4K8X

Binary complex of 9N DNA polymerase in the replicative state

Structural Biology Knowledgebase: 4K8X SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.195

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4K8X

Classification: TRANSFERASE / DNA

Total Structure Weight: 100033.73


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase A 775 Thermococcus sp. 9on-7 EC#: 2.7.7.7 IUBMB
Mutation: D141A, E143A
Gene Name(s): pol polA
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(P*AP*AP*AP*GP*GP*CP*GP*CP*AP*GP*TP*TP*CP*GP*CP*G)-3') T 16 synthetic DNA template
DNA (5'-D(*CP*GP*CP*GP*AP*AP*CP*TP*GP*CP*GP*(DOC))-3') P 12 synthetic DNA primer

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
5CY
Query on 5CY

T 1-(3-hydroxypropyl)-2-{(1E,3E,5E)-5-[1-(3- hydroxypropyl)-3,3-dimethyl-1,3-dihydro-2H- indol-2-ylidene]penta-1,3-dien-1-yl}-3,3- dimethyl-3H-indolium
N,N'-(dipropyl)-tetramethylindodicarbocyanine (Synonym)
C31 H39 N2 O2
VFBDPICHYNKCQJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

T 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
DOC
Query on DOC
P DNA LINKING C9 H14 N3 O6 P DC

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.195
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 112.21 α = 90.00
b = 142.62 β = 90.00
c = 66.70 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-04-19
  • Released Date: 2013-06-26
  • Deposition author(s): Betz, K., Diederichs, K., Marx, A.

Revision History

No revisions since initial release