Research workbench
Complement factor D in complex with the inhibitor 2-(2-(3'- (aminomethyl)-[1,1'-biphenyl]-3-CARBOXAMIDO)PHENYL)ACETIC acid
Analyse Complement factor D in complex with the inhibitor 2-(2-(3'… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QMT
- Type
- protein
- Length
- 454 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement factor D
- EC
- 3.4.21.46
- UniProt
- P00746
- Ligands
- J7B
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement factor D (EC 3.4.21.46) | protein | 230 | 10% helix, 36% strand | P00746 |
| B | Complement factor D (EC 3.4.21.46) | protein | 224 | 9% helix, 37% strand | P00746 |
Ligands and binding sites
- J7B · 2-[2-[[3-[3-(aminomethyl) phenyl]phenyl]carbonylamino]phenyl]ethanoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 347 | 0.71 | 0.83 | 31 | empty |
| 2 | 140 | 0.53 | 0.81 | 29 | J7B |
| 3 | 164 | 0.48 | 0.77 | 32 | J7B |
| 4 | 169 | 0.47 | 0.76 | 32 | empty |
| 5 | 94 | 0.35 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 842 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
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
- Elsewhere: RCSB PDB 6QMT · PDBe 6QMT · UniProt P00746
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