2YWH

Crystal structure of GDP-bound LepA from Aquifex aeolicus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal structures of GTP-binding protein LepA from Aquifex aeolicus.

Kawazoe, M.Takemoto, C.Kaminishi, T.Nishino, A.Nakayama-Ushikoshi, R.Hanawa-Suetsugu, K.Terada, T.Shirouzu, M.Yokoyama, S.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GTP-binding protein LepAA600Aquifex aeolicus VF5Mutation(s): 0 
Gene Names: aq_1725lepA
EC: 3.6.5
UniProt
Find proteins for O67618 (Aquifex aeolicus (strain VF5))
Explore O67618 
Go to UniProtKB:  O67618
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP (Subject of Investigation/LOI)
Query on GDP

Download Ideal Coordinates CCD File 
C [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.676α = 90
b = 116.118β = 90
c = 122.721γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2017-10-11
    Changes: Refinement description