Research workbench
Crystal structure of the human colony-stimulating factor 1 (hcsf-1) cytokine in complex with the viral receptor BARF1
Analyse Crystal structure of the human colony-stimulating factor 1 (hcsf-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
- 3UEZ
- Type
- protein
- Length
- 1,307 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
- P03228, P09603
- Ligands
- NAG, BMA
- Pockets
- 15 · best druggability 0.69
Structure
x-ray diffraction · 6 distinct chains · 35% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Secreted protein BARF1 | protein | 185 | 3% helix, 63% strand | P03228 |
| C, D | Secreted protein BARF1 | protein | 186 | 3% helix, 61% strand | P03228 |
| E | Macrophage colony-stimulating factor 1 | protein | 142 | 54% helix, 8% strand | P09603 |
| F | Macrophage colony-stimulating factor 1 | protein | 141 | 57% helix, 9% strand | P09603 |
| G | Macrophage colony-stimulating factor 1 | protein | 143 | 59% helix, 8% strand | P09603 |
| H | Macrophage colony-stimulating factor 1 | protein | 139 | 57% helix, 9% strand | P09603 |
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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.69 | 0.97 | 14 | empty |
| 2 | 386 | 0.63 | 0.78 | 42 | empty |
| 3 | 339 | 0.61 | 0.77 | 34 | empty |
| 4 | 183 | 0.55 | 0.79 | 32 | empty |
| 5 | 130 | 0.52 | 0.80 | 17 | empty |
Interfaces
15 interfaces between chains.
- E–F · 854 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 843 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 653 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 617 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 615 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 3UEZ · Crystal structure of the human Colony-Stimulating Factor 1 (hCSF-1) cytokine in complex… · the same entry in another collection · chain H against H, TM-score 1.00
- P09603 · AlphaFold monomer V2.0 prediction for macrophage colony-stimulating factor 1 (P09603) · a predicted model of the same protein · chain G against A, TM-score 0.98
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 P03228
- Every structure of UniProt P09603
- Elsewhere: RCSB PDB 3UEZ · PDBe 3UEZ · UniProt P03228 · UniProt P09603
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