3QFK

2.05 Angstrom Crystal Structure of Putative 5'-Nucleotidase from Staphylococcus aureus in complex with alpha-ketoglutarate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.221
  • R-Value Work: 0.173

Literature

Macromolecules
Sequence Display for 3QFK

Classification: HYDROLASE

Total Structure Weight: 61100.31

Macromolecule Entities
Molecule Chains Length Organism Details
Uncharacterized protein A 527 Staphylococcus aureus Gene Name(s): SAOUHSC_00107
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
AKG
Query on AKG

A 2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PEG
Query on PEG

A DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-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)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

Unit Cell:

Length (Å) Angle (°)
a = 90.44 α = 90.00
b = 84.69 β = 116.91
c = 95.97 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-01-21
  • Released Date: 2011-02-09
  • Deposition author(s): Minasov, G., Wawrzak, Z., Krishna, S.N., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Kiryukhina, O., Bagnoli, F., Falugi, F., Bottomley, M., Grandi, G., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History

  • Version 1_0: 2011-02-09

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Version format compliance

  • Version 1_2: 2017-11-08

    Type: Refinement description