MolNFT v1 · #98052 · protein
Crystal structure of DNPH1 (rcl) with N6-isopentenyl-AMP
4KXM · 2'-deoxynucleoside 5'-phosphate N-hydrolase 1: “Crystal structure of DNPH1 (rcl) with N6-isopentenyl-AMP”. X-ray diffraction, 1 ligand (6IA), 6 pockets (best druggability 0.64). MolNFT v1 #98052 on GenesisL1: 3D structure, binding…
- PDB
- 4KXM
- Type
- protein
- Length
- 525 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
- 6IA
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 (EC 3.2.2.-) | protein | 130 | 48% helix, 18% strand | O35820 |
| B, D | 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 (EC 3.2.2.-) | protein | 132 | 48% helix, 17% strand | O35820 |
| C | 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 (EC 3.2.2.-) | protein | 131 | 47% helix, 18% strand | O35820 |
Ligands and binding sites
- 6IA · N6-isopentenyl-adenosine-5'-monophosphate · ligand · 4 copies · chains A, B, 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 | 210 | 0.64 | 0.83 | 37 | 6IA |
| 2 | 331 | 0.63 | 0.79 | 34 | empty |
| 3 | 114 | 0.61 | 0.86 | 30 | 6IA |
| 4 | 177 | 0.60 | 0.82 | 33 | 6IA |
| 5 | 84 | 0.55 | 0.86 | 22 | 6IA |
Interfaces
6 interfaces between chains.
- A–B · 1477 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1470 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 349 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 313 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 27 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4KXM · Crystal structure of DNPH1 (RCL) WITH N6-ISOPENTENYL-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 A 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 O35820
- Elsewhere: RCSB PDB 4KXM · PDBe 4KXM · UniProt O35820
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