Research workbench
Conserved hypothetical protein pfu-367848-001 from pyrococcus furiosus
Analyse Conserved hypothetical protein pfu-367848-001 from pyrococcus furiosus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y82
- Type
- protein
- Length
- 578 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein
- UniProt
- Q8U3V0
- Ligands
- UNX
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 65% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein | protein | 147 | 66% helix, 14% strand | Q8U3V0 |
| B, C | Hypothetical protein | protein | 146 | 65% helix, 14% strand | Q8U3V0 |
| D | Hypothetical protein | protein | 139 | 65% helix, 14% strand | Q8U3V0 |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 42 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 295 | 0.59 | 0.78 | 35 | empty |
| 2 | 312 | 0.59 | 0.77 | 28 | empty |
| 3 | 80 | 0.33 | 0.74 | 21 | UNX |
| 4 | 61 | 0.28 | 0.74 | 18 | UNX |
Interfaces
4 interfaces between chains.
- A–B · 1412 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1364 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 494 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 69 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 31 modified (engineered).
Compared structures
- 1Y82 · Conserved hypothetical protein Pfu-367848-001 from Pyrococcus furiosus · the same entry in another collection · chain A against A, TM-score 1.00
- Q8U3V0 · AlphaFold monomer V2.0 prediction for vapc ribonuclease PF0355 (Q8U3V0) · a predicted model of the same protein · chain D 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 Q8U3V0
- Elsewhere: RCSB PDB 1Y82 · PDBe 1Y82 · UniProt Q8U3V0
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