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Crystal structure of human tdp-43 RRM1 domain in complex with an unmodified single-stranded DNA

Analyse Crystal structure of human tdp-43 RRM1 domain in complex with an unmodified… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
4Y0F
Type
protein + DNA
Length
169 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Tar DNA-binding protein 43; DNA (5'-D(*GP*TP*TP*GP*AP*GP*CP*GP*TP*T)-3')
UniProt
Q13148
Pockets
1 · best druggability 0.51

Structure

x-ray diffraction · 4 distinct chains · 21% helix, 39% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ATar DNA-binding protein 43protein7821% helix, 38% strandQ13148
BTar DNA-binding protein 43protein7721% helix, 39% strandQ13148
CDNA (5'-D(*GP*TP*TP*GP*AP*GP*CP*GP*TP*T)-3')dna10——
DDNA (5'-D(*GP*TP*TP*GP*AP*GP*CP*GP*TP*T)-3')dna4——

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
12790.510.7526empty

Interfaces

3 interfaces between chains.

  • A–C · 798 Ų buried · 18 hydrogen bonds · protein-nucleic
  • B–D · 553 Ų buried · 5 hydrogen bonds · protein-nucleic
  • B–C · 110 Ų buried · 1 hydrogen bond · protein-nucleic

Compared structures

  • 4Y0F · Crystal Structure of Human TDP-43 RRM1 Domain in Complex with an Unmodified… · the same entry in another collection · chain A against A, TM-score 1.00
  • Q13148 · AlphaFold monomer V2.0 prediction for tar DNA-binding protein 43 (Q13148) · a predicted model of the same protein · chain B against A, TM-score 0.98

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