5W2C

Structure of human DNA polymerase kappa in complex with Lucidin-derived DNA adduct and incoming dAMPNPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.211

Literature

Macromolecules
Sequence Display for 5W2C

Classification: REPLICATION

Total Structure Weight: 142148.27


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase kappa A, B 551 Homo sapiens EC#: 2.7.7.7 IUBMB
Fragment: UNP residues 1-526
Gene Name(s): POLK Gene View DINB1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(P*CP*GP*GP*AP*TP*CP*GP*AP*C)-3') C, P 9 Unidentified
DNA (5'-D(*CP*TP*AP*TP*(LDG)P*TP*CP*GP*AP*TP*CP*CP*G)-3') D, T 13 Unidentified

Small Molecules
Ligands 5 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)
PEG
Query on PEG

A, B DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-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
LDG
Query on LDG
D, T NON-POLYMER C27 H26 N5 O11 P DG

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.211
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 63.71 α = 90.00
b = 128.92 β = 90.00
c = 167.71 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2017-06-06
  • Released Date: 2017-10-18
  • Deposition author(s): Jha, V.K., Ling, H.

Revision History

  • Version 1_0: 2017-10-18

    Type: Initial release