Research workbench
Cycloalternan-degrading enzyme from trueperella pyogenes in complex with covalent intermediate
Analyse Cycloalternan-degrading enzyme from trueperella pyogenes in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I0F
- Type
- protein
- Length
- 729 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoside hydrolase family 31
- UniProt
- X4QP62
- Ligands
- GLC, BGC, CA
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Glycoside hydrolase family 31 | protein | 729 | 25% helix, 27% strand | X4QP62 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 3 copies · chains B
- BGC · beta-D-glucopyranose · sugar · chains B
- CA · Calcium ion · metal · 8 copies · chains B
- PGE · Triethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 642 | 0.75 | 0.81 | 52 | CA, PGE |
| 2 | 282 | 0.59 | 0.78 | 35 | GLC, BGC |
| 3 | 147 | 0.41 | 0.74 | 25 | empty |
| 4 | 87 | 0.33 | 0.74 | 20 | empty |
| 5 | 83 | 0.32 | 0.73 | 18 | empty |
Modifications
Observed in the structure: 1 glycan (glycosylation).
Compared structures
- 5I0F · Cycloalternan-degrading enzyme from Trueperella pyogenes in complex with covalent… · the same entry in another collection · chain B against B, 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 X4QP62
- Elsewhere: RCSB PDB 5I0F · PDBe 5I0F · UniProt X4QP62
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.