Research workbench
Bacillus circulans strain 251 cyclodextrin glycosyltransferase: a mutant Y89D/S146P complexed to an hexasaccharide inhibitor
Analyse Bacillus circulans strain 251 cyclodextrin glycosyltransferase: a mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DTU
- Type
- protein
- Length
- 686 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (cyclodextrin glycosyltransferase)
- EC
- 2.4.1.19
- UniProt
- P43379
- Ligands
- G6D, ADH, GLC, BGC, CA
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (cyclodextrin glycosyltransferase) (EC 2.4.1.19) | protein | 686 | 23% helix, 30% strand | P43379 |
Ligands and binding sites
- G6D · alpha-D-quinovopyranose · ligand · chains A
- ADH · 1-amino-2,3-dihydroxy-5-hydroxymethyl cyclohex-5-ene · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · 13 copies · chains A
- BGC · beta-D-glucopyranose · sugar · chains A
- CA · Calcium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 422 | 0.76 | 0.86 | 60 | empty |
| 2 | 354 | 0.62 | 0.78 | 30 | GLC, G6D, ADH |
| 3 | 104 | 0.38 | 0.75 | 20 | empty |
| 4 | 84 | 0.37 | 0.76 | 18 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1DTU · Bacillus circulans strain 251 cyclodextrin glycosyltransferase: a mutant Y89D/S146P… · the same entry in another collection · chain A against A, TM-score 1.00
- P43379 · AlphaFold monomer V2.0 prediction for cyclomaltodextrin glucanotransferase (P43379) · a predicted model of the same protein · 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 P43379
- Elsewhere: RCSB PDB 1DTU · PDBe 1DTU · UniProt P43379
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