Research workbench
Crystal structure of human interleukin-34 bound to human csf-1R
Analyse Crystal structure of human interleukin-34 bound to human csf-1R in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DKD
- Type
- protein
- Length
- 593 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-34; Macrophage colony-stimulating factor 1 receptor
- EC
- 2.7.10.1
- UniProt
- Q6ZMJ4, P07333
- Ligands
- NAG, BMA
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-34 | protein | 161 | 65% helix, 4% strand | Q6ZMJ4 |
| B | Interleukin-34 | protein | 160 | 64% helix, 3% strand | Q6ZMJ4 |
| C | Macrophage colony-stimulating factor 1 receptor (EC 2.7.10.1) | protein | 272 | 5% helix, 43% strand | P07333 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
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 | 200 | 0.71 | 0.88 | 30 | empty |
| 2 | 329 | 0.59 | 0.77 | 50 | empty |
| 3 | 152 | 0.49 | 0.78 | 28 | empty |
| 4 | 60 | 0.38 | 0.79 | 12 | NAG |
Interfaces
3 interfaces between chains.
- A–C · 1297 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 644 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 16 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 4DKD · Crystal Structure of Human Interleukin-34 Bound to Human CSF-1R · the same entry in another collection · chain A against A, TM-score 1.00
- Q6ZMJ4 · AlphaFold monomer V2.0 prediction for interleukin-34 (Q6ZMJ4) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P07333 · AlphaFold monomer V2.0 prediction for macrophage colony-stimulating factor 1 receptor… · a predicted model of the same protein · chain C against A, TM-score 0.68
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 Q6ZMJ4
- Every structure of UniProt P07333
- Elsewhere: RCSB PDB 4DKD · PDBe 4DKD · UniProt Q6ZMJ4 · UniProt P07333
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