6JMB | pdb_00006jmb

Crystal structure of Ostrinia furnacalis Group IV chitinase in complex with allosamidin

PDB DOI: https://doi.org/10.2210/pdb6JMB/pdb

Classification: HYDROLASE
Organism(s): Ostrinia furnacalis
Expression System: Pichia
Mutation(s): No

Deposited: 2019-03-07 Released: 2020-03-11
Deposition Author(s): Liu, T., Yang, Q.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.39 Å
R-Value Free:
0.160 (Depositor), 0.159 (DCC)
R-Value Work:
0.149 (Depositor), 0.149 (DCC)
R-Value Observed:
0.150 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Structure and property of group IV insect chitinase, a potential drug target and biopesticide

Liu, T., Guo, X., Bu, Y., Zhou, Y., Duan, Y., Yang, Q.

(2020) Insect Biochem Mol Biol 119

DOI: https://doi.org/10.1016/j.ibmb.2020.103326

Macromolecule Content

Total Structure Weight: 44.58 kDa
Atom Count: 3,282
Modeled Residue Count: 374
Deposited Residue Count: 393
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ofchtiv-allosamidin	A	393	Ostrinia furnacalis	Mutation(s): 0 EC: 3.2.1.14
UniProt
Find proteins for A0A482LWB1 (Ostrinia furnacalis) Explore A0A482LWB1 Go to UniProtKB: A0A482LWB1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A482LWB1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-allopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-allopyranose	B	2		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G77950XB GlyCosmos: G77950XB

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMI Query on AMI Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ALLOSAMIZOLINE C₉ H₁₆ N₂ O₄ MKJAYSJDHSEFRI-PVFLNQBWSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000468 Query on PRD_000468	B	Allosamidin	Oligosaccharide / Inhibitor		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.39 Å
R-Value Free: 0.160 (Depositor), 0.159 (DCC)
R-Value Work: 0.149 (Depositor), 0.149 (DCC)
R-Value Observed: 0.150 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.625	α = 90
b = 71.707	β = 90
c = 72.155	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-03-11

Deposition Author(s):

Liu, T.

Yang, Q.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31425021

Revision History (Full details and data files)

Version 1.0: 2020-03-11
Type: Initial release
Version 1.1: 2020-04-22
Changes: Database references
Version 2.0: 2022-04-13
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-11-22
Changes: Data collection, Refinement description
Version 2.2: 2024-11-13
Changes: Structure summary