Research workbench
Cycloalternan-degrading enzyme from trueperella pyogenes
Analyse Cycloalternan-degrading enzyme from trueperella pyogenes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F7S
- Type
- protein
- Length
- 1,403 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoside hydrolase family 31
- UniProt
- X4QP62
- Ligands
- CA
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoside hydrolase family 31 | protein | 701 | 25% helix, 28% strand | X4QP62 |
| B | Glycoside hydrolase family 31 | protein | 702 | 25% helix, 28% strand | X4QP62 |
Ligands and binding sites
- CA · Calcium ion · metal · 9 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 680 | 0.76 | 0.81 | 57 | PEG |
| 2 | 663 | 0.75 | 0.81 | 57 | PGE |
| 3 | 439 | 0.63 | 0.77 | 43 | CA |
| 4 | 255 | 0.58 | 0.78 | 27 | CA |
| 5 | 249 | 0.58 | 0.78 | 29 | CA |
Interfaces
1 interface between chains.
- A–B · 467 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5F7S · Cycloalternan-degrading enzyme from Trueperella pyogenes · 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 X4QP62
- Elsewhere: RCSB PDB 5F7S · PDBe 5F7S · UniProt X4QP62
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