MolNFT v1 · #116742 · protein
Beta-galactosidase - construct 33-930
5DMY: “Beta-galactosidase - construct 33-930”. X-ray diffraction, 3 ligands (MG, NA, NI), 20 pockets (best druggability 0.75). MolNFT v1 #116742 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DMY
- Type
- protein
- Length
- 2,568 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-galactosidase
- EC
- 3.2.1.23
- UniProt
- D4QAP3
- Ligands
- MG, NA, NI
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Beta-galactosidase (EC 3.2.1.23) | protein | 855 | 15% helix, 38% strand | D4QAP3 |
| B | Beta-galactosidase (EC 3.2.1.23) | protein | 858 | 14% helix, 38% strand | D4QAP3 |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 copies · chains A, B, C
- NA · Sodium ion · metal · 3 copies · chains A, C
- NI · Nickel (II) ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 932 | 0.75 | 0.78 | 84 | empty |
| 2 | 720 | 0.74 | 0.80 | 73 | empty |
| 3 | 60 | 0.74 | 0.99 | 20 | empty |
| 4 | 65 | 0.74 | 0.99 | 22 | empty |
| 5 | 799 | 0.73 | 0.78 | 73 | empty |
Interfaces
3 interfaces between chains.
- B–C · 540 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 335 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 184 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5DMY · Beta-galactosidase - construct 33-930 · 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 D4QAP3
- Elsewhere: RCSB PDB 5DMY · PDBe 5DMY · UniProt D4QAP3
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