Research workbench
Atomic resolution cryo-EM structure of beta-galactosidase
Analyse Atomic resolution cryo-EM structure of beta-galactosidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CVM
- Type
- protein
- Length
- 4,084 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 · 14% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-galactosidase (EC 3.2.1.23) | protein | 1021 | 14% helix, 41% 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 | 1183 | 0.82 | 0.84 | 114 | empty |
| 2 | 595 | 0.80 | 0.86 | 74 | empty |
| 3 | 1123 | 0.76 | 0.78 | 105 | empty |
| 4 | 1174 | 0.75 | 0.78 | 106 | empty |
| 5 | 1142 | 0.75 | 0.77 | 104 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2560 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 2558 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 2109 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 2108 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 111 Ų buried · 5 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 6CVM · PDBe 6CVM · UniProt P00722
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