4KHY

Ternary complex of rb69 mutant L415F with ribonucleotide at -3 position

Structural Biology Knowledgebase: 4KHY SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.198

Literature

Macromolecules
Sequence Display for 4KHY

Classification: TRANSFERASE / DNA

Total Structure Weight: 115359.97


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase A 903 Escherichia virus rb69 EC#: 2.7.7.7 IUBMB 3.1.11 IUBMB
Mutation: D222A, D327A, L415F
Gene Name(s): 43
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA/RNA (5'-D(*AP*CP*AP*GP*G)-R(P*U)-D(P*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3') T 18 synthetic TEMPLATE STRAND
DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*C)-3') P 14 synthetic PRIMER STRAND

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

A THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O14 P3
NHVNXKFIZYSCEB-XLPZGREQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.198
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 80.79 α = 90.00
b = 118.24 β = 90.00
c = 127.61 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-05-01
  • Released Date: 2013-10-09
  • Deposition author(s): Clausen, A.R., Pedersen, L.C.

Revision History

  • 2013-10-30
    Type: Citation | Details: Citation update