6L4X | pdb_00006l4x

Turning an asparaginyl endopeptidase into a peptide ligase

PDB DOI: https://doi.org/10.2210/pdb6L4X/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 (Singapore)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free:
0.236 (Depositor), 0.210 (DCC)
R-Value Work:
0.207 (Depositor)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.2 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 55.79 kDa
Atom Count: 3,434
Modeled Residue Count: 413
Deposited Residue Count: 502
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Asparaginyl endopeptidase	A	502	Clitoria ternatea	Mutation(s): 5 EC: 3.4.22.34
UniProt
Find proteins for A0A0P0QM28 (Clitoria ternatea) Explore A0A0P0QM28 Go to UniProtKB: A0A0P0QM28
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0P0QM28
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SNN Query on SNN	A	L-PEPTIDE LINKING	C₄ H₆ N₂ O₂		ASN

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free: 0.236 (Depositor), 0.210 (DCC)
R-Value Work: 0.207 (Depositor)
R-Value Observed: 0.208 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.9	α = 90
b = 79.29	β = 90
c = 134.86	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-10-07

Deposition Author(s):

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

Revision History (Full details and data files)

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
Version 2.2: 2024-11-06
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.