Research workbench
Crystal structure of F283Y mutant cyclodextrin glycosyltransferase complexed with a pseudo-tetraose derived from acarbose
Analyse Crystal structure of F283Y mutant cyclodextrin glycosyltransferase complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1V3M
- Type
- protein
- Length
- 1,372 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclomaltodextrin glucanotransferase
- EC
- 2.4.1.19
- UniProt
- P05618
- Ligands
- GLD, ACI, GLC, GAL, CA
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cyclomaltodextrin glucanotransferase (EC 2.4.1.19) | protein | 686 | 23% helix, 30% strand | P05618 |
Ligands and binding sites
- GLD · 4,6-dideoxy-alpha-D-xylo-hexopyranose · ligand · 2 copies · chains A, B
- ACI · 6-amino-4-hydroxymethyl-cyclohex-4-ene-1,2,3-triol · ligand · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 6 copies · chains B, A
- GAL · beta-D-galactopyranose · sugar · 5 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
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 419 | 0.72 | 0.82 | 65 | empty |
| 2 | 394 | 0.71 | 0.83 | 68 | empty |
| 3 | 1190 | 0.71 | 0.75 | 120 | empty |
| 4 | 368 | 0.65 | 0.80 | 35 | GAL, GLD, GLC, ACI |
| 5 | 363 | 0.64 | 0.79 | 34 | GAL, GLD, GLC, ACI |
Interfaces
1 interface between chains.
- A–B · 755 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1V3M · Crystal structure of F283Y mutant cyclodextrin glycosyltransferase complexed with a… · 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 B 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 1V3M · PDBe 1V3M · UniProt P05618
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