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Crystal structure of the gracilariopsis lemaneiformis alpha-1,4- glucan lyase covalent intermediate complex with 5-fluoro-idosyl- fluoride
Analyse Crystal structure of the gracilariopsis lemaneiformis alpha-1,4- glucan lyase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AMW
- Type
- protein
- Length
- 4,100 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-1,4-glucan lyase isozyme 1
- EC
- 4.2.2.13
- UniProt
- Q9STC1
- Ligands
- B9D, 5DI
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Alpha-1,4-glucan lyase isozyme 1 (EC 4.2.2.13) | protein | 1025 | 20% helix, 29% strand | Q9STC1 |
Ligands and binding sites
- B9D · 5-fluoro-alpha-L-idopyranose · ligand · 3 copies · chains A, B, C
- 5DI · alpha-D-threo-hexo-2,5-diulo-2,6-pyranosyl fluoride · ligand · chains D
- GOL · Glycerol · additive · 7 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.76 | 0.97 | 34 | empty |
| 2 | 65 | 0.75 | 0.99 | 18 | empty |
| 3 | 73 | 0.72 | 0.97 | 30 | empty |
| 4 | 61 | 0.71 | 0.98 | 24 | empty |
| 5 | 500 | 0.70 | 0.80 | 44 | empty |
Interfaces
3 interfaces between chains.
- A–C · 793 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 120 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 74 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified, 3 covalent (oxidation, covalent ligand).
Compared structures
- 4AMW · CRYSTAL STRUCTURE OF THE GRACILARIOPSIS LEMANEIFORMIS ALPHA-1,4- GLUCAN LYASE Covalent… · 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 Q9STC1
- Elsewhere: RCSB PDB 4AMW · PDBe 4AMW · UniProt Q9STC1
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