Research workbench
Crystal structure of pyrococcus furiosus pbaa (monoclinic form), an archaeal homolog of proteasome-assembly chaperone
Analyse Crystal structure of pyrococcus furiosus pbaa (monoclinic form), an archaeal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y9N
- Type
- protein
- Length
- 2,380 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pbaa
- UniProt
- Q8U4Q9
- Ligands
- CL
- Pockets
- 20 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Pbaa | protein | 238 | 43% helix, 26% strand | Q8U4Q9 |
Ligands and binding sites
- CL · Chloride ion · ion · 10 copies · chains A, H, B, C, F, D, E, I, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 332 | 0.61 | 0.78 | 45 | empty |
| 2 | 282 | 0.61 | 0.79 | 41 | empty |
| 3 | 338 | 0.60 | 0.77 | 44 | empty |
| 4 | 282 | 0.59 | 0.78 | 40 | empty |
| 5 | 266 | 0.58 | 0.78 | 40 | empty |
Interfaces
20 interfaces between chains.
- C–F · 1015 Ų buried · 13 hydrogen bonds · protein-protein
- D–J · 1015 Ų buried · 15 hydrogen bonds · protein-protein
- C–G · 1014 Ų buried · 4 hydrogen bonds · protein-protein
- B–G · 1010 Ų buried · 11 hydrogen bonds · protein-protein
- E–I · 1007 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5Y9N · Crystal structure of Pyrococcus furiosus PbaA (monoclinic form), an archaeal homolog of… · the same entry in another collection · chain A 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 Q8U4Q9
- Elsewhere: RCSB PDB 5Y9N · PDBe 5Y9N · UniProt Q8U4Q9
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