8J5G

Crystal structure of kinase AbmG in complex with 4'-hydroxy-4'-thiocytidine 5'-diphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

Starting Model: in silico
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Ligand Structure Quality Assessment 


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Literature

Crystal structure of kinase AbmG in complex with 4'-hydroxy-4'-thiocytidine 5'-diphosphate

Ushimaru, R.Mori, T.Liu, H.-w.Abe, I.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Deoxyadenosine/deoxycytidine kinase247Streptomyces sp. ATCC 700974Mutation(s): 1 
UniProt
Find proteins for A0A370RDE4 (Streptomyces sp. HB202)
Explore A0A370RDE4 
Go to UniProtKB:  A0A370RDE4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A370RDE4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TT9 (Subject of Investigation/LOI)
Query on TT9

Download Ideal Coordinates CCD File 
B [auth A][(2~{S},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-2-(hydroxymethyl)-3,4-bis(oxidanyl)thiolan-2-yl] phosphono hydrogen phosphate
C9 H15 N3 O11 P2 S
KEAXZHZTGMHPPH-AYHNYZOXSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.415α = 90
b = 78.344β = 90
c = 83.414γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-24
    Type: Initial release