6L4Y | pdb_00006l4y

Turning an asparaginyl endopeptidase into a peptide ligase

• PDB DOI: https://doi.org/10.2210/pdb6L4Y/pdb

• Classification: HYDROLASE
• Organism(s): Clitoria ternatea
• Expression System: Spodoptera aff. frugiperda 1 BOLD-2017
• Mutation(s): Yes 


• Deposited: 2019-10-21 Released: 2020-10-07 
• Deposition Author(s): El Sahili, A., Lescar, J.
• Funding Organization(s): Ministry of Education (MoE, Singapore)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Turning an Asparaginyl Endopeptidase into a Peptide Ligase

Hemu, X., El Sahili, A., Hu, S., Zhang, X., Serra, A., Goh, B.C., Darwis, D.A., Chen, M.W., Sze, S.K., Liu, C.F., Lescar, J., Tam, J.P.

(2020) ACS Catal 10: 8825-8834

• DOI: https://doi.org/10.1021/acscatal.0c02078

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: 112.28 kDa 
• Atom Count: 7,513 
• Modelled Residue Count: 825 
• Deposited Residue Count: 1,004 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Asparaginyl endopeptidase	A, B	502	Clitoria ternatea	Mutation(s): 2  EC: 3.4.22.34
UniProt
Find proteins for A0A0P0QM28 (Clitoria ternatea) Explore A0A0P0QM28  Go to UniProtKB:  A0A0P0QM28
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A], F [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PEG	E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS	A, B	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS
SNN	A, B	L-PEPTIDE LINKING	C4 H6 N2 O2		ASN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.61	α = 90
b = 79.6	β = 93.95
c = 136.47	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-10-07 
Deposition Author(s): El Sahili, A., Lescar, J.

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Funding Organization	Location	Grant Number
Ministry of Education (MoE, Singapore)	Singapore	MOE2016-T3-1-003

Revision History  

• Version 1.0: 2020-10-07
  Type: Initial release
  
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations
• Version 2.1: 2023-11-22
  Changes: Refinement description