Research workbench
Cryo-EM structure of beta-galactosidase at 2.9 A resolution plunged 205 ms after mixing with apoferritin
Analyse Cryo-EM structure of beta-galactosidase at 2.9 A resolution plunged 205 ms… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8BK8
- Type
- protein
- Length
- 4,044 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.9
- Source
- Escherichia coli
- Molecule
- Beta-galactosidase
- EC
- 3.2.1.23
- UniProt
- P00722
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · resolution 2.9 · 1 distinct chain · 13% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-galactosidase (EC 3.2.1.23) | protein | 1011 | 13% helix, 41% strand | P00722 |
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 | 924 | 0.82 | 0.84 | 97 | empty |
| 2 | 447 | 0.77 | 0.86 | 74 | empty |
| 3 | 1096 | 0.76 | 0.79 | 109 | empty |
| 4 | 1156 | 0.75 | 0.78 | 107 | empty |
| 5 | 384 | 0.75 | 0.85 | 49 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2488 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 2482 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 1968 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1968 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 130 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- P00722 · AlphaFold monomer V2.0 prediction for beta-galactosidase (P00722) · a predicted model of the same protein · chain B 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 8BK8 · PDBe 8BK8 · UniProt P00722
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