Research workbench
Crystal structure of the pathological D187N variant of calcium-free human gelsolin.
Analyse Crystal structure of the pathological D187N variant of calcium-free human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QBF
- Type
- protein
- Length
- 1,429 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gelsolin
- UniProt
- P06396
- Ligands
- NA, SO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gelsolin | protein | 714 | 24% helix, 28% strand | P06396 |
| B | Gelsolin | protein | 715 | 24% helix, 28% strand | P06396 |
Ligands and binding sites
- NA · Sodium ion · metal · chains B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 571 | 0.79 | 0.85 | 65 | empty |
| 2 | 840 | 0.78 | 0.81 | 83 | empty |
| 3 | 960 | 0.78 | 0.80 | 80 | GOL |
| 4 | 544 | 0.75 | 0.83 | 70 | SO4 |
| 5 | 607 | 0.73 | 0.81 | 69 | empty |
Interfaces
1 interface between chains.
- A–B · 596 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6QBF · Crystal structure of the pathological D187N 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 A 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 P06396
- Elsewhere: RCSB PDB 6QBF · PDBe 6QBF · UniProt P06396
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