MolNFT v1 · #58991 · protein
Crystal structure of a core domain of stomatin from pyrococcus horikoshii
3BK6 · PH stomatin: “Crystal structure of a core domain of stomatin from pyrococcus horikoshii”. X-ray diffraction, 8 pockets (best druggability 0.48). MolNFT v1 #58991 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3BK6
- Type
- protein
- Length
- 472 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PH stomatin
- UniProt
- O59180
- Pockets
- 8 · best druggability 0.48
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PH stomatin | protein | 170 | 56% helix, 24% strand | O59180 |
| B | PH stomatin | protein | 142 | 45% helix, 28% strand | O59180 |
| C | PH stomatin | protein | 160 | 56% helix, 25% strand | O59180 |
Pockets
8 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 184 | 0.48 | 0.76 | 29 | empty |
| 2 | 156 | 0.48 | 0.77 | 21 | empty |
| 3 | 159 | 0.46 | 0.76 | 23 | empty |
| 4 | 97 | 0.42 | 0.78 | 16 | empty |
| 5 | 88 | 0.42 | 0.79 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–C · 976 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 942 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 863 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3BK6 · Crystal structure of a core domain of stomatin from Pyrococcus horikoshii · the same entry in another collection · chain A against A, TM-score 1.00
- O59180 · AlphaFold monomer V2.0 prediction for stomatin homolog PH1511 (O59180) · a predicted model of the same protein · chain C against A, TM-score 0.90
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 O59180
- Elsewhere: RCSB PDB 3BK6 · PDBe 3BK6 · UniProt O59180
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