MolNFT v1 · #116061 · protein
Complex of gm-CSF/IL-2 inhibition factor with granulocyte-macrophage colony-stimulating factor
5D28: “Complex of gm-CSF/IL-2 inhibition factor with granulocyte-macrophage colony-stimulating factor”. X-ray diffraction, 4 ligands (NAG, BMA, MAN), 12 pockets (best druggability 0.67). MolNFT v1 #116061 on GenesisL1: 3D structure…
- PDB
- 5D28
- Type
- protein
- Length
- 688 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gm-CSF/IL-2 inhibition factor; Granulocyte-macrophage colony-stimulating factor
- UniProt
- Q9J5U5, P28773
- Ligands
- NAG, BMA, MAN, SO4
- Pockets
- 12 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gm-CSF/IL-2 inhibition factor | protein | 231 | 12% helix, 43% strand | Q9J5U5 |
| B | Granulocyte-macrophage colony-stimulating factor | protein | 111 | 54% helix, 9% strand | P28773 |
| C | Granulocyte-macrophage colony-stimulating factor | protein | 120 | 52% helix, 8% strand | P28773 |
| D | Gm-CSF/IL-2 inhibition factor | protein | 226 | 12% helix, 44% strand | Q9J5U5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, D
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- SO4 · Sulfate ion · ion · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 536 | 0.67 | 0.78 | 43 | empty |
| 2 | 280 | 0.66 | 0.82 | 48 | empty |
| 3 | 308 | 0.65 | 0.81 | 48 | empty |
| 4 | 379 | 0.63 | 0.78 | 37 | empty |
| 5 | 224 | 0.53 | 0.77 | 31 | empty |
Interfaces
4 interfaces between chains.
- C–D · 992 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 915 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 895 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 23 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 5D28 · Complex of GM-CSF/IL-2 inhibition factor with Granulocyte-macrophage colony-stimulating… · the same entry in another collection · chain A against A, TM-score 1.00
- P28773 · AlphaFold monomer V2.0 prediction for granulocyte-macrophage colony- stimulating factor… · a predicted model of the same protein · chain B 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 Q9J5U5
- Every structure of UniProt P28773
- Elsewhere: RCSB PDB 5D28 · PDBe 5D28 · UniProt Q9J5U5 · UniProt P28773
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