6MN8 | pdb_00006mn8

Crystal Structure of Prolyl-tRNA Synthetase from Onchocerca volvulus with bound Halofuginone and nucleotide

• PDB DOI: https://doi.org/10.2210/pdb6MN8/pdb

• Classification: LIGASE
• Organism(s): Onchocerca volvulus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-10-01 Released: 2018-10-17 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.179 (Depositor), 0.184 (DCC) 
• R-Value Work: 
  0.142 (Depositor), 0.146 (DCC) 
• R-Value Observed: 
  0.144 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Prolyl-tRNA Synthetase from Onchocerca volvulus with bound Halofuginone and nucleotide

Dranow, D.M., Conrady, D.G., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 60.15 kDa 
• Atom Count: 3,479 
• Modeled Residue Count: 399 
• Deposited Residue Count: 505 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A	505	Onchocerca volvulus	Mutation(s): 0  EC: 6.1.1.15
UniProt
Find proteins for A0A2K6VKP7 (Onchocerca volvulus) Explore A0A2K6VKP7  Go to UniProtKB:  A0A2K6VKP7

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP (Subject of Investigation/LOI)	E [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
HFG (Subject of Investigation/LOI)	D [auth A]	7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one C16 H17 Br Cl N3 O3 LVASCWIMLIKXLA-CABCVRRESA-N
AMP (Subject of Investigation/LOI)	F [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
2PN (Subject of Investigation/LOI)	G [auth A]	IMIDODIPHOSPHORIC ACID H5 N O6 P2 GNGSOPFGGKKDQP-UHFFFAOYSA-N
SER	K [auth A], L [auth A]	SERINE C3 H7 N O3 MTCFGRXMJLQNBG-REOHCLBHSA-N
GLY	H [auth A], I [auth A], J [auth A]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.179 (Depositor), 0.184 (DCC) 
• R-Value Work:  0.142 (Depositor), 0.146 (DCC) 
• R-Value Observed: 0.144 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36mn8

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.72	α = 90
b = 159.72	β = 90
c = 143.72	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
MoRDa	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-10-17 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2018-10-17
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description