MolNFT v1 · #35551 · protein
Mutant Y29M structure of PH0725 from pyrococcus horikoshii OT3
2EEQ · Diphthine synthase: “Mutant Y29M structure of PH0725 from pyrococcus horikoshii OT3”. X-ray diffraction, 2 ligands (SAH, SO4), 8 pockets (best druggability 0.75). MolNFT v1 #35551 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2EEQ
- Type
- protein
- Length
- 530 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diphthine synthase
- EC
- 2.1.1.98
- UniProt
- O58456
- Ligands
- SAH, SO4
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Diphthine synthase (EC 2.1.1.98) | protein | 265 | 38% helix, 23% strand | O58456 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
- SO4 · Sulfate ion · ion · 5 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
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 484 | 0.75 | 0.83 | 50 | SO4 |
| 2 | 428 | 0.74 | 0.83 | 60 | SAH |
| 3 | 146 | 0.43 | 0.75 | 19 | empty |
| 4 | 103 | 0.39 | 0.76 | 18 | empty |
| 5 | 87 | 0.36 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2600 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
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 2EEQ · PDBe 2EEQ · UniProt O58456
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