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Crystal structure analysis of TRF2-dbd-DNA complex

Analyse Crystal structure analysis of TRF2-dbd-DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
3SJM
Type
protein + DNA
Length
144 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'- D(*CP*TP*CP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3'); DNA (5'…
UniProt
Q15554
Pockets
3 · best druggability 0.36

Structure

x-ray diffraction · 3 distinct chains · 62% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
CDNA (5'- D(*CP*TP*CP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')dna17——
DDNA (5'- D(*TP*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*GP*A)-3')dna17——
A, BTelomeric repeat-binding factor 2protein5562% helix, 0% strandQ15554

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11040.360.7513empty
2670.340.7712empty
3500.300.769empty

Interfaces

6 interfaces between chains.

  • C–D · 755 Ų buried · 59 hydrogen bonds · nucleic-nucleic
  • D–A · 478 Ų buried · 13 hydrogen bonds · protein-nucleic
  • D–B · 457 Ų buried · 7 hydrogen bonds · protein-nucleic
  • C–B · 432 Ų buried · 10 hydrogen bonds · protein-nucleic
  • C–A · 398 Ų buried · 8 hydrogen bonds · protein-nucleic

Compared structures

  • 3SJM · Crystal Structure Analysis of TRF2-Dbd-DNA complex · the same entry in another collection · chain C against C, TM-score 1.00
  • Q15554 · AlphaFold monomer V2.0 prediction for telomeric repeat-binding factor 2 (Q15554) · a predicted model of the same protein · chain A against A, TM-score 0.98

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