MolNFT v1 · #141325 · protein
Crystal structure of glucosidase from croceicoccus marinus at 1.8 ångström resolution
5Z3K: “Crystal structure of glucosidase from croceicoccus marinus at 1.8 ångström resolution”. X-ray diffraction, 6 pockets (best druggability 0.76). MolNFT v1 #141325 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5Z3K
- Type
- protein
- Length
- 957 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucosidase
- UniProt
- A0A1Z1FG87
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucosidase | protein | 474 | 23% helix, 28% strand | A0A1Z1FG87 |
| B | Glucosidase | protein | 483 | 23% helix, 30% strand | A0A1Z1FG87 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, B
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 | 303 | 0.76 | 0.88 | 50 | GOL |
| 2 | 489 | 0.73 | 0.82 | 71 | empty |
| 3 | 126 | 0.44 | 0.77 | 29 | empty |
| 4 | 127 | 0.43 | 0.77 | 18 | empty |
| 5 | 55 | 0.32 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1084 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 5Z3K · Crystal structure of glucosidase from Croceicoccus marinus at 1.8 Angstrom resolution · 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 A0A1Z1FG87
- Elsewhere: RCSB PDB 5Z3K · PDBe 5Z3K · UniProt A0A1Z1FG87
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