Research workbench
Crystal structure of purp from pyrococcus furiosus complexed with ADP
Analyse Crystal structure of purp from pyrococcus furiosus complexed with ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R87
- Type
- protein
- Length
- 2,004 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purp protein PF1517
- UniProt
- Q8U0R7
- Ligands
- ADP, PO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Purp protein PF1517 | protein | 334 | 38% helix, 24% strand | Q8U0R7 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 19 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 251 | 0.86 | 0.98 | 33 | empty |
| 2 | 263 | 0.86 | 0.98 | 36 | empty |
| 3 | 241 | 0.85 | 0.97 | 28 | empty |
| 4 | 217 | 0.84 | 0.97 | 26 | empty |
| 5 | 645 | 0.82 | 0.86 | 79 | PO4, ADP |
Interfaces
9 interfaces between chains.
- D–F · 2146 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 2142 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 2064 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 2053 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 2053 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 2R87 · Crystal structure of PurP from Pyrococcus furiosus complexed with ADP · the same entry in another collection · chain C against C, 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 A against A, TM-score 0.98
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 2R87 · PDBe 2R87 · UniProt Q8U0R7
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