MolNFT v1 · #47836 · protein
Crystal structure of the lactose repressor bound to anti-inducer onpf in induced state
2PAF · Lactose operon repressor: “Crystal structure of the lactose repressor bound to anti-inducer onpf in induced state”. X-ray diffraction, 1 ligand (NPF), 4 pockets (best druggability 0.73). MolNFT v1 #47836 on GenesisL1: 3D structure…
- PDB
- 2PAF
- Type
- protein
- Length
- 538 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactose operon repressor
- UniProt
- P03023
- Ligands
- NPF
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lactose operon repressor | protein | 269 | 40% helix, 17% strand | P03023 |
Ligands and binding sites
- NPF · 2-nitrophenyl beta-D-fucopyranoside · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 398 | 0.73 | 0.84 | 58 | NPF |
| 2 | 421 | 0.72 | 0.83 | 61 | NPF |
| 3 | 62 | 0.40 | 0.80 | 13 | empty |
| 4 | 51 | 0.32 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1579 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 2PAF · Crystal Structure of the Lactose Repressor bound to anti-inducer ONPF in induced state · the same entry in another collection · chain A against A, TM-score 1.00
- P03023 · AlphaFold monomer V2.0 prediction for lactose operon repressor (P03023) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 2PAF · PDBe 2PAF · UniProt P03023
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