MolNFT v1 · #28824 · protein
Beta-galactosidase from arthrobacter sp. C2-2 (isoenzyme C2-2-1)
1YQ2: “Beta-galactosidase from arthrobacter sp. C2-2 (isoenzyme C2-2-1)”. X-ray diffraction, 4 ligands (NA, MG, SO4), 20 pockets (best druggability 0.80). MolNFT v1 #28824 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1YQ2
- Type
- protein
- Length
- 6,120 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-galactosidase
- EC
- 3.2.1.23
- UniProt
- Q8KRF6
- Ligands
- NA, MG, SO4, CL
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Beta-galactosidase (EC 3.2.1.23) | protein | 1020 | 15% helix, 36% strand | Q8KRF6 |
Ligands and binding sites
- NA · Sodium ion · metal · 12 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 11 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E, F
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B, C, D, E, F
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 | 1031 | 0.80 | 0.82 | 113 | SO4 |
| 2 | 1182 | 0.80 | 0.82 | 113 | empty |
| 3 | 1081 | 0.80 | 0.81 | 112 | SO4 |
| 4 | 1180 | 0.79 | 0.81 | 114 | SO4 |
| 5 | 1062 | 0.79 | 0.81 | 109 | SO4 |
Interfaces
12 interfaces between chains.
- A–F · 1326 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1314 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 1311 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1301 Ų buried · 22 hydrogen bonds · protein-protein
- D–F · 1290 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 1YQ2 · beta-galactosidase from Arthrobacter sp. C2-2 (isoenzyme C2-2-1) · 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 Q8KRF6
- Elsewhere: RCSB PDB 1YQ2 · PDBe 1YQ2 · UniProt Q8KRF6
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