MolNFT v1 · #5351 · protein + DNA
Crystal structure of the lac repressor dimer bound to operator and the anti-inducer onpf
1EFA · DNA (5'- D(*GP*AP*AP*T*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*C…: “Crystal structure of the lac repressor dimer bound to operator and the anti-inducer onpf”. X-ray diffraction, 1 ligand (NPF), 9 pockets (best druggability 0.82). MolNFT…
- PDB
- 1EFA
- Type
- protein + DNA
- Length
- 978 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*GP*AP*AP*T*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*T)-3'); Lac…
- UniProt
- P03023
- Ligands
- NPF
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | DNA (5'- D(*GP*AP*AP*T*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*T)-3') | dna | 17 | — | — |
| E | DNA (5'- D(*GP*AP*AP*T*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*T)-3') | dna | 17 | — | — |
| A | Lac repressor | protein | 328 | 45% helix, 17% strand | P03023 |
| B | Lac repressor | protein | 330 | 44% helix, 18% strand | P03023 |
| C | Lac repressor | protein | 286 | 42% helix, 20% strand | P03023 |
Ligands and binding sites
- NPF · 2-nitrophenyl beta-D-fucopyranoside · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 947 | 0.82 | 0.84 | 109 | NPF |
| 2 | 588 | 0.76 | 0.82 | 57 | empty |
| 3 | 281 | 0.73 | 0.86 | 44 | NPF |
| 4 | 250 | 0.55 | 0.77 | 31 | empty |
| 5 | 217 | 0.53 | 0.77 | 31 | empty |
Interfaces
7 interfaces between chains.
- A–B · 2257 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 804 Ų buried · 84 hydrogen bonds · nucleic-nucleic
- E–A · 581 Ų buried · 12 hydrogen bonds · protein-nucleic
- D–B · 572 Ų buried · 8 hydrogen bonds · protein-nucleic
- E–B · 555 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 1EFA · Crystal structure of the lac repressor dimer bound to operator and the anti-inducer onpf · 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 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 P03023
- Elsewhere: RCSB PDB 1EFA · PDBe 1EFA · UniProt P03023
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