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NMR structure of lac repressor HP62-DNA complex

Analyse NMR structure of lac repressor HP62-DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
1CJG
Type
protein + DNA
Length
168 residues
Chains
4
Method
solution nmr
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'- D(*GP*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*TP*C)- 3')…
UniProt
P03023
Pockets
4 · best druggability 0.55

Structure

solution nmr · 2 distinct chains · 58% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
C, DDNA (5'- D(*GP*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*TP*C)- 3')dna22——
A, BProtein (lac repressor)protein6258% helix, 0% strandP03023

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
12170.550.7920empty
22350.540.7726empty
31040.370.7512empty
4740.330.7610empty

Interfaces

6 interfaces between chains.

  • C–D · 987 Ų buried · 89 hydrogen bonds · nucleic-nucleic
  • D–A · 556 Ų buried · 9 hydrogen bonds · protein-nucleic
  • C–B · 550 Ų buried · 7 hydrogen bonds · protein-nucleic
  • D–B · 446 Ų buried · 3 hydrogen bonds · protein-nucleic
  • C–A · 424 Ų buried · 2 hydrogen bonds · protein-nucleic

Compared structures

  • 1CJG · NMR structure of lac repressor HP62-DNA complex · 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 0.79

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