5VZA

Pre-catalytic ternary complex of human Polymerase Mu (G433S) mutant with incoming nonhydrolyzable UMPNPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.184
  • R-Value Work: 0.169

Literature

Macromolecules
Sequence Display for 5VZA

Classification: TRANSFERASE / DNA

Total Structure Weight: 45676.54


Macromolecule Entities
Molecule Chains Length Organism Details
DNA-directed DNA/RNA polymerase mu A 354 Homo sapiens EC#: 2.7.7.7 IUBMB
Fragment: residues 134-494
Mutation: ΔP398, ΔG399, ΔA400, ΔA401, ΔV402, ΔG403, ΔG404, ΔS405, ΔT406, ΔR407, ΔP408, ΔC409, P410G, G433S
Gene Name(s): POLM Gene View polmu
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*CP*GP*GP*CP*AP*TP*AP*CP*G)-3') T 9 Synthetic construct
DNA (5'-D(*CP*GP*TP*A)-3') P 4 Synthetic construct
DNA (5'-D(P*GP*CP*CP*G)-3') D 4 Synthetic construct

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

A 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine
C9 H16 N3 O14 P3
OZIBFYOFLVBDIY-XVFCMESISA-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 MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-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: 1.5 Å
  • R-Value Free: 0.184
  • R-Value Work: 0.169
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 59.87 α = 90.00
b = 68.84 β = 90.00
c = 110.04 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-05-27
  • Released Date: 2017-07-05
  • Deposition author(s): Moon, A.F., Pryor, J.M., Ramsden, D.A., Kunkel, T.A., Bebenek, K., Pedersen, L.C.

Revision History

  • 2017-09-20
    Type: Author supporting evidence