› 6vmk

X-ray diffraction
3.01Å resolution

Crystal structure of human Complement Factor D with anti-Factor D Fab 20D12

Released:
DOI: 10.2210/pdb6vmk/pdb
PDB entry 6vmk coloured by chain, front view.
PDB entry 6vmk coloured by chain, side view.
PDB entry 6vmk coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Wu P, Harris SF, Eigenbrot C

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:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-208308 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Complement factor D Chains: C, F, I, N, Q, T, W, X, a, d, g, j, m, p, s, v
Molecule details ›
Chains: C, F, I, N, Q, T, W, X, a, d, g, j, m, p, s, v
Length: 228 amino acids
Theoretical weight: 24.44 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
UniProt:
  • Canonical: P00746 (Residues: 26-253; Coverage: 98%)
Gene names: CFD, DF, PFD
Sequence domains: Trypsin
Fab Y49R light chain Chains: A, D, G, J, L, O, R, U, Y, b, e, h, k, n, q, t
Molecule details ›
Chains: A, D, G, J, L, O, R, U, Y, b, e, h, k, n, q, t
Length: 214 amino acids
Theoretical weight: 23.35 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Fab Y49R heavy chain Chains: B, E, H, K, M, P, S, V, Z, c, f, i, l, o, r, u
Molecule details ›
Chains: B, E, H, K, M, P, S, V, Z, c, f, i, l, o, r, u
Length: 223 amino acids
Theoretical weight: 23.67 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli

Ligands and Environments

2 bound ligands:
Ligand GOL 16 x GOL
Ligand SO4 12 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: I222
Unit cell:
a: 263.704Å b: 301.454Å c: 458.842Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.174 0.174 0.215
Expression systems:
  • Cricetulus griseus
  • Escherichia coli

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