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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of CcbD with methylthiolincosamide

Mori, T.Lyu, S.Abe, I.

To be published.

Macromolecules
Find similar proteins by:  (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

View Full Validation Report



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: 2023-08-02
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Data collection