Research workbench
Structure of the complex of lac repressor headpiece and an 11 base- pair half-operator determined by nuclear magnetic resonance spectroscopy and restrained molecular dynamics
Analyse Structure of the complex of lac repressor headpiece and an 11 base- pair… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LCD
- Type
- protein + DNA
- Length
- 73 residues
- Chains
- 3
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*G)-3'); DNA…
- UniProt
- P03023
- Ligands
- NA
- Pockets
- 1 · best druggability 0.24
Structure
solution nmr · 3 distinct chains · 57% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA (5'-D(*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*G)-3') | dna | 11 | — | — |
| C | DNA (5'-D(*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*T)-3') | dna | 11 | — | — |
| A | Lac repressor | protein | 51 | 57% helix, 0% strand | P03023 |
Ligands and binding sites
- NA · Sodium ion · metal · chains C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.24 | 0.73 | 10 | empty |
Interfaces
3 interfaces between chains.
- C–A · 541 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–C · 497 Ų buried · 55 hydrogen bonds · nucleic-nucleic
- B–A · 331 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 1LCD · Structure of the complex of lac repressor headpiece and an 11 base-pair half-operator… · the same entry in another collection · chain B against B, 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 0.73
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 1LCD · PDBe 1LCD · UniProt P03023
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