3vi4

X-ray diffraction
2.9Å resolution

Crystal structure of alpha5beta1 integrin headpiece in complex with RGD peptide

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
PDBe Complex ID:
PDB-CPX-209246 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (7 distinct):
Integrin alpha-5 heavy chain Chains: A, C
Molecule details ›
Chains: A, C
Length: 632 amino acids
Theoretical weight: 68.19 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
UniProt:
  • Canonical: P08648 (Residues: 42-664; Coverage: 62%)
Gene names: FNRA, ITGA5
Sequence domains:
Structure domains:
Integrin beta-1 Chains: B, D
Molecule details ›
Chains: B, D
Length: 454 amino acids
Theoretical weight: 50.56 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
UniProt:
  • Canonical: P05556 (Residues: 21-465; Coverage: 57%)
Gene names: FNRB, ITGB1, MDF2, MSK12
Sequence domains:
Structure domains:
SG/19 Fab fragment (Light chain) Chains: E, L
Molecule details ›
Chains: E, L
Length: 219 amino acids
Theoretical weight: 24.22 KDa
Source organism: Mus musculus
Expression system: Mus musculus
Structure domains: Immunoglobulins
SG/19 Fab fragment (Heavy chain) Chains: F, H
Molecule details ›
Chains: F, H
Length: 218 amino acids
Theoretical weight: 23.48 KDa
Source organism: Mus musculus
Expression system: Mus musculus
Structure domains: Immunoglobulins
RGD peptide Chains: G, I
Molecule details ›
Chains: G, I
Length: 5 amino acids
Theoretical weight: 559 Da

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
3 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-17A
Spacegroup: P1
Unit cell:
a: 92.805Å b: 103.869Å c: 125.262Å
α: 75.72° β: 70.16° γ: 70.9°
R-values:
R R work R free
0.218 0.215 0.275
Expression systems:
  • Cricetulus griseus
  • Mus musculus