MolNFT v1 · #50094 · protein
Crystal structure of purp from pyrococcus furiosus complexed with AMP
2R85 · Purp protein PF1517: “Crystal structure of purp from pyrococcus furiosus complexed with AMP”. X-ray diffraction, 3 ligands (AMP, NA, CL), 4 pockets (best druggability 0.65). MolNFT v1 #50094 on GenesisL1: 3D structure, binding sites…
- PDB
- 2R85
- Type
- protein
- Length
- 659 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purp protein PF1517
- UniProt
- Q8U0R7
- Ligands
- AMP, NA, CL
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Purp protein PF1517 | protein | 330 | 39% helix, 24% strand | Q8U0R7 |
| B | Purp protein PF1517 | protein | 329 | 38% helix, 24% strand | Q8U0R7 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 4 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 · 4 copies · chains A, B
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 | 573 | 0.65 | 0.76 | 60 | NA, CL, AMP, MPD |
| 2 | 450 | 0.64 | 0.77 | 42 | AMP, MPD |
| 3 | 138 | 0.42 | 0.75 | 26 | NA, CL |
| 4 | 107 | 0.41 | 0.77 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 332 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2R85 · Crystal structure of PurP from Pyrococcus furiosus complexed with AMP · 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 0.93
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 2R85 · PDBe 2R85 · UniProt Q8U0R7
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