MolNFT v1 · #34411 · protein
Crystal structure of the PH0510 protein from pyrococcus horikoshii OT3 in complex with beta-D-fructopyranose-1-phosphate
2DF8 · 325AA long hypothetical protein: “Crystal structure of the PH0510 protein from pyrococcus horikoshii OT3 in complex with…”. X-ray diffraction, 1 ligand (F1P), 6 pockets (best druggability 0.88). MolNFT v1 #34411 on GenesisL1: 3D…
- PDB
- 2DF8
- Type
- protein
- Length
- 649 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 325AA long hypothetical protein
- UniProt
- O58246
- Ligands
- F1P
- Pockets
- 6 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 325AA long hypothetical protein | protein | 325 | 45% helix, 17% strand | O58246 |
| B | 325AA long hypothetical protein | protein | 324 | 46% helix, 17% strand | O58246 |
Ligands and binding sites
- F1P · 1-O-phosphono-beta-D-fructopyranose · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
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 | 655 | 0.88 | 0.92 | 71 | EDO |
| 2 | 105 | 0.77 | 0.97 | 26 | F1P |
| 3 | 134 | 0.75 | 0.94 | 31 | F1P |
| 4 | 141 | 0.62 | 0.85 | 23 | empty |
| 5 | 137 | 0.60 | 0.84 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2767 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 2DF8 · Crystal Structure of the PH0510 protein from Pyrococcus horikoshii OT3 in complex with… · 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 O58246
- Elsewhere: RCSB PDB 2DF8 · PDBe 2DF8 · UniProt O58246
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