MolNFT v1 · #167496 · protein
Crystal structure of human complement factor D with anti-factor D Fab 20D12
6VMJ · FAB20D12 light chain: “Crystal structure of human complement factor D with anti-factor D Fab 20D12”. X-ray diffraction, 20 pockets (best druggability 0.71). MolNFT v1 #167496 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6VMJ
- Type
- protein
- Length
- 2,610 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FAB20D12 light chain; FAB20D12 heavy chain; Complement factor D
- EC
- 3.4.21.46
- UniProt
- P00746
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I, L | FAB20D12 light chain | protein | 213 | 6% helix, 50% strand | — |
| B, F, J | FAB20D12 heavy chain | protein | 211 | 5% helix, 50% strand | — |
| M | FAB20D12 heavy chain | protein | 213 | 6% helix, 52% strand | — |
| W, X, Y, Z | Complement factor D (EC 3.4.21.46) | protein | 228 | 9% helix, 36% strand | P00746 |
Ligands and binding sites
- CIT · Citric acid · additive · 6 copies · chains B, F, J, M, W, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1197 | 0.71 | 0.75 | 107 | empty |
| 2 | 879 | 0.69 | 0.75 | 82 | empty |
| 3 | 834 | 0.66 | 0.74 | 86 | empty |
| 4 | 678 | 0.64 | 0.74 | 59 | empty |
| 5 | 110 | 0.57 | 0.85 | 28 | empty |
Interfaces
24 interfaces between chains.
- E–F · 1652 Ų buried · 12 hydrogen bonds · protein-protein
- L–M · 1637 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1611 Ų buried · 11 hydrogen bonds · protein-protein
- I–J · 1608 Ų buried · 13 hydrogen bonds · protein-protein
- E–Z · 538 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide (disulfide).
Compared structures
- 6VMJ · Crystal structure of human Complement Factor D with anti-Factor D Fab 20D12 · the same entry in another collection · chain Z against Z, 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 P00746
- Elsewhere: RCSB PDB 6VMJ · PDBe 6VMJ · UniProt P00746
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