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Structure of human DNA polymerase kappa with DNA

Analyse Structure of human DNA polymerase kappa with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
6CST
Type
protein + DNA
Length
932 residues
Chains
6
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA polymerase kappa; DNA (5'-D(P*AP*TP*AP*CP*AP*TP*AP*CP*C)-3'); DNA…
EC
2.7.7.7
UniProt
Q9UBT6
Ligands
DZ4, MG, K, CL, IOD
Pockets
15 · best druggability 0.87

Structure

x-ray diffraction · 4 distinct chains · 49% helix, 19% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ADNA polymerase kappa (EC 2.7.7.7)protein44649% helix, 19% strandQ9UBT6
BDNA polymerase kappa (EC 2.7.7.7)protein44250% helix, 19% strandQ9UBT6
C, PDNA (5'-D(P*AP*TP*AP*CP*AP*TP*AP*CP*C)-3')dna9——
D, TDNA (5'-D(P*TP*AP*CP*TP*GP*GP*TP*AP*TP*GP*TP*AP*T)-3')dna13——

Ligands and binding sites

  • DZ4 · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]adenosine · ligand · 2 copies · chains A, C, D, B, P, T
  • MG · Magnesium ion · metal · 4 copies · chains A, C, B, P
  • K · Potassium ion · metal · 4 copies · chains A, B, D
  • CL · Chloride ion · ion · 9 copies · chains A, B, T, D
  • IOD · Iodide ion · ion · 6 copies · chains A, B
  • EDO · 1,2-ethanediol · additive · 10 copies · chains A, C, B
  • PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B
  • PGE · Triethylene glycol · additive · chains A

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

Pockets

15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
112000.870.88102MG, IOD, EDO, DZ4, CL
26220.820.8771CL
33270.760.8836MG, DZ4
42300.700.8730K
55800.700.7947empty

Interfaces

9 interfaces between chains.

  • A–B · 1392 Ų buried · 33 hydrogen bonds · protein-protein
  • A–D · 1045 Ų buried · 24 hydrogen bonds · protein-nucleic
  • B–T · 1000 Ų buried · 21 hydrogen bonds · protein-nucleic
  • A–C · 664 Ų buried · 18 hydrogen bonds · protein-nucleic
  • B–P · 643 Ų buried · 18 hydrogen bonds · protein-nucleic

Compared structures

  • 6CST · Structure of human DNA polymerase kappa with DNA · the same entry in another collection · chain T against T, TM-score 1.00
  • Q9UBT6 · AlphaFold monomer V2.0 prediction for DNA polymerase kappa (Q9UBT6) · a predicted model of the same protein · chain B against A, TM-score 0.99

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