MolNFT v1 · #34390 · protein
Crystal structure of project id PH0725 from pyrococcus horikoshii OT3 at 1.65 a resolution
2DEK · Probable diphthine synthase: “Crystal structure of project id PH0725 from pyrococcus horikoshii OT3 at 1.65 a resolution”. X-ray diffraction, 2 ligands (SAH, NA), 7 pockets (best druggability 0.75). MolNFT v1 #34390 on GenesisL1: 3D…
- PDB
- 2DEK
- Type
- protein
- Length
- 530 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable diphthine synthase
- EC
- 2.1.1.98
- UniProt
- O58456
- Ligands
- SAH, NA
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable diphthine synthase (EC 2.1.1.98) | protein | 265 | 39% helix, 23% strand | O58456 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 473 | 0.75 | 0.83 | 48 | empty |
| 2 | 417 | 0.74 | 0.84 | 57 | SAH |
| 3 | 146 | 0.41 | 0.74 | 19 | empty |
| 4 | 113 | 0.41 | 0.76 | 17 | empty |
| 5 | 92 | 0.39 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2544 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 2DEK · Crystal structure of project ID PH0725 from Pyrococcus horikoshii OT3 at 1.65 A resolution · the same entry in another collection · chain A against A, TM-score 1.00
- O58456 · AlphaFold monomer V2.0 prediction for diphthine synthase (O58456) · a predicted model of the same protein · chain B 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 O58456
- Elsewhere: RCSB PDB 2DEK · PDBe 2DEK · UniProt O58456
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