Research workbench
2.2 a resolution cryo-EM structure of beta-galactosidase in complex with a cell-permeant inhibitor
Analyse 2.2 a resolution cryo-EM structure of beta-galactosidase in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A1A
- Type
- protein
- Length
- 4,088 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-galactosidase
- EC
- 3.2.1.23
- UniProt
- P00722
- Ligands
- PTQ, MG, NA
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 1 distinct chain · 12% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-galactosidase (EC 3.2.1.23) | protein | 1022 | 12% helix, 39% strand | P00722 |
Ligands and binding sites
- PTQ · 2-phenylethyl 1-thio-beta-D-galactopyranoside · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- NA · Sodium ion · metal · 8 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 | 754 | 0.82 | 0.86 | 99 | empty |
| 2 | 654 | 0.82 | 0.87 | 75 | empty |
| 3 | 800 | 0.80 | 0.83 | 119 | empty |
| 4 | 861 | 0.80 | 0.82 | 113 | empty |
| 5 | 586 | 0.74 | 0.82 | 74 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2705 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 2698 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 2242 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 2242 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 149 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5A1A · 2.2 A resolution cryo-EM structure of beta-galactosidase in complex with a cell-permeant… · 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 5A1A · PDBe 5A1A · UniProt P00722
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