Research workbench
Solution structure of a dimer of lac repressor DNA-binding domain complexed to its natural operator O3
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
- 2KEK
- Type
- protein + DNA
- Length
- 170 residues
- Chains
- 4
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactose operon repressor; DNA (5'- D(*CP*GP*GP*CP*AP*GP*TP*GP*AP*GP*CP*GP*CP*AP*AP*CP*GP*C…
- UniProt
- P03023
- Pockets
- 6 · best druggability 0.59
Structure
solution nmr · 3 distinct chains · 50% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lactose operon repressor | protein | 62 | 50% helix, 0% strand | P03023 |
| C | DNA (5'- D(*CP*GP*GP*CP*AP*GP*TP*GP*AP*GP*CP*GP*CP*AP*AP*CP*GP*CP*AP*AP*TP*TP* C)-3') | dna | 23 | — | — |
| D | DNA (5'- D(P*GP*AP*AP*TP*TP*GP*CP*GP*TP*TP*GP*CP*GP*CP*TP*CP*AP*CP*TP*GP*CP*CP *G)-3') | dna | 23 | — | — |
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 240 | 0.59 | 0.80 | 25 | empty |
| 2 | 65 | 0.35 | 0.77 | 14 | empty |
| 3 | 75 | 0.33 | 0.75 | 14 | empty |
| 4 | 59 | 0.33 | 0.77 | 14 | empty |
| 5 | 62 | 0.32 | 0.76 | 13 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1101 Ų buried · 93 hydrogen bonds · nucleic-nucleic
- A–D · 597 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–C · 554 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–C · 511 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–D · 446 Ų buried · 12 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2KEK · Solution structure of a dimer of LAC repressor DNA-binding domain complexed to its… · 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 0.74
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 2KEK · PDBe 2KEK · UniProt P03023
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