5TWQ

Post-catalytic nicked complex of human Polymerase Mu with newly incorporated UTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.205
  • R-Value Work: 0.168

Literature

Macromolecules
Sequence Display for 5TWQ

Classification: TRANSFERASE / DNA

Total Structure Weight: 45775.65


Macromolecule Entities
Molecule Chains Length Organism Details
human DNA 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
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 Unidentified
DNA/RNA (5'-D(*CP*GP*TP*A)-R(P*U)-3') P 5 Unidentified
DNA (5'-D(P*GP*CP*CP*G)-3') D 4 Unidentified

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PPV
Query on PPV

A PYROPHOSPHATE
H4 O7 P2
XPPKVPWEQAFLFU-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)
MN
Query on MN

A MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
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: 1.8 Å
  • R-Value Free: 0.205
  • R-Value Work: 0.168
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 59.97 α = 90.00
b = 68.71 β = 90.00
c = 110.41 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-11-14
  • 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

No revisions since initial release