7YN2

Crystal structure of CcbD with methylthiolincosamide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history. 


Literature

Crystal structure of CcbD with methylthiolincosamide

Mori, T., Lyu, S., Abe, I.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CcbD
A, B
365Streptomyces caelestisMutation(s): 0 
Gene Names: HDA41_002772
UniProt
Find proteins for E9JES9 (Streptomyces caelestis)
Explore E9JES9 
Go to UniProtKB:  E9JES9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9JES9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IYV (Subject of Investigation/LOI)
Query on IYV
Download Ideal Coordinates CCD File 
C [auth A](2R,3R,4S,5R,6R)-2-[(1R,2R)-1-azanyl-2-oxidanyl-propyl]-6-methylsulfanyl-oxane-3,4,5-triol
C9 H19 N O5 S
AEEIMWYSDWZKAT-HJTGYUAHSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 192.059α = 90
b = 52.903β = 91.103
c = 90.938γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-02
    Type: Initial release