MolNFT v1 · #47949 · protein + DNA
Crystal structure of the lac repressor bound to onpg in repressed state
2PE5 · DNA (5'- D(*DAP*DAP*DTP*DTP*DGP*DTP*DGP*DAP*DGP*DCP*DGP*DCP*…: “Crystal structure of the lac repressor bound to onpg in repressed state”. X-ray diffraction, 1 ligand (145), 14 pockets (best druggability 0.76). MolNFT v1 #47949 on…
- 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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