5HNK

Crystal structure of T5Fen in complex intact substrate and metal ions.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.183

Literature

Macromolecules
Sequence Display for 5HNK

Classification: HYDROLASE

Total Structure Weight: 70091.62


Macromolecule Entities
Molecule Chains Length Organism Details
Exodeoxyribonuclease A, B 272 Escherichia virus t5 Fragment: UNP residues 20-291
Mutation: D153K
Details: Corresponds to residues 20-291 of Uniprot P06229 but with mutation D153K
Gene Name(s): D15 exo5 T5.130 T5p128
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*AP*AP*AP*AP*GP*CP*GP*TP*AP*CP*GP*C)-3') X, Y 12 Synthetic construct

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

B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

Y POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

Y MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.183
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 44.72 α = 90.00
b = 109.94 β = 90.00
c = 127.34 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-01-18
  • Released Date: 2016-06-01
  • Deposition author(s): Almalki, F.A., Feng, M., Zhang, J., Sedelnikova, S.E., Rafferty, J.B., Sayers, J.R., Artymiuk, P.J.

Revision History

  • Version 1_0: 2016-06-01

    Type: Initial release

  • Version 1_1: 2016-06-08

    Type: Database references

  • Version 1_2: 2016-06-22

    Type: Database references

  • Version 1_3: 2016-07-20

    Type: Database references