MolNFT v1 · #22956 · protein
Unprecedented quaternary structure of E. COLI lac repressor core tetramer: implications for DNA looping
1TLF: “Unprecedented quaternary structure of E. COLI lac repressor core tetramer: implications for DNA looping”. X-ray diffraction, 2 ligands (EMC, IPT), 11 pockets (best druggability 0.81). MolNFT v1 #22956 on GenesisL1: 3D structure…
- PDB
- 1TLF
- Type
- protein
- Length
- 1,184 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lac repressor
- UniProt
- P03023
- Ligands
- EMC, IPT
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Lac repressor | protein | 296 | 45% helix, 20% strand | P03023 |
Ligands and binding sites
- EMC · Ethyl mercury ion · ligand · 4 copies · chains A, B, C, D
- IPT · 1-methylethyl 1-thio-beta-D-galactopyranoside · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.81 | 0.97 | 31 | IPT |
| 2 | 164 | 0.81 | 0.96 | 30 | IPT |
| 3 | 165 | 0.81 | 0.96 | 33 | IPT |
| 4 | 208 | 0.78 | 0.92 | 40 | IPT |
| 5 | 1105 | 0.73 | 0.77 | 112 | EMC |
Interfaces
6 interfaces between chains.
- A–B · 2251 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 2165 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 796 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 481 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 138 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1TLF · Unprecedented quaternary structure of E. COLI lac repressor core tetramer: implications… · 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 0.91
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 1TLF · PDBe 1TLF · UniProt P03023
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