Research workbench
Inhibiting alternative pathway complement activation by targeting the exosite on factor D
Analyse Inhibiting alternative pathway complement activation by targeting the exosite… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D9Q
- Type
- protein
- Length
- 1,310 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Factor D; Anti-factor D, light chain; Anti-factor D, heavy chain
- UniProt
- F6YBP7, Q8TCD0, P01857
- Ligands
- ZN, SO4
- Pockets
- 17 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Factor D | protein | 228 | 10% helix, 35% strand | F6YBP7 |
| D, L | Anti-factor D, light chain | protein | 213 | 6% helix, 50% strand | Q8TCD0 |
| E | Anti-factor D, heavy chain | protein | 212 | 10% helix, 50% strand | P01857 |
| H | Anti-factor D, heavy chain | protein | 216 | 10% helix, 49% strand | P01857 |
Ligands and binding sites
- ZN · Zinc ion · metal · 7 copies · chains A, B, D, E, H, L
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 10 copies · chains A, H, L, B, E, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 610 | 0.68 | 0.77 | 63 | empty |
| 2 | 355 | 0.60 | 0.77 | 48 | GOL |
| 3 | 300 | 0.58 | 0.77 | 38 | empty |
| 4 | 56 | 0.53 | 0.88 | 22 | empty |
| 5 | 194 | 0.51 | 0.77 | 26 | empty |
Interfaces
7 interfaces between chains.
- H–L · 1822 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1646 Ų buried · 12 hydrogen bonds · protein-protein
- D–L · 934 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 576 Ų buried · 15 hydrogen bonds · protein-protein
- A–H · 576 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 4D9Q · Inhibiting Alternative Pathway Complement Activation by Targeting the Exosite on Factor D · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt F6YBP7
- Every structure of UniProt Q8TCD0
- Every structure of UniProt P01857
- Elsewhere: RCSB PDB 4D9Q · PDBe 4D9Q · UniProt F6YBP7 · UniProt Q8TCD0 · UniProt P01857
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