3Q80

Structure of Mtb 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase (IspD) Complexed with CDP-ME


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of Mycobacterium tuberculosis 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase (IspD): a candidate antitubercular drug target

Reddy, M.C.M.Bruning, J.B.Thurman, C.Ioerger, T.R.Sacchettini, J.C.

(2011) Proteins --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2-C-methyl-D-erythritol 4-phosphate cytidyltransferase
A, B
231Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: ispD
EC: 2.7.7.60
Find proteins for P9WKG9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WKG9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CDM
Query on CDM

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Download CCD File 
A, B
4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL
C14 H25 N3 O14 P2
YFAUKWZNPVBCFF-XHIBXCGHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.165 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 41.581α = 90.00
b = 92.668β = 90.00
c = 146.421γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data collection
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-05-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-11-12
    Type: Structure summary
  • Version 1.3: 2017-11-08
    Type: Refinement description