MolNFT v1 · #155040 · protein
E.COLI beta-galactosidase (E537Q) in complex with fluorescent probe KSL01
6KUZ: “E.COLI beta-galactosidase (E537Q) in complex with fluorescent probe KSL01”. X-ray diffraction, 3 ligands (DVL, NA, MG), 20 pockets (best druggability 0.80). MolNFT v1 #155040 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6KUZ
- Type
- protein
- Length
- 4,083 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
- DVL, NA, MG
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Beta-galactosidase (EC 3.2.1.23) | protein | 1021 | 14% helix, 41% strand | P00722 |
| D | Beta-galactosidase (EC 3.2.1.23) | protein | 1020 | 15% helix, 40% strand | P00722 |
Ligands and binding sites
- DVL · 3-(1,3-benzothiazol-2-yl)-2-[[4-[(2~{S},3~{R},4~{S}, 5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl) oxan-2-yl]oxyphenyl]methoxy]-5-methyl-benzaldehyde · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 12 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 35 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains 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 | 913 | 0.80 | 0.83 | 101 | empty |
| 2 | 652 | 0.77 | 0.83 | 75 | DMS |
| 3 | 430 | 0.72 | 0.82 | 41 | DMS |
| 4 | 397 | 0.70 | 0.82 | 37 | empty |
| 5 | 409 | 0.70 | 0.82 | 39 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1767 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1712 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 727 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6KUZ · E.coli beta-galactosidase (E537Q) in complex with fluorescent probe KSL01 · 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 D 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 6KUZ · PDBe 6KUZ · UniProt P00722
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