MolNFT v1 · #34935 · protein
Structure of PH1917 protein with the complex of imp from pyrococcus horikoshii
2DVN · Hypothetical protein PH1917: “Structure of PH1917 protein with the complex of imp from pyrococcus horikoshii”. X-ray diffraction, 2 ligands (IMP, SO4), 3 pockets (best druggability 0.78). MolNFT v1 #34935 on GenesisL1: 3D structure…
- PDB
- 2DVN
- Type
- protein
- Length
- 372 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein PH1917
- UniProt
- O59580
- Ligands
- IMP, SO4
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 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
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