Research workbench
Structure of M-csf bound to the first three domains of fms
Analyse Structure of M-csf bound to the first three domains of fms in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EJJ
- Type
- protein
- Length
- 565 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Colony stimulating factor-1; Macrophage colony-stimulating factor 1 receptor
- EC
- 2.7.10.1
- UniProt
- Q3U395, P09581
- Ligands
- NAG
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Colony stimulating factor-1 | protein | 148 | 54% helix, 8% strand | Q3U395 |
| B | Colony stimulating factor-1 | protein | 145 | 52% helix, 8% strand | Q3U395 |
| X | Macrophage colony-stimulating factor 1 receptor (EC 2.7.10.1) | protein | 272 | 5% helix, 51% strand | P09581 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 623 | 0.75 | 0.81 | 70 | empty |
| 2 | 177 | 0.51 | 0.78 | 21 | empty |
| 3 | 66 | 0.49 | 0.85 | 17 | empty |
| 4 | 53 | 0.26 | 0.74 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–X · 987 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 807 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3EJJ · Structure of M-CSF bound to the first three domains of FMS · the same entry in another collection · chain A against A, TM-score 1.00
- P09581 · AlphaFold monomer V2.0 prediction for macrophage colony-stimulating factor 1 receptor… · a predicted model of the same protein · chain X against A, TM-score 0.64
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 Q3U395
- Every structure of UniProt P09581
- Elsewhere: RCSB PDB 3EJJ · PDBe 3EJJ · UniProt Q3U395 · UniProt P09581
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