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Crystal structure of TET3 in complex with a cpg dsdna

Analyse Crystal structure of TET3 in complex with a cpg dsdna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
4HP3
Type
protein + DNA
Length
75 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3'); LOC100036628 protein
UniProt
A0JP82
Ligands
ZN, UNX
Pockets
2 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains · 24% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, BDNA (5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3')dna12——
CLOC100036628 proteinprotein5124% helix, 0% strandA0JP82

Ligands and binding sites

  • ZN · Zinc ion · metal · 2 copies · chains C
  • UNX · Unknown atom or ion · ion · 3 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
12380.590.8021UNX
21080.450.7914empty

Interfaces

3 interfaces between chains.

  • A–B · 541 Ų buried · 43 hydrogen bonds · nucleic-nucleic
  • A–C · 480 Ų buried · 12 hydrogen bonds · protein-nucleic
  • B–C · 452 Ų buried · 10 hydrogen bonds · protein-nucleic

Compared structures

  • 4HP3 · Crystal structure of Tet3 in complex with a CpG dsDNA · the same entry in another collection · chain A against A, TM-score 1.00
  • A0JP82 · AlphaFold monomer V2.0 prediction for methylcytosine dioxygenase TET3 (A0JP82) · a predicted model of the same protein · chain C against A, TM-score 0.81

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