5T14

DNA polymerase kappa extending beyond a bulky major benzo[a]pyrene adduct

Structural Biology Knowledgebase: 5T14 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.266
  • R-Value Work: 0.204

Literature

Macromolecules
Sequence Display for 5T14

Classification: TRANSFERASE / DNA

Total Structure Weight: 135883.08


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase kappa A, B 527 Homo sapiens EC#: 2.7.7.7 IUBMB
Gene Name(s): POLK Gene View DINB1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA C, P 9 Unidentified
DNA D, T 13 Unidentified

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DZ4
Query on DZ4

A, B 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine
C10 H17 N6 O11 P3
WKIPJDSLGCBQCU-RRKCRQDMSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PGE
Query on PGE

B TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
VKJ
Query on VKJ
D, T NON-POLYMER C30 H28 N5 O10 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.266
  • R-Value Work: 0.204
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 65.25 α = 90.00
b = 128.82 β = 90.00
c = 167.46 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-08-17
  • Released Date: 2016-12-21
  • Deposition author(s): Jha, V.K., Ling, H.

Revision History

  • 2017-01-18
    Type: Citation | Details: Citation