MolNFT v1 · #161289 · protein
Crystal structure of the pathological N184K variant of calcium-free human gelsolin
6Q9R: “Crystal structure of the pathological N184K variant of calcium-free human gelsolin”. X-ray diffraction, 2 ligands (CL, SO4), 20 pockets (best druggability 0.83). MolNFT v1 #161289 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6Q9R
- Type
- protein
- Length
- 1,428 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gelsolin
- UniProt
- P06396
- Ligands
- CL, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gelsolin | protein | 715 | 25% helix, 30% strand | P06396 |
| B | Gelsolin | protein | 713 | 25% helix, 29% strand | P06396 |
Ligands and binding sites
- CL · Chloride ion · ion · 9 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 17 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 410 | 0.83 | 0.91 | 58 | CL, GOL, SO4 |
| 2 | 1005 | 0.83 | 0.84 | 104 | CL, GOL, TRS |
| 3 | 818 | 0.79 | 0.82 | 93 | GOL |
| 4 | 883 | 0.76 | 0.79 | 76 | CL, GOL |
| 5 | 324 | 0.59 | 0.77 | 44 | GOL |
Interfaces
1 interface between chains.
- A–B · 722 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6Q9R · Crystal structure of the pathological N184K variant of calcium-free human gelsolin · the same entry in another collection · chain A against A, TM-score 1.00
- P06396 · AlphaFold monomer V2.0 prediction for gelsolin (P06396) · a predicted model of the same protein · chain B against A, 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 P06396
- Elsewhere: RCSB PDB 6Q9R · PDBe 6Q9R · UniProt P06396
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