Research workbench
Crystal structure of purp from pyrococcus furiosus complexed with ATP
Analyse Crystal structure of purp from pyrococcus furiosus complexed with ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R86
- Type
- protein
- Length
- 652 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purp protein PF1517
- UniProt
- Q8U0R7
- Ligands
- ATP, NA, PO4
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Purp protein PF1517 | protein | 334 | 38% helix, 24% strand | Q8U0R7 |
| B | Purp protein PF1517 | protein | 318 | 38% helix, 25% strand | Q8U0R7 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 627 | 0.69 | 0.77 | 64 | PO4, NA, ATP, MPD |
| 2 | 474 | 0.63 | 0.76 | 44 | NA, ATP |
| 3 | 55 | 0.35 | 0.79 | 17 | PO4 |
Interfaces
1 interface between chains.
- A–B · 353 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2R86 · Crystal structure of PurP from Pyrococcus furiosus complexed with ATP · the same entry in another collection · chain A against A, TM-score 1.00
- Q8U0R7 · AlphaFold monomer V2.0 prediction for 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofu… · a predicted model of the same protein · chain B against A, TM-score 0.94
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 Q8U0R7
- Elsewhere: RCSB PDB 2R86 · PDBe 2R86 · UniProt Q8U0R7
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