Research workbench
The mechanism of gm-csf inhibition by human gm-csf auto-antibodies
Analyse The mechanism of gm-csf inhibition by human gm-csf auto-antibodies in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BFS
- Type
- protein
- Length
- 535 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab light chain; Fab heavy chain; Granulocyte-macrophage colony-stimulating factor
- UniProt
- P04141
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Fab light chain | protein | 212 | 6% helix, 52% strand | — |
| H | Fab heavy chain | protein | 211 | 6% helix, 54% strand | — |
| C | Granulocyte-macrophage colony-stimulating factor | protein | 112 | 53% helix, 9% strand | P04141 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 569 | 0.60 | 0.74 | 66 | empty |
| 2 | 90 | 0.34 | 0.74 | 23 | empty |
| 3 | 82 | 0.33 | 0.75 | 20 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1771 Ų buried · 15 hydrogen bonds · protein-protein
- H–C · 664 Ų buried · 10 hydrogen bonds · protein-protein
- L–C · 293 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6BFS · The mechanism of GM-CSF inhibition by human GM-CSF auto-antibodies · the same entry in another collection · chain L against L, TM-score 1.00
- P04141 · AlphaFold monomer V2.0 prediction for granulocyte-macrophage colony- stimulating factor… · a predicted model of the same protein · chain C against A, TM-score 0.96
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 P04141
- Elsewhere: RCSB PDB 6BFS · PDBe 6BFS · UniProt P04141
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