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Eukaryotic sliding clamp PCNA bound to DNA

Analyse Eukaryotic sliding clamp PCNA bound to DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
3K4X
Type
protein + DNA
Length
778 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Proliferating cell nuclear antigen; DNA (5'-D(*CP*CP*CP*AP*TP*CP*GP*TP*AP*T)-3'); DNA…
UniProt
P15873
Pockets
9 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 45% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AProliferating cell nuclear antigenprotein75819% helix, 45% strandP15873
BDNA (5'-D(*CP*CP*CP*AP*TP*CP*GP*TP*AP*T)-3')dna10——
CDNA (5'-D(*TP*TP*TP*TP*AP*TP*AP*CP*GP*AP*TP*GP*GP*G)-3')dna10——

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
14680.770.8639empty
24760.650.7845empty
31550.440.7522empty
41600.430.7429empty
5960.360.7514empty

Interfaces

3 interfaces between chains.

  • A–B · 474 Ų buried · 4 hydrogen bonds · protein-nucleic
  • B–C · 461 Ų buried · 33 hydrogen bonds · nucleic-nucleic
  • A–C · 218 Ų buried · 2 hydrogen bonds · protein-nucleic

Compared structures

  • 3K4X · Eukaryotic Sliding Clamp PCNA Bound to DNA · the same entry in another collection · chain A against A, TM-score 1.00
  • P15873 · AlphaFold monomer V2.0 prediction for proliferating cell nuclear antigen (P15873) · a predicted model of the same protein · chain A against A, TM-score 0.33

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