5Y9B | pdb_00005y9b

Crystal structure of Bacillus licheniformis Gamma glutamyl transpeptidase with DON

• PDB DOI: https://doi.org/10.2210/pdb5Y9B/pdb

• Classification: TRANSFERASE
• Organism(s): Bacillus licheniformis
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2017-08-24 Released: 2018-08-29 
• Deposition Author(s): Goel, M., Kumari, S., Pal, R., Gupta, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.236 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Bacillus licheniformis Gamma glutamyl transpeptidase with Azaserine

Goel, M., Kumari, S., Pal, R., Gupta, R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 64.39 kDa 
• Atom Count: 4,271 
• Modeled Residue Count: 542 
• Deposited Residue Count: 585 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma glutamyl transpeptidase	A	398	Bacillus licheniformis	Mutation(s): 0  EC: 2.3.2.2 (PDB Primary Data), 3.4.19.13 (UniProt)
UniProt
Find proteins for Q65KZ6 (Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / CCUG 7422 / NBRC 12200 / NCIMB 9375 / NCTC 10341 / NRRL NRS-1264 / Gibson 46)) Explore Q65KZ6  Go to UniProtKB:  Q65KZ6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma glutamyl transpeptidase	B	187	Bacillus licheniformis	Mutation(s): 0  EC: 2.3.2.2 (PDB Primary Data), 3.4.19.13 (UniProt)
UniProt
Find proteins for Q65KZ6 (Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / CCUG 7422 / NBRC 12200 / NCIMB 9375 / NCTC 10341 / NRRL NRS-1264 / Gibson 46)) Explore Q65KZ6  Go to UniProtKB:  Q65KZ6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DON	E [auth B]	6-DIAZENYL-5-OXO-L-NORLEUCINE C6 H11 N3 O3 CKRLZVNSTCQAJW-YFKPBYRVSA-N
EDO	F [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	C [auth A], D [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.236 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.56	α = 90
b = 61.396	β = 90
c = 145.81	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data processing
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-29 
Deposition Author(s): Goel, M., Kumari, S., Pal, R., Gupta, R.

Revision History  

• Version 1.0: 2018-08-29
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2025-09-17
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary