7YP8 | pdb_00007yp8

Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Leucyl-sulfamoyl 3-deazaadenosine

• PDB DOI: https://doi.org/10.2210/pdb7YP8/pdb

• Classification: LIGASE
• Organism(s): Neisseria gonorrhoeae NCCP11945
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-08-02 Released: 2024-02-07 
• Deposition Author(s): Pang, L., De Graef, S., Strelkov, S.V., Weeks, S.D.
• Funding Organization(s): Research Foundation - Flanders (FWO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.231 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

The essential role of a structured water in base recognition of Class II aminoacyl-tRNA synthetases

Pang, L., De Graef, S., Zhang, B., Strelkov, S.V., Van Aerschot, A., Weeks, S.D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 98.8 kDa 
• Atom Count: 6,958 
• Modeled Residue Count: 866 
• Deposited Residue Count: 877 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine--tRNA ligase	A	877	Neisseria gonorrhoeae NCCP11945	Mutation(s): 1  Gene Names: leuS, NGK_0009 EC: 6.1.1.4
UniProt
Find proteins for B4RNT1 (Neisseria gonorrhoeae (strain NCCP11945)) Explore B4RNT1  Go to UniProtKB:  B4RNT1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JIE (Subject of Investigation/LOI)	C [auth A]	[(2R,3S,4R,5R)-5-(4-azanylimidazo[4,5-c]pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl N-[(2S)-2-azanyl-4-methyl-pentanoyl]sulfamate C17 H26 N6 O7 S SLTGASQMUPNMPQ-JHTGIODLSA-N
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.231 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.794	α = 90
b = 82.979	β = 90
c = 229.25	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-02-07 
Deposition Author(s): Pang, L., De Graef, S., Strelkov, S.V., Weeks, S.D.

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Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	G077814N
Research Foundation - Flanders (FWO)	Belgium	G0A4616N
Research Foundation - Flanders (FWO)	Belgium	1S53516N

Revision History  

• Version 1.0: 2024-02-07
  Type: Initial release
  
• Version 1.1: 2026-03-04
  Changes: Refinement description, Structure summary