MolNFT v1 · #59427 · protein
Crystal structure of streptomyces venezuelae desvi
3BXO · N,N-dimethyltransferase: “Crystal structure of streptomyces venezuelae desvi”. X-ray diffraction, 2 ligands (UPP, SAM), 2 pockets (best druggability 0.75). MolNFT v1 #59427 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3BXO
- Type
- protein
- Length
- 472 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N,N-dimethyltransferase
- UniProt
- Q9ZGH6
- Ligands
- UPP, SAM
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | N,N-dimethyltransferase | protein | 236 | 31% helix, 36% strand | Q9ZGH6 |
Ligands and binding sites
- UPP · Phenyl-uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 612 | 0.75 | 0.81 | 57 | UPP, SAM |
| 2 | 572 | 0.74 | 0.81 | 54 | UPP, SAM |
Interfaces
1 interface between chains.
- A–B · 814 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3BXO · Crystal Structure of Streptomyces venezuelae DesVI · the same entry in another collection · chain A against A, TM-score 1.00
- Q9ZGH6 · AlphaFold monomer V2.0 prediction for dtdp-3-amino-3,4,6-trideoxy- alpha-D-glucopyranose… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9ZGH6
- Elsewhere: RCSB PDB 3BXO · PDBe 3BXO · UniProt Q9ZGH6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.