5DEZ | pdb_00005dez

Crystal structure of AcMNPV Chitinase A

• PDB DOI: https://doi.org/10.2210/pdb5DEZ/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: 2.30 Å
• R-Value Free: 
  0.229 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

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: 125.78 kDa 
• Atom Count: 9,207 
• Modeled Residue Count: 1,056 
• Deposited Residue Count: 1,102 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ac-ChiA	A, B	551	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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], F [auth A], G [auth A], J [auth B], K [auth B], L [auth B], M [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	N [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	H [auth A], I [auth A], O [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.229 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.931	α = 90
b = 111.927	β = 90
c = 129.516	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 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-10-30
  Changes: Data collection, Database references, Structure summary