5U2R

PRECATALYTIC TERNARY COMPLEX OF HUMAN DNA POLYMERASE BETA WITH GAPPED DNA SUBSTARTE, INCOMING L-DCTP AND CA2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.191

Literature

Macromolecules
Sequence Display for 5U2R

Classification: TRANSFERASE / DNA

Total Structure Weight: 49495.41


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase beta A 343 Homo sapiens EC#: 2.7.7.7 IUBMB 4.2.99 IUBMB
Gene Name(s): POLB Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
16- MER TEMPLATE T 16 Synthetic construct
10- MER PRIMER P 10 Synthetic construct
5-MER PHOSPHORYLATED DOWNSTREAM PRIMER D 5 Synthetic construct

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
1S0
Query on 1S0

A 4-amino-1-{2-deoxy-5-O-[(R)-hydroxy{[(S)- hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]- beta-L-erythro-pentofuranosyl}pyrimidin-2(1H)- one
C9 H16 N3 O13 P3
RGWHQCVHVJXOKC-CHKWXVPMSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
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: 1.8 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.191
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 50.91 α = 90.00
b = 80.16 β = 107.68
c = 55.64 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-11-30
  • Released Date: 2017-05-24
  • Deposition author(s): Vyas, R., Suo, Z.

Revision History

  • Version 1_0: 2017-05-24

    Type: Initial release

  • Version 1_1: 2017-06-14

    Type: Database references

  • Version 1_2: 2017-09-13

    Type: Author supporting evidence