Research workbench
Crystal structure of the mouse colony-stimulating factor 1 (mcsf-1) cytokine in complex with the viral receptor BARF1
Analyse Crystal structure of the mouse colony-stimulating factor 1 (mcsf-1) cytokine in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ADQ
- Type
- protein
- Length
- 1,313 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Secreted protein BARF1; Macrophage colony-stimulating factor 1
- UniProt
- P0CW72, P07141
- Ligands
- NAG, BMA, MAN
- Pockets
- 14 · best druggability 0.59
Structure
x-ray diffraction · 5 distinct chains · 32% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Secreted protein BARF1 | protein | 185 | 3% helix, 62% strand | P0CW72 |
| C, D | Secreted protein BARF1 | protein | 186 | 2% helix, 62% strand | P0CW72 |
| E | Macrophage colony-stimulating factor 1 | protein | 144 | 58% helix, 8% strand | P07141 |
| F, H | Macrophage colony-stimulating factor 1 | protein | 142 | 58% helix, 8% strand | P07141 |
| G | Macrophage colony-stimulating factor 1 | protein | 143 | 58% helix, 8% strand | P07141 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 4 copies
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 279 | 0.59 | 0.78 | 33 | empty |
| 2 | 198 | 0.58 | 0.80 | 23 | empty |
| 3 | 130 | 0.55 | 0.82 | 25 | empty |
| 4 | 199 | 0.54 | 0.79 | 21 | empty |
| 5 | 172 | 0.54 | 0.79 | 29 | empty |
Interfaces
15 interfaces between chains.
- G–H · 781 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 763 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 615 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 611 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 587 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4ADQ · Crystal structure of the mouse colony-stimulating factor 1 (mcsf-1) cytokine in complex… · the same entry in another collection · chain H against H, TM-score 1.00
- P07141 · AlphaFold monomer V2.0 prediction for macrophage colony-stimulating factor 1 (P07141) · a predicted model of the same protein · chain E against A, TM-score 0.99
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 P07141
- Elsewhere: RCSB PDB 4ADQ · PDBe 4ADQ · UniProt P0CW72 · UniProt P07141
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