5DF0 | pdb_00005df0

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free: 
  0.286 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.232 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of AcMNPV Chitinase A

Mou, T.-C., Sprang, S.R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

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

Macromolecules

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
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SN5	F [auth A], O [auth B]	2-deoxy-2-(ethanethioylamino)-beta-D-glucopyranose C8 H15 N O5 S BIHKKHHUWVSGSD-FMDGEEDCSA-N
58Y	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
NAG	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
SO4	I [auth A], J [auth A], K [auth A], Q [auth B], R [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free:  0.286 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.232 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

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

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-09-07 
Deposition Author(s): Mou, T.-C., Sprang, S.R.

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

Revision History  

• 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
• Version 1.5: 2024-11-20
  Changes: Structure summary