4HVC

Crystal structure of human prolyl-tRNA synthetase in complex with halofuginone and ATP analogue

Structural Biology Knowledgebase: 4HVC SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.204

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4HVC

Classification: ligase / ligase inhibitor

Total Structure Weight: 120149.31

Macromolecule Entities
Molecule Chains Length Organism Details
Bifunctional glutamate/proline--tRNA ligase A, B 519 Homo sapiens EC#: 6.1.1.15 IUBMB 6.1.1.17 IUBMB
Fragment: ProRS part of EPRS (unp residues 1003-1513)
Gene Name(s): EPRS Gene View GLNS PARS QARS Gene View QPRS PIG32

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

A, B PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HFG
Query on HFG

A, B 7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin- 2-yl]-2-oxopropyl}quinazolin-4(3H)-one
Halofuginone (Synonym)
C16 H17 Br Cl N3 O3
LVASCWIMLIKXLA-CABCVRRESA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.204
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 72.54 α = 90.00
b = 93.10 β = 107.95
c = 87.00 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-11-06
  • Released Date: 2013-01-02
  • Deposition author(s): Zhou, H., Sun, L., Yang, X.L., Schimmel, P.

Revision History

No revisions since initial release