Research workbench
Structure of cyclodextrin glycosyltransferase complexed with a thio- maltopentaose
Analyse Structure of cyclodextrin glycosyltransferase complexed with a thio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 9CGT
- Type
- protein
- Length
- 684 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
- P30920
- Ligands
- 4SG, Z9E, GLC, 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 | 684 | 23% helix, 30% strand | P30920 |
Ligands and binding sites
- 4SG · 4-thio-alpha-D-glucopyranose · ligand · 2 copies · chains A
- Z9E · 1-thio-alpha-D-glucopyranose · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · 2 copies · 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 | 428 | 0.76 | 0.85 | 71 | empty |
| 2 | 390 | 0.64 | 0.78 | 34 | Z9E, 4SG, GLC |
| 3 | 160 | 0.43 | 0.74 | 25 | empty |
| 4 | 59 | 0.31 | 0.76 | 20 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 9CGT · Structure of cyclodextrin glycosyltransferase complexed with a thio-maltopentaose · the same entry in another collection · chain A against A, TM-score 1.00
- P30920 · AlphaFold monomer V2.0 prediction for cyclomaltodextrin glucanotransferase (P30920) · 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 P30920
- Elsewhere: RCSB PDB 9CGT · PDBe 9CGT · UniProt P30920
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