PDB entry 5kjr coloured by chain, side view.
PDB entry 5kjr coloured by chain, top view.
Source organisms:
Primary publication:
A Highly Conserved gp120 Inner Domain Residue Modulates Env Conformation and Trimer Stability.
Ding S, Tolbert WD, Prévost J, Pacheco B, Coutu M, Debbeche O, Xiang SH, Pazgier M, Finzi A
J Virol 90 8395-409 (2016)
PMID: 27384653

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-229613 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Human immunodeficiency virus 1 envelope glycoprotein Gp120 domain-containing protein Chain: G
Molecule details ›
Chain: G
Length: 353 amino acids
Theoretical weight: 39.14 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: A0A0M3KKW9 (Residues: 1-353; Coverage: 100%)
Gene name: HIV-1 Env
Sequence domains: Envelope glycoprotein GP120
Structure domains: Human immunodeficiency virus 1, Gp160, envelope glycoprotein
M48U1 CD4 MIMETIC PEPTIDE Chain: N
Molecule details ›
Chain: N
Length: 28 amino acids
Theoretical weight: 3.06 KDa
Source organism: synthetic construct
Expression system: Not provided
N60-I3 FAB HEAVY CHAIN Chain: H
Molecule details ›
Chain: H
Length: 229 amino acids
Theoretical weight: 24.41 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
N60-I3 FAB LIGHT CHAIN Chain: L
Molecule details ›
Chain: L
Length: 221 amino acids
Theoretical weight: 23.34 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins

Ligands and Environments

2 bound ligands:
Ligand NAG 10 x NAG
Ligand MPD 1 x MPD
2 modified residues:
Ligand DPR 1 x DPR
Ligand U2X 1 x U2X

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL14-1
Spacegroup: P21212
Unit cell:
a: 95.191Å b: 101.944Å c: 108.747Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.252 0.249 0.306
Expression systems:
  • Homo sapiens
  • Not provided

Quick links

Citations

1 review citation

Beyond Viral Neutralization.
Lewis et al. (2017)
13 other articles

1 mention without citation

A Highly Conserved gp120 Inner Domain Residue Modulates Env Conformation and Trimer Stability.
Ding et al. (2016)