› 7t0r

X-ray diffraction
3.65Å resolution

Crystal structure of the anti-CD4 adnectin 6940_B01 as a complex with the extracellular domains of CD4 and ibalizumab fAb

Released:
DOI: 10.2210/pdb7t0r/pdb
PDB entry 7t0r coloured by chain, front view.
PDB entry 7t0r coloured by chain, side view.
PDB entry 7t0r coloured by chain, top view.
Source organisms:
Primary publication:
Novel Bent Conformation of CD4 Induced by HIV-1 Inhibitor Indirectly Prevents Productive Viral Attachment.
Wensel D, Williams S, Dixon DP, Ward P, McCormick P, Concha N, Stewart E, Hong X, Mazzucco C, Pal S, Ding B, Fellinger C, Krystal M
J Mol Biol 434 167395 (2022)
PMID: 34896364

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-208499 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Ibalizumab Light Chain Chains: B, L
Molecule details ›
Chains: B, L
Length: 219 amino acids
Theoretical weight: 24.25 KDa
Source organism: Mus musculus
Expression system: Cricetulus griseus
Ibalizumab Heavy Chain Chains: C, H
Molecule details ›
Chains: C, H
Length: 229 amino acids
Theoretical weight: 24.79 KDa
Source organism: Mus musculus
Expression system: Cricetulus griseus
T-cell surface glycoprotein CD4 Chains: A, D
Molecule details ›
Chains: A, D
Length: 373 amino acids
Theoretical weight: 41.67 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P01730 (Residues: 26-389; Coverage: 84%)
Gene name: CD4
Sequence domains:
Adnectin 6940_B01 Chains: G, I
Molecule details ›
Chains: G, I
Length: 94 amino acids
Theoretical weight: 10.31 KDa
Source organism: synthetic construct
Expression system: Escherichia coli BL21(DE3)

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Unit cell:
a: 83.51Å b: 164.014Å c: 167.053Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.23 0.226 0.292
Expression systems:
  • Cricetulus griseus
  • Homo sapiens
  • Escherichia coli BL21(DE3)

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