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Structure of the DNA binding domain of PSK1 par partition protein bound to centromere DNA

Analyse Structure of the DNA binding domain of PSK1 par partition protein bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
8CSH
Type
protein + DNA
Length
138 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'-D(P*TP*GP*TP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*AP*C)- 3'); Par; DNA (5'…
UniProt
Q9L8I7
Pockets
1 · best druggability 0.63

Structure

x-ray diffraction · 3 distinct chains · 58% helix, 17% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
TDNA (5'-D(P*TP*GP*TP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*AP*C)- 3')dna15——
D, AParprotein5358% helix, 17% strandQ9L8I7
YDNA (5'- D(*TP*AP*GP*TP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*AP*CP*A)-3')dna17——

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
14950.630.7645empty

Interfaces

5 interfaces between chains.

  • T–Y · 671 Ų buried · 61 hydrogen bonds · nucleic-nucleic
  • T–D · 373 Ų buried · 9 hydrogen bonds · protein-nucleic
  • A–Y · 340 Ų buried · 9 hydrogen bonds · protein-nucleic
  • D–Y · 314 Ų buried · 4 hydrogen bonds · protein-nucleic
  • T–A · 298 Ų buried · 6 hydrogen bonds · protein-nucleic

Compared structures

  • 8CSH · Structure of the DNA binding domain of pSK1 Par partition protein bound to centromere DNA · the same entry in another collection · chain T against T, TM-score 1.00

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