1H48

The structure of 2C-Methyl-D-erythritol 2,4-cyclodiphosphate synthase in complex with CMP and product


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.202

Literature

Macromolecules
Sequence Display for 1H48

Classification: SYNTHASE

Total Structure Weight: 107715.30

Macromolecule Entities
Molecule Chains Length Organism Details
2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE A, B, C..., D, E, FA, B, C, D, E, F 161 Escherichia coli EC#: 4.6.1.12 IUBMB
Gene Name(s): ispF mecS ygbB b2746 JW2716
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
C5P
Query on C5P

A, B, C, D, E, F CYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O8 P
IERHLVCPSMICTF-XVFCMESISA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GPP
Query on GPP

C, E GERANYL DIPHOSPHATE
C10 H20 O7 P2
GVVPGTZRZFNKDS-JXMROGBWSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CDI
Query on CDI

A, B, C, D, E, F 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE
C5 H12 O9 P2
SFRQRNJMIIUYDI-UHNVWZDZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B, C, D, E, F ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A, D MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.202
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 198.12 α = 90.00
b = 150.29 β = 106.52
c = 57.56 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-02-24
  • Released Date: 2004-12-22
  • Deposition author(s): Kemp, L.E., Alphey, M.S., Bond, C.S., Hunter, W.N.

Revision History

  • Version 1_0: 2004-12-22

    Type: Initial release

  • Version 1_1: 2011-05-08

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance

  • Version 1_3: 2017-07-12

    Type: Derived calculations