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
- 4D9R
- Type
- protein
- Length
- 1,317 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement factor D; Fab light chain; Fab heavy chain
- EC
- 3.4.21.46
- UniProt
- P00746, P01834, P01857
- Ligands
- CL
- Pockets
- 12 · best druggability 0.63
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Complement factor D (EC 3.4.21.46) | protein | 228 | 9% helix, 34% strand | P00746 |
| L | Fab light chain | protein | 214 | 7% helix, 50% strand | P01834 |
| H | Fab heavy chain | protein | 218 | 8% helix, 49% strand | P01857 |
| E | Fab heavy chain | protein | 216 | 8% helix, 50% strand | P01857 |
| D | Fab light chain | protein | 213 | 7% helix, 50% strand | P01834 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains E, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 630 | 0.63 | 0.74 | 59 | empty |
| 2 | 626 | 0.62 | 0.74 | 61 | empty |
| 3 | 457 | 0.61 | 0.75 | 59 | empty |
| 4 | 156 | 0.56 | 0.81 | 24 | empty |
| 5 | 101 | 0.41 | 0.77 | 18 | empty |
Interfaces
8 interfaces between chains.
- L–H · 1926 Ų buried · 19 hydrogen bonds · protein-protein
- E–D · 1848 Ų buried · 17 hydrogen bonds · protein-protein
- B–E · 584 Ų buried · 16 hydrogen bonds · protein-protein
- A–H · 577 Ų buried · 14 hydrogen bonds · protein-protein
- A–L · 399 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide (disulfide).
Compared structures
- 4D9R · Inhibiting Alternative Pathway Complement Activation by Targeting the Exosite on Factor D · the same entry in another collection · chain D against D, TM-score 1.00
- P00746 · AlphaFold monomer V2.0 prediction for complement factor D (P00746) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P01834 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa constant (P01834) · a predicted model of the same protein · chain L against A, TM-score 0.50
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 P00746
- Every structure of UniProt P01834
- Every structure of UniProt P01857
- Elsewhere: RCSB PDB 4D9R · PDBe 4D9R · UniProt P00746 · UniProt P01834 · UniProt P01857
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