MolNFT v1 · #77609 · protein
'X-ray crystal structure of the putative N-type ATP pyrophosphatase (PF0828) in complex with ATP from pyrococcus furiosus, northeast structural genomics consortium target PFR23
3RK1 · N-type ATP pyrophosphatase superfamily: “'X-ray crystal structure of the putative N-type ATP pyrophosphatase (PF0828) in complex with ATP from…”. X-ray diffraction, 2 ligands (ATP, PO4), 5 pockets (best druggability 0.76). MolNFT v1…
- PDB
- 3RK1
- Type
- protein
- Length
- 444 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-type ATP pyrophosphatase superfamily
- UniProt
- Q8U2K6
- Ligands
- ATP, PO4
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-type ATP pyrophosphatase superfamily | protein | 221 | 34% helix, 30% strand | Q8U2K6 |
| B | N-type ATP pyrophosphatase superfamily | protein | 223 | 32% helix, 30% strand | Q8U2K6 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 527 | 0.76 | 0.83 | 49 | ATP |
| 2 | 390 | 0.74 | 0.85 | 45 | ATP, PO4 |
| 3 | 791 | 0.69 | 0.75 | 61 | empty |
| 4 | 111 | 0.44 | 0.78 | 21 | PO4 |
| 5 | 57 | 0.30 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1002 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 3RK1 · 'X-ray crystal Structure of the putative N-type ATP pyrophosphatase (PF0828) in complex… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q8U2K6
- Elsewhere: RCSB PDB 3RK1 · PDBe 3RK1 · UniProt Q8U2K6
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