MolNFT v1 · #47363 · protein
Structure of a covalent intermediate in thermus thermophilus amylomaltase
2OWC · 4-alpha-glucanotransferase: “Structure of a covalent intermediate in thermus thermophilus amylomaltase”. X-ray diffraction, 3 ligands (SUI, AC1, GLC), 7 pockets (best druggability 0.78). MolNFT v1 #47363 on GenesisL1: 3D structure…
- PDB
- 2OWC
- 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, GLC
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-alpha-glucanotransferase (EC 2.4.1.25) | protein | 498 | 46% helix, 13% 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
- GLC · alpha-D-glucopyranose · sugar · chains A
- GOL · Glycerol · additive · chains A
- MLI · Malonate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.78 | 0.98 | 29 | empty |
| 2 | 803 | 0.74 | 0.79 | 61 | GLC, AC1, GOL |
| 3 | 146 | 0.46 | 0.76 | 24 | MLI |
| 4 | 62 | 0.40 | 0.80 | 18 | empty |
| 5 | 101 | 0.39 | 0.76 | 20 | empty |
Modifications
Observed in the structure: 2 covalent, 1 glycan (covalent ligand, glycosylation).
Compared structures
- 2OWC · Structure of a covalent intermediate in Thermus thermophilus amylomaltase · 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 2OWC · PDBe 2OWC · UniProt Q72J82
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