MolNFT v1 · #174375 · protein
E.COLI beta-galactosidase (E537Q) in complex with fluorescent probe KSA01
7BTK: “E.COLI beta-galactosidase (E537Q) in complex with fluorescent probe KSA01”. X-ray diffraction, 3 ligands (F6L, MG, NA), 20 pockets (best druggability 0.77). MolNFT v1 #174375 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7BTK
- Type
- protein
- Length
- 4,086 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
- F6L, MG, NA
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Beta-galactosidase (EC 3.2.1.23) | protein | 1021 | 15% helix, 40% strand | P00722 |
| C | Beta-galactosidase (EC 3.2.1.23) | protein | 1023 | 14% helix, 40% strand | P00722 |
Ligands and binding sites
- F6L · 4-[[2-[(E)-2-[4-[(2S,3R,4S,5R,6R)-6-(hydroxymethyl)-3, 4,5-tris(oxidanyl)oxan-2-yl]oxyphenyl]ethenyl]-3,3-dimethyl-2H-indol-1-yl]methyl]benzoic acid · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, D
- NA · Sodium ion · metal · 7 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 38 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains B
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 | 688 | 0.77 | 0.82 | 87 | empty |
| 2 | 621 | 0.76 | 0.82 | 85 | empty |
| 3 | 450 | 0.73 | 0.83 | 45 | DMS |
| 4 | 428 | 0.72 | 0.82 | 43 | DMS |
| 5 | 50 | 0.71 | 0.99 | 19 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1877 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1741 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 706 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7BTK · E.coli beta-galactosidase (E537Q) in complex with fluorescent probe KSA01 · 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 7BTK · PDBe 7BTK · UniProt P00722
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