› 5mt4

X-ray diffraction
1.65Å resolution

COMPLEMENT FACTOR D IN COMPLEX WITH A REVERSIBLE BENZOIC ACID BASED INHIBITOR

Released:
DOI: 10.2210/pdb5mt4/pdb
PDB entry 5mt4 coloured by chain, front view.
PDB entry 5mt4 coloured by chain, side view.
PDB entry 5mt4 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure-Based Library Design and Fragment Screening for the Identification of Reversible Complement Factor D Protease Inhibitors.
Vulpetti A, Randl S, Rüdisser S, Ostermann N, Erbel P, Mac Sweeney A, Zoller T, Salem B, Gerhartz B, Cumin F, Hommel U, Dalvit C, Lorthiois E, Maibaum J
J Med Chem 60 1946-1958 (2017)
PMID: 28157311

Function and Biology Details

Reaction catalysed: 
Selective cleavage of Arg-|-Lys bond in complement factor B when in complex with complement subcomponent C3b or with cobra venom factor.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133224 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Complement factor D Chain: A
Molecule details ›
Chain: A
Length: 232 amino acids
Theoretical weight: 24.74 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P00746 (Residues: 26-253; Coverage: 98%)
Gene names: CFD, DF, PFD
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases

Ligands and Environments

1 bound ligand:
Ligand M7O 1 x M7O
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P21
Unit cell:
a: 55.476Å b: 50.839Å c: 39.366Å
α: 90° β: 104.93° γ: 90°
R-values:
R R work R free
0.19 0.19 0.239
Expression system: Escherichia coli

Quick links

Citations

2 review citations

The renaissance of complement therapeutics.
Ricklin et al. (2018)
1 more