Research workbench
Crystal structure of DNPH1 (rcl) with 6-cyclopentyl-AMP
Analyse Crystal structure of DNPH1 (rcl) with 6-cyclopentyl-AMP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KXL
- Type
- protein
- Length
- 531 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
- 6C6, SO4
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 (EC 3.2.2.-) | protein | 135 | 47% helix, 17% strand | O35820 |
| B | 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 (EC 3.2.2.-) | protein | 126 | 49% helix, 18% strand | O35820 |
| C | 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 (EC 3.2.2.-) | protein | 134 | 49% helix, 17% strand | O35820 |
| D | 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 (EC 3.2.2.-) | protein | 136 | 43% helix, 17% strand | O35820 |
Ligands and binding sites
- 6C6 · N-cyclopentyladenosine 5'-(dihydrogen phosphate) · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 304 | 0.64 | 0.81 | 49 | empty |
| 2 | 214 | 0.64 | 0.83 | 34 | 6C6 |
| 3 | 176 | 0.61 | 0.83 | 33 | 6C6 |
| 4 | 122 | 0.61 | 0.86 | 31 | 6C6 |
| 5 | 206 | 0.58 | 0.80 | 35 | 6C6 |
Interfaces
5 interfaces between chains.
- A–B · 1453 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1438 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 458 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 456 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 42 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4KXL · Crystal structure of DNPH1 (RCL) with 6-CYCLOPENTYL-AMP · 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 B 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 4KXL · PDBe 4KXL · UniProt O35820
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