› 4m1d

X-ray diffraction
1.8Å resolution

Crystal structure of anti-HIV-1 Fab 447-52D in complex with V3 cyclic peptide MN

Released:
DOI: 10.2210/pdb4m1d/pdb
PDB entry 4m1d coloured by chain, front view.
PDB entry 4m1d coloured by chain, side view.
PDB entry 4m1d coloured by chain, top view.
Source organisms:
Primary publication:
Thermodynamic Signatures of the Antigen Binding Site of mAb 447-52D Targeting the Third Variable Region of HIV-1 gp120.
Killikelly A, Zhang HT, Spurrier B, Williams C, Gorny MK, Zolla-Pazner S, Kong XP
Biochemistry (2013)
PMID: 23944979

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-207570 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ig-like domain-containing protein Chains: L, M
Molecule details ›
Chains: L, M
Length: 216 amino acids
Theoretical weight: 22.79 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: A2NUT2 (Residues: 20-118, 119-234; Coverage: 100%)
Sequence domains:
Structure domains: Immunoglobulins
Fab mAb 447-52D Heavy Chain Chains: H, I
Molecule details ›
Chains: H, I
Length: 231 amino acids
Theoretical weight: 24.76 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
Surface protein gp120 Chains: P, Q
Molecule details ›
Chains: P, Q
Length: 14 amino acids
Theoretical weight: 1.6 KDa
Source organism: HIV-1 M:B_MN
Expression system: Not provided
UniProt:
  • Canonical: P05877 (Residues: 311-322; Coverage: 2%)
Gene name: env

Ligands and Environments

1 bound ligand:
Ligand GOL 17 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X6A
Spacegroup: C2
Unit cell:
a: 179.836Å b: 59.781Å c: 137.066Å
α: 90° β: 127.35° γ: 90°
R-values:
R R work R free
0.188 0.186 0.216
Expression systems:
  • Homo sapiens
  • Not provided

Quick links

Citations

10 citation in other articles

Structures of HIV-1 Env V1V2 with broadly neutralizing antibodies reveal commonalities that enable vaccine design.
Gorman et al. (2016)
9 more

11 mentions without citation

Crystal structure, conformational fixation and entry-related interactions of mature ligand-free HIV-1 Env.
Kwon et al. (2015)
10 more