6LE7 | pdb_00006le7

Crystal structure of nematode family I chitinase,CeCht1, in complex with dihydropyrrolopyrazol-6-one derivate 2

PDB DOI: https://doi.org/10.2210/pdb6LE7/pdb

Classification: HYDROLASE
Organism(s): Caenorhabditis elegans
Expression System: Komagataella phaffii GS115
Mutation(s): No

Deposited: 2019-11-24 Released: 2021-05-26
Deposition Author(s): Chen, Q., Yang, Q., Zhou, Y.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free:
0.257 (Depositor), 0.258 (DCC)
R-Value Work:
0.216 (Depositor), 0.217 (DCC)
R-Value Observed:
0.219 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of nematode family I chitinase,CeCht1, in complex with dihydropyrrolopyrazol-6-one derivate 2

Chen, Q., Yang, Q., Zhou, Y.

To be published.

Macromolecule Content

Total Structure Weight: 42.62 kDa
Atom Count: 3,273
Modeled Residue Count: 381
Deposited Residue Count: 381
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable endochitinase	A	381	Caenorhabditis elegans	Mutation(s): 0 Gene Names: cht-1, C04F6.3 EC: 3.2.1.14
UniProt
Find proteins for Q11174 (Caenorhabditis elegans) Explore Q11174 Go to UniProtKB: Q11174
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q11174
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EA9 (Subject of Investigation/LOI) Query on EA9 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(4R)-3-(2-hydroxyphenyl)-4-(3-methoxy-4-propoxy-phenyl)-5-(pyridin-3-ylmethyl)-1,4-dihydropyrrolo[3,4-c]pyrazol-6-one C₂₇ H₂₆ N₄ O₄ VDJNZGXOMKRJML-AREMUKBSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.257 (Depositor), 0.258 (DCC)
R-Value Work: 0.216 (Depositor), 0.217 (DCC)
R-Value Observed: 0.219 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.634	α = 90
b = 67.119	β = 103.657
c = 57.062	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-05-26

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31801776

Revision History (Full details and data files)

Version 1.0: 2021-05-26
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-16
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.