MolNFT v1 · #53699 · protein
Crystal structure of the gracilariopsis lemaneiformis alpha-1,4- glucan lyase
2X2H · Alpha-1,4-glucan lyase isozyme 1: “Crystal structure of the gracilariopsis lemaneiformis alpha-1,4- glucan lyase”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability 0.74). MolNFT v1 #53699 on GenesisL1: 3D structure…
- PDB
- 2X2H
- 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
- CL
- Pockets
- 20 · best druggability 0.74
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
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 16 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 9 copies · chains A, C, 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 | 59 | 0.74 | 0.99 | 18 | empty |
| 2 | 55 | 0.74 | 1.00 | 18 | empty |
| 3 | 170 | 0.72 | 0.90 | 51 | empty |
| 4 | 53 | 0.71 | 0.99 | 25 | empty |
| 5 | 683 | 0.71 | 0.78 | 64 | empty |
Interfaces
3 interfaces between chains.
- A–C · 773 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 131 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 111 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 2X2H · Crystal structure of the Gracilariopsis lemaneiformis alpha-1,4- glucan lyase · 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 2X2H · PDBe 2X2H · UniProt Q9STC1
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