3I0O

Crystal Structure of Spectinomycin Phosphotransferase, APH(9)-Ia, in complex with ADP and Spectinomcyin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.275
  • R-Value Work: 0.229

Literature

Macromolecules
Sequence Display for 3I0O

Classification: TRANSFERASE

Total Structure Weight: 40505.38

Macromolecule Entities
Molecule Chains Length Organism Details
Spectinomycin phosphotransferase A 339 Legionella pneumophila Gene Name(s): aph
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SMI
Query on SMI

A SPECTINOMYCIN
4,,6S (Synonym)
C14 H26 N2 O8
JEBSYFSDBYNEEU-GOZOPVAMSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NI
Query on NI

A NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
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: 2.4 Å
  • R-Value Free: 0.275
  • R-Value Work: 0.229
  • Space Group: P 31 2 1

Unit Cell:

Length (Å) Angle (°)
a = 75.01 α = 90.00
b = 75.01 β = 90.00
c = 139.94 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-06-25
  • Released Date: 2010-01-19
  • Deposition author(s): Fong, D.H., Lemke, C.T., Hwang, J., Xiong, B., Berghuis, A.M.

Revision History

  • Version 1_0: 2010-01-19

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Version format compliance