Research workbench
Crystal structure of purp from pyrococcus furiosus complexed with AMP and aicar
Analyse Crystal structure of purp from pyrococcus furiosus complexed with AMP and aicar in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R84
- Type
- protein
- Length
- 642 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purp protein PF1517
- UniProt
- Q8U0R7
- Ligands
- AMP, AMZ, NA, CL
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Purp protein PF1517 | protein | 329 | 38% helix, 24% strand | Q8U0R7 |
| B | Purp protein PF1517 | protein | 313 | 39% helix, 24% strand | Q8U0R7 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- AMZ · Aminoimidazole 4-carboxamide ribonucleotide · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, B
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 | 551 | 0.66 | 0.77 | 54 | NA, CL, AMP, AMZ, MPD |
| 2 | 480 | 0.62 | 0.76 | 51 | NA, CL, AMP, AMZ |
| 3 | 63 | 0.33 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 350 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2R84 · Crystal structure of PurP from Pyrococcus furiosus complexed with AMP and AICAR · 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 0.95
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 2R84 · PDBe 2R84 · UniProt Q8U0R7
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