MolNFT v1 · #34918 · protein
Crystal structure of LEU65 to ala mutant of diphthine synthase
2DV5: “Crystal structure of LEU65 to ala mutant of diphthine synthase”. X-ray diffraction, 2 ligands (SAH, SO4), 7 pockets (best druggability 0.74). MolNFT v1 #34918 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2DV5
- 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
- 7 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Diphthine synthase (EC 2.1.1.98) | protein | 265 | 37% helix, 23% strand | O58456 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
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 | 435 | 0.74 | 0.84 | 57 | SO4, SAH |
| 2 | 454 | 0.73 | 0.83 | 49 | SO4 |
| 3 | 110 | 0.41 | 0.76 | 16 | empty |
| 4 | 139 | 0.40 | 0.74 | 19 | empty |
| 5 | 95 | 0.37 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2594 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 2DV5 · PDBe 2DV5 · UniProt O58456
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