› 3h6n

X-ray diffraction
2Å resolution

Crystal Structure of the ubiquitin-like domain of plexin D1

Released:
DOI: 10.2210/pdb3h6n/pdb
PDB entry 3h6n coloured by chain, front view.
PDB entry 3h6n coloured by chain, side view.
PDB entry 3h6n coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Tong Y, Nedyalkova L, Tempel W, MacKenzie F, Arrowsmith CH, Edwards AM, Bountra C, Weigelt J, Bochkarev A, Buck M, Park H, Structural Genomics Consortium (SGC)

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-195232 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Plexin-D1 Chain: A
Molecule details ›
Chain: A
Length: 127 amino acids
Theoretical weight: 14.52 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Y4D7 (Residues: 1553-1678; Coverage: 7%)
Gene names: KIAA0620, PLXND1
Sequence domains: Plexin cytoplasmic RhoGTPase-binding domain
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Ligands and Environments

2 bound ligands:
Ligand ARS 2 x ARS
Ligand UNX 1 x UNX
1 modified residue:
Ligand MSE 3 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: C2
Unit cell:
a: 81.777Å b: 27.051Å c: 52.653Å
α: 90° β: 114.06° γ: 90°
R-values:
R R work R free
0.244 0.243 0.276
Expression system: Escherichia coli

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