Research workbench
E. coli (lacZ) beta-galactosidase (N460S) in complex with L-ribose
Analyse E. coli (lacZ) beta-galactosidase (N460S) in complex with L-ribose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DUX
- Type
- protein
- Length
- 4,060 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Escherichia coli
- Molecule
- Beta-galactosidase
- EC
- 3.2.1.23
- UniProt
- P00722
- Ligands
- 0MK, NA, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.3 · 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 | 1015 | 14% helix, 41% strand | P00722 |
Ligands and binding sites
- 0MK · beta-L-ribopyranose · sugar · 9 copies · chains A, B, C, D
- NA · Sodium ion · metal · 14 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 65 copies · chains A, B, C, D
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 | 1034 | 0.81 | 0.83 | 116 | empty |
| 2 | 1021 | 0.81 | 0.83 | 113 | empty |
| 3 | 1182 | 0.81 | 0.82 | 147 | DMS |
| 4 | 773 | 0.79 | 0.83 | 105 | DMS |
| 5 | 402 | 0.72 | 0.83 | 39 | DMS |
Interfaces
6 interfaces between chains.
- A–D · 2540 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 2525 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2051 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2045 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 140 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
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 4DUX · PDBe 4DUX · UniProt P00722
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