MolNFT v1 · #50401 · protein
Structure of xac npp for evaluation of refinement methodology
2RH6 · Phosphodiesterase-nucleotide pyrophosphatase: “Structure of xac npp for evaluation of refinement methodology”. X-ray diffraction, 2 ligands (AMP, ZN), 3 pockets (best druggability 0.81). MolNFT v1 #50401 on GenesisL1: 3D structure…
- PDB
- 2RH6
- Type
- protein
- Length
- 764 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphodiesterase-nucleotide pyrophosphatase
- EC
- 3.6.1.9
- UniProt
- Q8PIS1
- Ligands
- AMP, ZN
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphodiesterase-nucleotide pyrophosphatase (EC 3.6.1.9) | protein | 382 | 35% helix, 22% strand | Q8PIS1 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 3 copies · chains A, B
- ZN · Zinc ion · metal · 4 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 965 | 0.81 | 0.82 | 115 | empty |
| 2 | 462 | 0.67 | 0.79 | 46 | AMP |
| 3 | 461 | 0.66 | 0.78 | 44 | AMP |
Interfaces
1 interface between chains.
- A–B · 692 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2RH6 · Structure of Xac NPP for evaluation of refinement methodology · 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 Q8PIS1
- Elsewhere: RCSB PDB 2RH6 · PDBe 2RH6 · UniProt Q8PIS1
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