4G5F

Pantothenate synthetase in complex with racemate (2S)-2,3-DIHYDRO-1,4-BENZODIOXINE-2-CARBOXYLIC ACID and (2R)-2,3-DIHYDRO-1,4-BENZODIOXINE-2-CARBOXYLIC ACID

Structural Biology Knowledgebase: 4G5F SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.240
  • R-Value Work: 0.170

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4G5F

Classification: Ligase / Ligase inhibitor

Total Structure Weight: 66356.36

Macromolecule Entities
Molecule Chains Length Organism Details
Pantothenate synthetase A, B 309 Mycobacterium tuberculosis EC#: 6.3.2.1 IUBMB
Mutation: T2A, E77G
Gene Name(s): panC Rv3602c MTCY07H7B.20

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
0JD
Query on 0JD

A, B (2S)-2,3-dihydro-1,4-benzodioxine-2-carboxylic acid
C9 H8 O4
HMBHAQMOBKLWRX-QMMMGPOBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
15N
Query on 15N

A, B (2R)-2,3-dihydro-1,4-benzodioxine-2-carboxylic acid
C9 H8 O4
HMBHAQMOBKLWRX-MRVPVSSYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

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

A, 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 %)
0JD N/A in BindingDB
Kd: 880000 nM  BindingMOAD
N/A in PDBbind
15N N/A in BindingDB
Kd: 880000 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.240
  • R-Value Work: 0.170
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 48.41 α = 90.00
b = 70.99 β = 99.58
c = 81.68 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-07-17
  • Released Date: 2013-07-17
  • Deposition author(s): Silvestre, H.L., Blundell, T.L., Abell, C., Ciulli, A.

Revision History

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