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Transcriptional repressor COPG/DNA complex

Analyse Transcriptional repressor COPG/DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
1B01
Type
protein + DNA
Length
124 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'- D(*CP*CP*CP*GP*TP*GP*CP*AP*CP*TP*CP*AP*AP*TP*GP*CP*AP*AP*T) -3'); DNA (5'…
UniProt
P13920
Pockets
1 · best druggability 0.31

Structure

x-ray diffraction · 3 distinct chains · 67% helix, 19% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
EDNA (5'- D(*CP*CP*CP*GP*TP*GP*CP*AP*CP*TP*CP*AP*AP*TP*GP*CP*AP*AP*T) -3')dna19——
FDNA (5'- D(*GP*AP*TP*TP*GP*CP*AP*TP*TP*GP*AP*GP*TP*GP*CP*AP*CP*GP*G) -3')dna19——
A, BTranscriptional repressor copgprotein4367% helix, 19% strandP13920

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1720.310.7520empty

Interfaces

6 interfaces between chains.

  • A–B · 1724 Ų buried · 18 hydrogen bonds · protein-protein
  • E–F · 1708 Ų buried · 774 hydrogen bonds · nucleic-nucleic
  • E–A · 492 Ų buried · 12 hydrogen bonds · protein-nucleic
  • E–B · 484 Ų buried · 11 hydrogen bonds · protein-nucleic
  • F–A · 474 Ų buried · 12 hydrogen bonds · protein-nucleic

Compared structures

  • 1B01 · Transcriptional repressor COPG/DNA complex · the same entry in another collection · chain E against E, TM-score 1.00
  • P13920 · AlphaFold monomer V2.0 prediction for protein copg (P13920) · a predicted model of the same protein · chain A against A, TM-score 0.89

Analyse

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