Research workbench
E. COLI (lacz) beta-galactosidase (N460T) in complex with D- galctopyranosyl-1-one
Analyse E. COLI (lacz) beta-galactosidase (N460T) in complex with D… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CZJ
- 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
- 149, NA, MG
- Pockets
- 20 · best druggability 0.82
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
- 149 · D-galactonolactone · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 16 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 9 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 94 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 | 1006 | 0.82 | 0.83 | 113 | empty |
| 2 | 660 | 0.77 | 0.83 | 72 | empty |
| 3 | 1123 | 0.76 | 0.79 | 100 | DMS |
| 4 | 1053 | 0.76 | 0.79 | 105 | DMS |
| 5 | 1162 | 0.76 | 0.78 | 108 | DMS |
Interfaces
6 interfaces between chains.
- B–C · 2283 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 2267 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2055 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 1966 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 136 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3CZJ · E. COLI (lacZ) BETA-GALACTOSIDASE (N460T) IN COMPLEX WITH D-GALCTOPYRANOSYL-1-ONE · 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 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 P00722
- Elsewhere: RCSB PDB 3CZJ · PDBe 3CZJ · UniProt P00722
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