MolNFT v1 · #91332 · protein
Multi-pronged modulation of cytokine signaling
4FA8 · Secreted protein BARF1: “Multi-pronged modulation of cytokine signaling”. X-ray diffraction, 2 ligands (NAG, BMA), 10 pockets (best druggability 0.62). MolNFT v1 #91332 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4FA8
- Type
- protein
- Length
- 1,003 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Secreted protein BARF1; Macrophage colony-stimulating factor 1
- UniProt
- P0CW72, P09603
- Ligands
- NAG, BMA
- Pockets
- 10 · best druggability 0.62
Structure
x-ray diffraction · 5 distinct chains · 33% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Secreted protein BARF1 | protein | 188 | 3% helix, 61% strand | P0CW72 |
| B | Secreted protein BARF1 | protein | 189 | 3% helix, 61% strand | P0CW72 |
| E | Macrophage colony-stimulating factor 1 | protein | 145 | 58% helix, 8% strand | P09603 |
| F | Macrophage colony-stimulating factor 1 | protein | 146 | 60% helix, 8% strand | P09603 |
| G | Macrophage colony-stimulating factor 1 | protein | 147 | 61% helix, 8% strand | P09603 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B, D, E, F, G
- BMA · beta-D-mannopyranose · sugar · 3 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.62 | 0.93 | 16 | empty |
| 2 | 170 | 0.60 | 0.83 | 29 | empty |
| 3 | 263 | 0.54 | 0.76 | 35 | empty |
| 4 | 209 | 0.50 | 0.76 | 23 | empty |
| 5 | 73 | 0.48 | 0.83 | 22 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1488 Ų buried · 28 hydrogen bonds · protein-protein
- F–G · 886 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 601 Ų buried · 10 hydrogen bonds · protein-protein
- D–G · 554 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 535 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 6 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 P0CW72
- Every structure of UniProt P09603
- Elsewhere: RCSB PDB 4FA8 · PDBe 4FA8 · UniProt P0CW72 · UniProt P09603
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