4B13

Plasmodium vivax N-myristoyltransferase with a bound benzofuran inhibitor (compound 25)

Structural Biology Knowledgebase: 4B13 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.291
  • R-Value Work: 0.238

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4B13

Classification: TRANSFERASE

Total Structure Weight: 139653.70

Macromolecule Entities
Molecule Chains Length Organism Details
GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE A, B, C 385 Plasmodium vivax EC#: 2.3.1.97 IUBMB
Fragment: RESIDUES 27-410
Gene Name(s): PVX_085815

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

A, B, C 2-oxopentadecyl-CoA
C36 H64 N7 O17 P3 S
JKWHUJMJVNMKEF-UOCZADIYSA-J
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
X25
Query on X25

A, B, C 4-{[2-(3-benzyl-1,2,4-oxadiazol-5-yl)-3-methyl- 1-benzofuran-4-yl]oxy}piperidine
C23 H23 N3 O3
QVBWWXFSCCHYFK-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B, C CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, C MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
X25 N/A in BindingDB
IC50: 2000 nM  BindingMOAD
IC50: 2000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.291
  • R-Value Work: 0.238
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 57.32 α = 90.00
b = 119.13 β = 90.00
c = 178.46 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-07-06
  • Released Date: 2012-10-17
  • Deposition author(s): Yu, Z., Brannigan, J.A., Moss, D.K., Brzozowski, A.M., Wilkinson, A.J., Holder, A.A., Tate, E.W., Leatherbarrow, R.J.

Revision History

  • 2012-11-07
    Type: Citation | Details: JRNL