5YCD

Crystal structure of Poecilia reticulata adenylate kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of Poecilia reticulata adenylate kinase

Bae, E.Kim, J.Moon, S.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Adenylayte kinaseA, B193Poecilia reticulataMutation(s): 0 
Gene Names: AK1
EC: 2.7.4.3 (UniProt), 2.7.4.6 (UniProt)
UniProt
Find proteins for A0A452CSM2 (Poecilia reticulata)
Explore A0A452CSM2 
Go to UniProtKB:  A0A452CSM2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AP5 (Subject of Investigation/LOI)
Query on AP5

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]BIS(ADENOSINE)-5'-PENTAPHOSPHATE
C20 H29 N10 O22 P5
OIMACDRJUANHTJ-XPWFQUROSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.79α = 90
b = 81.505β = 90
c = 120.123γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Rural Development AdministrationKorea, Republic OfPJ01111201
National Research Foundation of KoreaKorea, Republic OfNRF-2016R1D1A1A09916821

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-12
    Type: Initial release
  • Version 1.1: 2018-09-19
    Changes: Data collection, Database references