4DDK

Pantothenate synthetase in complex with 1,3-benzodioxole-5-carboxylic acid

Structural Biology Knowledgebase: 4DDK SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.184

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DDK

Classification: ligase / ligase inhibitor

Total Structure Weight: 64163.85

Macromolecule Entities
Molecule Chains Length Organism Details
Pantothenate synthetase A, B 301 Mycobacterium tuberculosis EC#: 6.3.2.1 IUBMB
Mutation: T2A, E77G
Gene Name(s): panC MT3707

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
0HN
Query on 0HN

A, B 1,3-benzodioxole-5-carboxylic acid
benzo[d][1,3]dioxole-5-carboxylic acid (Synonym)
C8 H6 O4
VDVJGIYXDVPQLP-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EOH
Query on EOH

A, B ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
0HN N/A in BindingDB
Kd: 5130000 nM  BindingMOAD
Kd: 5100000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.184
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 48.19 α = 90.00
b = 70.71 β = 99.14
c = 81.69 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-01-18
  • Released Date: 2013-02-13
  • Deposition author(s): Silvestre, H.L.

Revision History

  • 2013-09-04
    Type: Citation | Details: Citation update
  • 2013-08-07
    Type: Citation | Details: Citation update