MolNFT v1 · #71988 · protein
E. COLI (lacz) beta-galactosidase (R599A)
3MUY · Beta-D-galactosidase: “E. COLI (lacz) beta-galactosidase (R599A)”. X-ray diffraction, 2 ligands (NA, MG), 20 pockets (best druggability 0.81). MolNFT v1 #71988 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3MUY
- Type
- protein
- Length
- 4,044 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-D-galactosidase
- EC
- 3.2.1.23
- UniProt
- C6UB28
- Ligands
- NA, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1, 2, 3, 4 | Beta-D-galactosidase (EC 3.2.1.23) | protein | 1011 | 14% helix, 41% strand | C6UB28 |
Ligands and binding sites
- NA · Sodium ion · metal · 16 copies · chains 1, 2, 3, 4
- MG · Magnesium ion · metal · 10 copies · chains 1, 2, 3, 4
- DMS · Dimethyl sulfoxide · additive · 130 copies · chains 1, 2, 3, 4
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 | 940 | 0.81 | 0.83 | 110 | DMS |
| 2 | 1172 | 0.81 | 0.82 | 150 | DMS |
| 3 | 773 | 0.79 | 0.83 | 82 | empty |
| 4 | 389 | 0.75 | 0.86 | 75 | DMS |
| 5 | 320 | 0.71 | 0.85 | 49 | DMS |
Interfaces
6 interfaces between chains.
- 1–4 · 2377 Ų buried · 34 hydrogen bonds · protein-protein
- 2–3 · 2332 Ų buried · 33 hydrogen bonds · protein-protein
- 3–4 · 2078 Ų buried · 32 hydrogen bonds · protein-protein
- 1–2 · 2036 Ų buried · 39 hydrogen bonds · protein-protein
- 2–4 · 138 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3MUY · E. coli (lacZ) beta-galactosidase (R599A) · the same entry in another collection · chain 1 against 1, 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 C6UB28
- Elsewhere: RCSB PDB 3MUY · PDBe 3MUY · UniProt C6UB28
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