MolNFT v1 · #103077 · protein
Crystal structure of human DNPH1 (rcl) with 6-naphthyl-purine- riboside-monophosphate
4P5E · 2'-deoxynucleoside 5'-phosphate N-hydrolase 1: “Crystal structure of human DNPH1 (rcl) with 6-naphthyl-purine- riboside-monophosphate”. X-ray diffraction, 2 ligands (N6P, CA), 5 pockets (best druggability 0.53). MolNFT v1 #103077 on…
- PDB
- 4P5E
- Type
- protein
- Length
- 276 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
- O43598
- Ligands
- N6P, CA
- Pockets
- 5 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 (EC 3.2.2.-) | protein | 140 | 46% helix, 16% strand | O43598 |
| B | 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 (EC 3.2.2.-) | protein | 136 | 44% helix, 16% strand | O43598 |
Ligands and binding sites
- N6P · 6-(naphthalen-2-yl)-9-(5-O-phosphono-beta-D-ribofuranosyl)-9H-purine · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · chains 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 226 | 0.53 | 0.77 | 24 | N6P |
| 2 | 140 | 0.51 | 0.80 | 19 | empty |
| 3 | 197 | 0.49 | 0.76 | 26 | N6P |
| 4 | 117 | 0.39 | 0.75 | 22 | empty |
| 5 | 92 | 0.34 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 448 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4P5E · Crystal structure of human DNPH1 (rcl) with 6-naphthyl-purine-riboside-monophosphate · the same entry in another collection · chain A against A, TM-score 1.00
- O43598 · AlphaFold monomer V2.0 prediction for 2'-deoxynucleoside 5'-phosphate N-hydrolase 1… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 O43598
- Elsewhere: RCSB PDB 4P5E · PDBe 4P5E · UniProt O43598
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