MolNFT v1 · #143980 · protein
The mechanism of gm-csf inhibition by human gm-csf auto-antibodies
6BFQ · Fab heavy chain: “The mechanism of gm-csf inhibition by human gm-csf auto-antibodies”. X-ray diffraction, 20 pockets (best druggability 0.70). MolNFT v1 #143980 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6BFQ
- Type
- protein
- Length
- 2,086 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab heavy chain; Fab light chain; Granulocyte-macrophage colony-stimulating factor
- UniProt
- P04141
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 10 distinct chains · 19% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fab heavy chain | protein | 213 | 9% helix, 50% strand | — |
| L, B | Fab light chain | protein | 212 | 6% helix, 51% strand | — |
| A | Fab heavy chain | protein | 210 | 10% helix, 50% strand | — |
| C | Fab heavy chain | protein | 211 | 10% helix, 50% strand | — |
| D, F | Fab light chain | protein | 213 | 6% helix, 51% strand | — |
| E | Fab heavy chain | protein | 210 | 10% helix, 50% strand | — |
| G | Granulocyte-macrophage colony-stimulating factor | protein | 94 | 48% helix, 9% strand | P04141 |
| J | Granulocyte-macrophage colony-stimulating factor | protein | 102 | 53% helix, 8% strand | P04141 |
| I | Granulocyte-macrophage colony-stimulating factor | protein | 94 | 52% helix, 9% strand | P04141 |
| K | Granulocyte-macrophage colony-stimulating factor | protein | 102 | 53% helix, 8% strand | P04141 |
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1069 | 0.70 | 0.74 | 85 | empty |
| 2 | 415 | 0.63 | 0.77 | 41 | empty |
| 3 | 611 | 0.62 | 0.74 | 60 | empty |
| 4 | 525 | 0.60 | 0.74 | 54 | empty |
| 5 | 301 | 0.56 | 0.76 | 41 | empty |
Interfaces
18 interfaces between chains.
- E–F · 1680 Ų buried · 18 hydrogen bonds · protein-protein
- H–L · 1679 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1669 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1634 Ų buried · 18 hydrogen bonds · protein-protein
- C–G · 692 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 6BFQ · The mechanism of GM-CSF inhibition by human GM-CSF auto-antibodies · the same entry in another collection · chain K against K, TM-score 1.00
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 6BFQ · PDBe 6BFQ · UniProt P04141
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