Research workbench
Crystal structure of thermus aquaticus amylomaltase (GH77) in complex with a 34-meric cycloamylose
Analyse Crystal structure of thermus aquaticus amylomaltase (GH77) in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JIW
- Type
- protein
- Length
- 499 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
- O87172
- Ligands
- SNN, GLC, BGC, CO3
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-alpha-glucanotransferase (EC 2.4.1.25) | protein | 499 | 47% helix, 13% strand | O87172 |
Ligands and binding sites
- SNN · L-3-aminosuccinimide · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · 16 copies · chains A
- BGC · beta-D-glucopyranose · sugar · chains A
- CO3 · Carbonate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · 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 | 104 | 0.76 | 0.97 | 27 | empty |
| 2 | 811 | 0.70 | 0.76 | 74 | GLC |
| 3 | 168 | 0.49 | 0.77 | 24 | GLC |
| 4 | 94 | 0.41 | 0.77 | 21 | empty |
| 5 | 79 | 0.40 | 0.78 | 17 | empty |
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5JIW · Crystal structure of Thermus aquaticus amylomaltase (GH77) in complex with a 34-meric… · the same entry in another collection · chain A against A, TM-score 1.00
- O87172 · AlphaFold monomer V2.0 prediction for 4-alpha-glucanotransferase (O87172) · 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 O87172
- Elsewhere: RCSB PDB 5JIW · PDBe 5JIW · UniProt O87172
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