MolNFT v1 · #174320 · protein
E.COLI beta-galactosidase (E537Q) in complex with fluorescent probe KSA02
7BRS: “E.COLI beta-galactosidase (E537Q) in complex with fluorescent probe KSA02”. X-ray diffraction, 3 ligands (F4X, MG, NA), 20 pockets (best druggability 0.81). MolNFT v1 #174320 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7BRS
- Type
- protein
- Length
- 4,063 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
- F4X, MG, NA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-galactosidase (EC 3.2.1.23) | protein | 1021 | 14% helix, 40% strand | P00722 |
| B | Beta-galactosidase (EC 3.2.1.23) | protein | 1012 | 14% helix, 41% strand | P00722 |
| C | Beta-galactosidase (EC 3.2.1.23) | protein | 1015 | 14% helix, 41% strand | P00722 |
| D | Beta-galactosidase (EC 3.2.1.23) | protein | 1015 | 14% helix, 41% strand | P00722 |
Ligands and binding sites
- F4X · 8-[2-[(E)-2-[4-[(2S,3R,4S,5R,6R)-6-(hydroxymethyl)-3,4, 5-tris(oxidanyl)oxan-2-yl]oxyphenyl]ethenyl]-3,3-dimethyl-indol-1-ium-1-yl]octanoic acid · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- NA · Sodium ion · metal · 7 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 46 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains A
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 | 229 | 0.81 | 0.94 | 56 | empty |
| 2 | 1080 | 0.77 | 0.80 | 129 | empty |
| 3 | 734 | 0.74 | 0.80 | 83 | empty |
| 4 | 83 | 0.74 | 0.97 | 23 | empty |
| 5 | 56 | 0.72 | 0.99 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1768 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1652 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 572 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7BRS · E.coli beta-galactosidase (E537Q) in complex with fluorescent probe KSA02 · the same entry in another collection · chain B against B, TM-score 1.00
- P00722 · AlphaFold monomer V2.0 prediction for beta-galactosidase (P00722) · a predicted model of the same protein · chain C 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 7BRS · PDBe 7BRS · UniProt P00722
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