MolNFT v1 · #167497 · protein
Crystal structure of human complement factor D with anti-factor D Fab 20D12
6VMK: “Crystal structure of human complement factor D with anti-factor D Fab 20D12”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.77). MolNFT v1 #167497 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6VMK
- Type
- protein
- Length
- 10,464 residues
- Chains
- 48
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement factor D; Fab Y49R light chain; Fab Y49R heavy chain
- EC
- 3.4.21.46
- UniProt
- P00746
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| W, C, F, I, N, Q, T, X, a, d, g, j, m, p, s, v | Complement factor D (EC 3.4.21.46) | protein | 228 | 9% helix, 36% strand | P00746 |
| L, A, D, G, J, O, R, U, Y, b, e, h, k, n, q, t | Fab Y49R light chain | protein | 213 | 5% helix, 50% strand | — |
| M, B, E, H, K, P, S, V, Z, c, f, i, l, o, r, u | Fab Y49R heavy chain | protein | 213 | 7% helix, 52% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 12 copies · chains W, C, N, Q, T, X, g, j, m, p, s, v
- GOL · Glycerol · additive · 16 copies · chains W, C, F, I, N, Q, T, X, a, d, g, j, m, p, s, v
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 539 | 0.77 | 0.84 | 69 | empty |
| 2 | 508 | 0.77 | 0.85 | 76 | empty |
| 3 | 550 | 0.77 | 0.84 | 76 | empty |
| 4 | 870 | 0.70 | 0.76 | 93 | empty |
| 5 | 916 | 0.69 | 0.75 | 87 | empty |
Interfaces
122 interfaces between chains.
- n–o · 1751 Ų buried · 15 hydrogen bonds · protein-protein
- k–l · 1735 Ų buried · 15 hydrogen bonds · protein-protein
- e–f · 1721 Ų buried · 13 hydrogen bonds · protein-protein
- O–P · 1717 Ų buried · 10 hydrogen bonds · protein-protein
- q–r · 1716 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 128 disulfide (disulfide).
Compared structures
- 6VMK · Crystal structure of human Complement Factor D with anti-Factor D Fab 20D12 · the same entry in another collection · chain I against I, 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 6VMK · PDBe 6VMK · UniProt P00746
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