2AMT

Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase complexed with a CDP derived fluorescent inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.280
  • R-Value Work: 0.243

Literature

Macromolecules
Sequence Display for 2AMT

Classification: LYASE

Total Structure Weight: 105942.16

Macromolecule Entities
Molecule Chains Length Organism Details
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase A, B, C..., D, E, FA, B, C, D, E, F 159 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 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
1AA
Query on 1AA

A, C, D, E 5'-O-[({[(2-{[(2-AMINOPHENYL)CARBONYL]OXY}ETHYL)OXY]PHOSPHINATO}OXY)PHOSPHINATO]CYTIDINE
C18 H24 N4 O13 P2
PGXVRIOOHRVKLC-DTZQCDIJSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GPP
Query on GPP

A, D GERANYL DIPHOSPHATE
C10 H20 O7 P2
GVVPGTZRZFNKDS-JXMROGBWSA-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)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
1AA N/A in BindingDB
Kd: 36000 nM  BindingMOAD
Kd: 36000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.280
  • R-Value Work: 0.243
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 54.03 α = 90.00
b = 115.27 β = 90.18
c = 87.61 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-08-10
  • Released Date: 2006-02-28
  • Deposition author(s): Ramsden, N.L., Hunter, W.N.

Revision History

  • Version 1_0: 2006-02-28

    Type: Initial release

  • Version 1_1: 2008-04-30

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance