MolNFT v1 · #142059 · protein
Crystal structure of agl-ka catalytic domain
5ZRU · Alpha-1,3-glucanase: “Crystal structure of agl-ka catalytic domain”. X-ray diffraction, 3 ligands (CA, ZN, SO4), 11 pockets (best druggability 0.76). MolNFT v1 #142059 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ZRU
- Type
- protein
- Length
- 1,152 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-1,3-glucanase
- UniProt
- Q0WYG9
- Ligands
- CA, ZN, SO4
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Alpha-1,3-glucanase | protein | 576 | 6% helix, 44% strand | Q0WYG9 |
Ligands and binding sites
- CA · Calcium ion · metal · 10 copies · chains A, C
- ZN · Zinc ion · metal · 4 copies · chains A, C
- SO4 · Sulfate ion · ion · 4 copies · chains A, C
- PE5 · 3,6,9,12,15,18,21,24-octaoxahexacosan-1-ol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 97 | 0.76 | 0.97 | 25 | empty |
| 2 | 320 | 0.66 | 0.81 | 48 | CA |
| 3 | 327 | 0.64 | 0.80 | 43 | CA |
| 4 | 265 | 0.58 | 0.78 | 36 | empty |
| 5 | 221 | 0.49 | 0.75 | 23 | PE5 |
Interfaces
1 interface between chains.
- A–C · 742 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5ZRU · Crystal structure of Agl-KA catalytic domain · 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 Q0WYG9
- Elsewhere: RCSB PDB 5ZRU · PDBe 5ZRU · UniProt Q0WYG9
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