5DF0

Crystal structure of AcMNPV Chitinase A in complex WITH CHITOTRIO-THIAZOLINE DITHIOAMIDE

PDB DOI: https://doi.org/10.2210/pdb5DF0/pdb

Classification: HYDROLASE
Organism(s): Autographa californica nucleopolyhedrovirus
Expression System: Alphabaculovirus
Mutation(s): No

Deposited: 2015-08-26 Released: 2016-09-07
Deposition Author(s): Mou, T.-C., Sprang, S.R.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.25 Å
R-Value Free: 0.286
R-Value Work: 0.226
R-Value Observed: 0.232

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of AcMNPV Chitinase A

Mou, T.-C., Sprang, S.R.

To be published.

Macromolecule Content

Total Structure Weight: 124.51 kDa
Atom Count: 8,521
Modelled Residue Count: 1,056
Deposited Residue Count: 1,090
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ac-ChiA	A, B	545	Autographa californica nucleopolyhedrovirus	Mutation(s): 0 Gene Names: ChiA, Ac-ChiA EC: 3.2.1.14
UniProt
Find proteins for Q70SQ1 (Autographa californica nuclear polyhedrosis virus) Explore Q70SQ1 Go to UniProtKB: Q70SQ1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q70SQ1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SN5 Query on SN5 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain O [auth B] MOL2 format, chain F [auth A] MOL2 format, chain O [auth B]	F [auth A], O [auth B]	2-deoxy-2-(ethanethioylamino)-beta-D-glucopyranose C₈ H₁₅ N O₅ S BIHKKHHUWVSGSD-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Focus chain O [auth B] Interactions & Density Focus chain F [auth A] Focus chain O [auth B]
58Y Query on 58Y Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain P [auth B] MOL2 format, chain G [auth A] MOL2 format, chain P [auth B]	G [auth A], P [auth B]	(2R,3aR,5R,6R,7R,7aR)-5-(hydroxymethyl)-2-methylhexahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol C₈ H₁₅ N O₄ S XWPUWEBFKDEDIF-CVBHLRHXSA-N		Interactions Focus chain G [auth A] Focus chain P [auth B] Interactions & Density Focus chain G [auth A] Focus chain P [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B]	C [auth A] D [auth A] E [auth A] L [auth B] M [auth B] C [auth A], D [auth A], E [auth A], L [auth B], M [auth B], N [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B]	I [auth A], J [auth A], K [auth A], Q [auth B], R [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A]	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.25 Å
R-Value Free: 0.286
R-Value Work: 0.226
R-Value Observed: 0.232
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.712	α = 90
b = 112.766	β = 90
c = 129.591	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-09-07

Deposition Author(s):

Mou, T.-C.

Sprang, S.R.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P20GM103546

Revision History (Full details and data files)

Version 1.0: 2016-09-07
Type: Initial release
Version 1.1: 2017-09-20
Changes: Author supporting evidence, Derived calculations
Version 1.2: 2019-12-25
Changes: Author supporting evidence
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.4: 2023-09-27
Changes: Data collection, Database references, Refinement description, Structure summary

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5DF0

Crystal structure of AcMNPV Chitinase A in complex WITH CHITOTRIO-THIAZOLINE DITHIOAMIDE

Crystal structure of AcMNPV Chitinase A

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)