Research workbench
Crystal structure of the middle domain of human HSP90-beta refined at 2.3 a resolution
Analyse Crystal structure of the middle domain of human HSP90-beta refined at 2.3 a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PRY
- Type
- protein
- Length
- 756 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heat shock protein HSP 90-beta
- UniProt
- P08238
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heat shock protein HSP 90-beta | protein | 255 | 42% helix, 20% strand | P08238 |
| B | Heat shock protein HSP 90-beta | protein | 251 | 39% helix, 20% strand | P08238 |
| C | Heat shock protein HSP 90-beta | protein | 250 | 42% helix, 20% strand | P08238 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains B, C
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 815 | 0.76 | 0.80 | 76 | empty |
| 2 | 1103 | 0.75 | 0.78 | 96 | empty |
| 3 | 197 | 0.57 | 0.80 | 20 | empty |
| 4 | 194 | 0.49 | 0.76 | 23 | empty |
| 5 | 129 | 0.46 | 0.77 | 19 | EDO |
Interfaces
3 interfaces between chains.
- A–B · 757 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 631 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 114 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3PRY · Crystal structure of the middle domain of human HSP90-beta refined at 2.3 A resolution · the same entry in another collection · chain A against A, TM-score 1.00
- P08238 · AlphaFold monomer V2.0 prediction for heat shock protein HSP 90-beta (P08238) · 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 P08238
- Elsewhere: RCSB PDB 3PRY · PDBe 3PRY · UniProt P08238
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