MolNFT v1 · #129445 · protein
Human afamin monoclinic crystal form
5OKL: “Human afamin monoclinic crystal form”. X-ray diffraction, 4 ligands (PAM, NAG, BMA), 20 pockets (best druggability 0.79). MolNFT v1 #129445 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5OKL
- Type
- protein
- Length
- 1,119 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Afamin
- UniProt
- P43652
- Ligands
- PAM, NAG, BMA, CL
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Afamin | protein | 561 | 69% helix, 1% strand | P43652 |
| B | Afamin | protein | 558 | 68% helix, 1% strand | P43652 |
Ligands and binding sites
- PAM · Palmitoleic acid · ligand · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A
- CL · Chloride ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 863 | 0.79 | 0.81 | 74 | CL |
| 2 | 551 | 0.75 | 0.82 | 46 | PAM |
| 3 | 680 | 0.69 | 0.77 | 59 | empty |
| 4 | 170 | 0.65 | 0.85 | 23 | empty |
| 5 | 164 | 0.60 | 0.83 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 88 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 31 disulfide, 4 glycan (disulfide, N-glycosylation).
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 P43652
- Elsewhere: RCSB PDB 5OKL · PDBe 5OKL · UniProt P43652
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