Research workbench
Plant nucleoside hydrolase - PPNRH1 enzyme
Analyse Plant nucleoside hydrolase - PPNRH1 enzyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KPN
- Type
- protein
- Length
- 2,544 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside N-ribohydrolase 1
- EC
- 3.2.2.1
- UniProt
- M1FQT3
- Ligands
- CA
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Nucleoside N-ribohydrolase 1 (EC 3.2.2.1) | protein | 318 | 39% helix, 19% strand | M1FQT3 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 970 | 0.80 | 0.81 | 81 | empty |
| 2 | 470 | 0.75 | 0.84 | 46 | CA |
| 3 | 306 | 0.75 | 0.87 | 37 | empty |
| 4 | 344 | 0.74 | 0.85 | 40 | CA |
| 5 | 446 | 0.73 | 0.83 | 50 | CA |
Interfaces
14 interfaces between chains.
- A–B · 1421 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1340 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 1239 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1235 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 889 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4KPN · Plant nucleoside hydrolase - PpNRh1 enzyme · the same entry in another collection · chain A against A, TM-score 1.00
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 M1FQT3
- Elsewhere: RCSB PDB 4KPN · PDBe 4KPN · UniProt M1FQT3
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