Research workbench
SYRB2 with alpha-ketoglutarate
Analyse SYRB2 with alpha-ketoglutarate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FCU
- Type
- protein
- Length
- 608 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Syringomycin biosynthesis enzyme 2
- Ligands
- AKG, DSU
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Syringomycin biosynthesis enzyme 2 | protein | 309 | 19% helix, 28% strand | — |
| B | Syringomycin biosynthesis enzyme 2 | protein | 299 | 19% helix, 29% strand | — |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, B
- DSU · ((2R,3S,4S,5S)-3,4-dihydroxy-5-(hydroxymethyl)-5-((2R,3S,4S,5S,6R)-3,4,5-trihydroxy-6-methoxy-tetrahydro-2H-pyran-2-yloxy)-tetrahydrofuran-2-yl)methyl nonanoate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 344 | 0.85 | 0.94 | 44 | AKG |
| 2 | 417 | 0.82 | 0.89 | 42 | AKG |
| 3 | 423 | 0.67 | 0.79 | 50 | empty |
| 4 | 415 | 0.64 | 0.78 | 49 | empty |
| 5 | 231 | 0.55 | 0.78 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 877 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 2FCU · SyrB2 with alpha-ketoglutarate · the same entry in another collection · chain A 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
- Elsewhere: RCSB PDB 2FCU · PDBe 2FCU
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.