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Covalent intermediate in amylomaltase in complex with the acceptor analog 4-deoxyglucose
Analyse Covalent intermediate in amylomaltase in complex with the acceptor analog… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OWW
- Type
- protein
- Length
- 498 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-alpha-glucanotransferase
- EC
- 2.4.1.25
- UniProt
- Q72J82
- Ligands
- SUI, AC1, G4D, GLC
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-alpha-glucanotransferase (EC 2.4.1.25) | protein | 498 | 46% helix, 12% strand | Q72J82 |
Ligands and binding sites
- SUI · (3-amino-2,5-dioxo-1-pyrrolidinyl)acetic acid · ligand · chains A
- 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 · chains A
- G4D · 4-deoxy-alpha-D-glucopyranose · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- MLI · Malonate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 108 | 0.79 | 0.98 | 28 | GOL |
| 2 | 796 | 0.76 | 0.80 | 70 | GLC, AC1, G4D, GOL |
| 3 | 155 | 0.47 | 0.76 | 27 | MLI |
| 4 | 76 | 0.42 | 0.80 | 19 | empty |
| 5 | 57 | 0.35 | 0.78 | 15 | empty |
Modifications
Observed in the structure: 2 covalent, 1 glycan (covalent ligand, glycosylation).
Compared structures
- 2OWW · Covalent intermediate in amylomaltase in complex with the acceptor analog 4-deoxyglucose · 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 Q72J82
- Elsewhere: RCSB PDB 2OWW · PDBe 2OWW · UniProt Q72J82
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