› 8ckm

X-ray diffraction
2.72Å resolution

Semaphorin-5A TSR 3-4 domains

Released:
DOI: 10.2210/pdb8ckm/pdb
PDB entry 8ckm coloured by chain, front view.
PDB entry 8ckm coloured by chain, side view.
PDB entry 8ckm coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure and function of Semaphorin-5A glycosaminoglycan interactions.
Nagy GN, Zhao XF, Karlsson R, Wang K, Duman R, Harlos K, El Omari K, Wagner A, Clausen H, Miller RL, Giger RJ, Jones EY
Nat Commun 15 2723 (2024)
PMID: 38548715

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-274529 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Semaphorin-5A Chains: A, B
Molecule details ›
Chains: A, B
Length: 125 amino acids
Theoretical weight: 14.05 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q13591 (Residues: 652-768; Coverage: 11%)
Gene names: SEMA5A, SEMAF
Sequence domains: Thrombospondin type 1 domain

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: C2
Unit cell:
a: 104.11Å b: 27.65Å c: 92.24Å
α: 90° β: 99.1° γ: 90°
R-values:
R R work R free
0.29 0.288 0.331
Expression system: Homo sapiens

Quick links

Citations

1 citations in other articles

A Toxoplasma gondii thioredoxin with cell adhesion and antioxidant function.
Wang et al. (2024)