2VKQ

Crystal structure of human cytosolic 5'-nucleotidase III (cN-III, NT5C3) in complex with beryllium trifluoride

Structural Biology Knowledgebase: 2VKQ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.210

Literature

Macromolecules
Sequence Display for 2VKQ

Classification: HYDROLASE

Total Structure Weight: 33289.62

Macromolecule Entities
Molecule Chains Length Organism Details
CYTOSOLIC 5'-NUCLEOTIDASE III A 292 Homo sapiens EC#: 3.1.3.5 IUBMB
Fragment: RESIDUES 13-285
Gene Name(s): NT5C3A Gene View NT5C3 P5N1 UMPH1 HSPC233
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.210
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 88.26 α = 90.00
b = 99.39 β = 90.00
c = 78.04 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-12-21
  • Released Date: 2008-01-08
  • Deposition author(s): Wallden, K., Moche, M., Arrowsmith, C.H., Berglund, H., Busam, R., Collins, R., Dahlgren, L.G., Edwards, A., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Herman, M.D., Johansson, A., Johansson, I., Kallas, A., Karlberg, T., Kotenyova, T., Lehtio, L., Nilsson, M.E., Nyman, T., Persson, C., Sagemark, J., Thorsell, A.G., Tresaugues, L., van den Berg, S., Weigelt, J., Welin, M., Nordlund, P., Structural Genomics Consortium (SGC)

Revision History

  • 2015-04-22
    Type: Entry authorship | Details: AUTHOR
  • 2015-04-22
    Type: Source and taxonomy | Details: SOURCE
  • 2011-07-13
    Type: Version format compliance | Details: Compliance with PDBx exchange dictionary V4
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor