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Crystal structure of rat DNPH1 (rcl) with 6-naphthyl-purine-riboside- monophosphate
Analyse Crystal structure of rat DNPH1 (rcl) with 6-naphthyl-purine-riboside… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P5D
- Type
- protein
- Length
- 286 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2'-deoxynucleoside 5'-phosphate N-hydrolase 1
- EC
- 3.2.2.-
- UniProt
- O35820
- Ligands
- N6P, SO4
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 (EC 3.2.2.-) | protein | 142 | 45% helix, 15% strand | O35820 |
| A | 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 (EC 3.2.2.-) | protein | 144 | 44% helix, 15% strand | O35820 |
Ligands and binding sites
- N6P · 6-(naphthalen-2-yl)-9-(5-O-phosphono-beta-D-ribofuranosyl)-9H-purine · ligand · 2 copies · chains C, A
- SO4 · Sulfate ion · ion · chains A
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 | 322 | 0.62 | 0.79 | 33 | N6P |
| 2 | 365 | 0.60 | 0.76 | 36 | N6P |
| 3 | 138 | 0.41 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- C–A · 296 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4P5D · Crystal structure of rat DNPH1 (rcl) with 6-naphthyl-purine-riboside-monophosphate · the same entry in another collection · chain C against C, TM-score 1.00
- O35820 · AlphaFold monomer V2.0 prediction for 2'-deoxynucleoside 5'-phosphate N-hydrolase 1… · a predicted model of the same protein · chain C against A, TM-score 0.97
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 O35820
- Elsewhere: RCSB PDB 4P5D · PDBe 4P5D · UniProt O35820
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