Research workbench
Structure of PH1917 protein with the complex of IMP from Pyrococcus horikoshii
Analyse Structure of PH1917 protein with the complex of IMP from Pyrococcus horikoshii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DVN
- Type
- protein
- Length
- 372 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.6
- Source
- Pyrococcus horikoshii
- Molecule
- Hypothetical protein PH1917
- UniProt
- O59580
- Ligands
- IMP, SO4
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · resolution 1.6 · 1 distinct chain · 39% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hypothetical protein PH1917 | protein | 186 | 39% helix, 26% strand | O59580 |
Ligands and binding sites
- IMP · Inosinic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 13 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 841 | 0.78 | 0.81 | 86 | SO4, IMP, GOL |
| 2 | 343 | 0.60 | 0.77 | 48 | IMP, GOL |
| 3 | 59 | 0.29 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 715 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2DVN · Structure of PH1917 protein with the complex of imp from pyrococcus horikoshii · the same entry in another collection · chain A against A, TM-score 1.00
- O59580 · AlphaFold monomer V2.0 prediction for DITP/XTP pyrophosphatase (O59580) · 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 O59580
- Elsewhere: RCSB PDB 2DVN · PDBe 2DVN · UniProt O59580
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.