MolNFT v1 · #4143 · protein
Crystal structure of alkalophilic asparagine 233-replaced cyclodextrin glucanotransferase complexed with an inhibitor, acarbose, at 2.0 a resolution
1DED: “Crystal structure of alkalophilic asparagine 233-replaced cyclodextrin glucanotransferase complexed with an…”. X-ray diffraction, 4 ligands (AC1, BGC, GLC), 9 pockets (best druggability 0.74). MolNFT v1 #4143 on GenesisL1: 3D…
- PDB
- 1DED
- Type
- protein
- Length
- 1,372 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclodextrin glucanotransferase
- EC
- 2.4.1.19
- UniProt
- P05618
- Ligands
- AC1, BGC, GLC, CA
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cyclodextrin glucanotransferase (EC 2.4.1.19) | protein | 686 | 22% helix, 30% strand | P05618 |
Ligands and binding sites
- AC1 · 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose · ligand · 3 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 3 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 3 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 441 | 0.74 | 0.84 | 58 | empty |
| 2 | 408 | 0.72 | 0.83 | 61 | empty |
| 3 | 883 | 0.70 | 0.76 | 105 | empty |
| 4 | 391 | 0.66 | 0.80 | 39 | BGC, GLC, AC1 |
| 5 | 343 | 0.63 | 0.79 | 30 | BGC, GLC, AC1 |
Interfaces
1 interface between chains.
- A–B · 700 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1DED · Crystal structure of alkalophilic asparagine 233-replaced cyclodextrin glucanotransferase… · the same entry in another collection · chain A against A, TM-score 1.00
- P05618 · AlphaFold monomer V2.0 prediction for cyclomaltodextrin glucanotransferase (P05618) · 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 P05618
- Elsewhere: RCSB PDB 1DED · PDBe 1DED · UniProt P05618
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