MolNFT v1 · #34916 · protein
Crystal structure of LEU65 to arg mutant of diphthine synthase
2DV3: “Crystal structure of LEU65 to arg mutant of diphthine synthase”. X-ray diffraction, 3 ligands (SAH, NA, CL), 8 pockets (best druggability 0.74). MolNFT v1 #34916 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2DV3
- 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, NA, CL
- Pockets
- 8 · 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
- NA · Sodium ion · metal · chains A, B
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · 2 copies · chains B, A
- FMT · Formic acid · additive · chains 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 | 412 | 0.74 | 0.84 | 55 | SAH |
| 2 | 468 | 0.74 | 0.83 | 48 | GOL |
| 3 | 105 | 0.40 | 0.76 | 16 | empty |
| 4 | 125 | 0.39 | 0.74 | 17 | empty |
| 5 | 96 | 0.39 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2546 Ų buried · 29 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 2DV3 · PDBe 2DV3 · UniProt O58456
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