Research workbench
Crystal structure of DNPH1 (rcl) with kinetine riboside monophosphate
Analyse Crystal structure of DNPH1 (rcl) with kinetine riboside monophosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KXN
- Type
- protein
- Length
- 513 residues
- Chains
- 4
- 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
- 6K6
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 (EC 3.2.2.-) | protein | 131 | 47% helix, 18% strand | O35820 |
| B | 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 (EC 3.2.2.-) | protein | 126 | 47% helix, 18% strand | O35820 |
| C | 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 (EC 3.2.2.-) | protein | 125 | 47% helix, 18% strand | O35820 |
Ligands and binding sites
- 6K6 · N-(furan-2-ylmethyl)adenosine 5'-(dihydrogen phosphate) · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.65 | 0.82 | 32 | empty |
| 2 | 204 | 0.64 | 0.84 | 35 | 6K6 |
| 3 | 174 | 0.64 | 0.85 | 35 | 6K6 |
| 4 | 162 | 0.56 | 0.81 | 32 | 6K6 |
| 5 | 145 | 0.49 | 0.78 | 24 | 6K6 |
Interfaces
6 interfaces between chains.
- A–B · 1475 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1469 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 374 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 373 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 29 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4KXN · Crystal structure of DNPH1 (RCL) with kinetine riboside monophosphate · the same entry in another collection · chain D against D, 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 0.98
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 O35820
- Elsewhere: RCSB PDB 4KXN · PDBe 4KXN · UniProt O35820
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