MolNFT v1 · #11854 · protein
E. COLI (lacz) beta-galactosidase-trapped 2-deoxy-galactosyl enzyme intermediate
1JZ3: “E. COLI (lacz) beta-galactosidase-trapped 2-deoxy-galactosyl enzyme intermediate”. X-ray diffraction, 3 ligands (2DG, MG, NA), 20 pockets (best druggability 0.81). MolNFT v1 #11854 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1JZ3
- Type
- protein
- Length
- 4,044 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-galactosidase
- EC
- 3.2.1.23
- UniProt
- P00722
- Ligands
- 2DG, MG, NA
- 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 |
|---|---|---|---|---|---|
| A, B, C, D | Beta-galactosidase (EC 3.2.1.23) | protein | 1011 | 14% helix, 41% strand | P00722 |
Ligands and binding sites
- 2DG · 2-deoxy-alpha-D-galactopyranose · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 17 copies · chains A, B, C, D
- NA · Sodium ion · metal · 16 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 110 copies · chains A, D, B, C
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, D, B, C
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 | 1132 | 0.81 | 0.82 | 140 | DMS |
| 2 | 861 | 0.80 | 0.83 | 93 | empty |
| 3 | 755 | 0.79 | 0.83 | 108 | DMS |
| 4 | 729 | 0.78 | 0.82 | 94 | empty |
| 5 | 397 | 0.72 | 0.83 | 37 | DMS |
Interfaces
6 interfaces between chains.
- B–C · 2348 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 2344 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2016 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 1983 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 142 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 1JZ3 · E. COLI (lacZ) BETA-GALACTOSIDASE-TRAPPED 2-DEOXY-GALACTOSYL ENZYME INTERMEDIATE · the same entry in another collection · chain D against D, TM-score 1.00
- P00722 · AlphaFold monomer V2.0 prediction for beta-galactosidase (P00722) · a predicted model of the same protein · chain D 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 P00722
- Elsewhere: RCSB PDB 1JZ3 · PDBe 1JZ3 · UniProt P00722
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