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Structure of CDX2-DNA(TCG)

Analyse Structure of CDX2-DNA(TCG) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
6ES3
Type
protein + DNA
Length
216 residues
Chains
6
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'- D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*CP*GP*AP*CP*CP*TP*CP*C)-3'); Homeobox protein…
UniProt
Q99626
Pockets
4 · best druggability 0.72

Structure

x-ray diffraction · 3 distinct chains · 72% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, BDNA (5'- D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*CP*GP*AP*CP*CP*TP*CP*C)-3')dna18——
K, MHomeobox protein cdx-2protein7272% helix, 0% strandQ99626
F, EDNA (5'- D(P*GP*GP*AP*GP*GP*TP*CP*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')dna18——

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
16540.720.7955empty
26320.700.7853empty
3850.420.7913empty
4710.330.7512empty

Interfaces

9 interfaces between chains.

  • B–E · 789 Ų buried · 63 hydrogen bonds · nucleic-nucleic
  • A–F · 788 Ų buried · 62 hydrogen bonds · nucleic-nucleic
  • K–M · 748 Ų buried · 5 hydrogen bonds · protein-protein
  • A–K · 613 Ų buried · 22 hydrogen bonds · protein-nucleic
  • B–M · 591 Ų buried · 21 hydrogen bonds · protein-nucleic

Compared structures

  • 6ES3 · Structure of CDX2-DNA(TCG) · the same entry in another collection · chain E against E, TM-score 1.00
  • Q99626 · AlphaFold monomer V2.0 prediction for homeobox protein cdx-2 (Q99626) · a predicted model of the same protein · chain K against A, TM-score 0.92

Analyse

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