MolNFT v1 · #121604 · protein
Cycloalternan-forming enzyme from listeria monocytogenes in complex with cycloalternan
5I0D · LMO2446 protein: “Cycloalternan-forming enzyme from listeria monocytogenes in complex with cycloalternan”. X-ray diffraction, 4 ligands (GLC, MG, CA), 19 pockets (best druggability 0.68). MolNFT v1 #121604 on GenesisL1: 3D…
- PDB
- 5I0D
- Type
- protein
- Length
- 2,120 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LMO2446 protein
- UniProt
- Q8Y4J2
- Ligands
- GLC, MG, CA, CL
- Pockets
- 19 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | LMO2446 protein | protein | 1060 | 18% helix, 37% strand | Q8Y4J2 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 37 copies · chains A, B
- MG · Magnesium ion · metal · 8 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 932 | 0.68 | 0.74 | 104 | empty |
| 2 | 487 | 0.66 | 0.78 | 60 | CL |
| 3 | 358 | 0.63 | 0.79 | 43 | CL |
| 4 | 201 | 0.55 | 0.79 | 29 | GLC |
| 5 | 225 | 0.53 | 0.77 | 32 | GLC |
Interfaces
1 interface between chains.
- A–B · 387 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 60 modified (engineered).
Compared structures
- 5I0D · Cycloalternan-forming enzyme from Listeria monocytogenes in complex with cycloalternan · 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
- Every structure of UniProt Q8Y4J2
- Elsewhere: RCSB PDB 5I0D · PDBe 5I0D · UniProt Q8Y4J2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.