Research workbench
Solution structure of a dimer of lac repressor DNA-binding domain complexed to its natural operator O1
Analyse Solution structure of a dimer of lac repressor DNA-binding domain complexed to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1L1M
- Type
- protein + DNA
- Length
- 170 residues
- Chains
- 4
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*GP*GP*AP*TP*AP*AP*CP *AP*AP*TP*TP*T)-3'…
- UniProt
- P03023
- Pockets
- 3 · best druggability 0.37
Structure
solution nmr · 3 distinct chains · 60% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'-D(*GP*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*GP*GP*AP*TP*AP*AP*CP *AP*AP*TP*TP*T)-3' | dna | 23 | — | — |
| D | 5'-D(*AP*AP*AP*TP*TP*GP*TP*TP*AP*TP*CP*CP*GP*CP*TP*CP*AP*CP *AP*AP*TP*TP*C)-3' | dna | 23 | — | — |
| A, B | Lactose operon repressor | protein | 62 | 60% helix, 0% strand | P03023 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 109 | 0.37 | 0.74 | 14 | empty |
| 2 | 66 | 0.29 | 0.74 | 18 | empty |
| 3 | 54 | 0.29 | 0.75 | 16 | empty |
Interfaces
6 interfaces between chains.
- C–D · 962 Ų buried · 89 hydrogen bonds · nucleic-nucleic
- C–A · 647 Ų buried · 20 hydrogen bonds · protein-nucleic
- C–B · 624 Ų buried · 14 hydrogen bonds · protein-nucleic
- D–B · 559 Ų buried · 22 hydrogen bonds · protein-nucleic
- D–A · 536 Ų buried · 16 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1L1M · Solution structure of a dimer of lac repressor DNA-binding domain complexed to its… · 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 A against A, TM-score 0.84
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 1L1M · PDBe 1L1M · UniProt P03023
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