Research workbench
Crystal structure of the lac repressor bound to onpg in repressed state
Analyse Crystal structure of the lac repressor bound to onpg in repressed state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PE5
- Type
- protein + DNA
- Length
- 1,037 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*DAP*DAP*DTP*DTP*DGP*DTP*DGP*DAP*DGP*DCP*DGP*DCP*DTP*DCP*DAP*DCP*DA…
- UniProt
- P03023
- Ligands
- 145
- Pockets
- 14 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | DNA (5'- D(*DAP*DAP*DTP*DTP*DGP*DTP*DGP*DAP*DGP*DCP*DGP*DCP*DTP*DCP*DAP*DCP*DA P*DAP*DTP*DT)-3') | dna | 17 | — | — |
| E, F | DNA (5'- D(*DAP*DAP*DTP*DTP*DGP*DTP*DGP*DAP*DGP*DCP*DGP*DCP*DTP*DCP*DAP*DCP*DA P*DAP*DTP*DT)-3') | dna | 17 | — | — |
| A, C | Lactose operon repressor | protein | 328 | 47% helix, 17% strand | P03023 |
| B | Lactose operon repressor | protein | 330 | 46% helix, 16% strand | P03023 |
Ligands and binding sites
- 145 · 2-nitrophenyl beta-D-galactopyranoside · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 639 | 0.76 | 0.82 | 82 | 145 |
| 2 | 272 | 0.74 | 0.87 | 41 | 145 |
| 3 | 267 | 0.73 | 0.87 | 42 | 145 |
| 4 | 111 | 0.73 | 0.93 | 18 | empty |
| 5 | 273 | 0.55 | 0.76 | 27 | empty |
Interfaces
8 interfaces between chains.
- A–B · 2404 Ų buried · 26 hydrogen bonds · protein-protein
- D–E · 736 Ų buried · 59 hydrogen bonds · nucleic-nucleic
- E–A · 612 Ų buried · 9 hydrogen bonds · protein-nucleic
- F–C · 594 Ų buried · 9 hydrogen bonds · protein-nucleic
- D–B · 572 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 2PE5 · Crystal Structure of the Lac Repressor bound to ONPG in repressed state · the same entry in another collection · chain C against C, TM-score 1.00
- P03023 · AlphaFold monomer V2.0 prediction for lactose operon repressor (P03023) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P03023
- Elsewhere: RCSB PDB 2PE5 · PDBe 2PE5 · UniProt P03023
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