Research workbench
Crystal structure of pyrococcus furiosus pbab, an archaeal proteasome activator
Analyse Crystal structure of pyrococcus furiosus pbab, an archaeal proteasome activator in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VR0
- Type
- protein
- Length
- 984 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein
- UniProt
- Q8U1R3
- Ligands
- AU
- Pockets
- 12 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative uncharacterized protein | protein | 244 | 36% helix, 26% strand | Q8U1R3 |
| C | Putative uncharacterized protein | protein | 248 | 34% helix, 26% strand | Q8U1R3 |
| D | Putative uncharacterized protein | protein | 248 | 35% helix, 26% strand | Q8U1R3 |
Ligands and binding sites
- AU · Gold ion · metal · 18 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 754 | 0.69 | 0.76 | 61 | AU |
| 2 | 120 | 0.50 | 0.80 | 17 | empty |
| 3 | 123 | 0.47 | 0.79 | 29 | AU |
| 4 | 102 | 0.46 | 0.79 | 17 | empty |
| 5 | 118 | 0.44 | 0.77 | 26 | AU |
Interfaces
4 interfaces between chains.
- A–D · 1241 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1211 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1191 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1125 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3VR0 · Crystal structure of Pyrococcus furiosus PbaB, an archaeal proteasome activator · 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 Q8U1R3
- Elsewhere: RCSB PDB 3VR0 · PDBe 3VR0 · UniProt Q8U1R3
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