2QV4

Human pancreatic alpha-amylase complexed with nitrite and acarbose

• PDB DOI: https://doi.org/10.2210/pdb2QV4/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2007-08-07 Released: 2008-03-25 
• Deposition Author(s): Williams, L.K., Maurus, R., Brayer, G.D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 0.224 
• R-Value Work: 0.176 

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 57.05 kDa 
• Atom Count: 4,430 
• Modelled Residue Count: 496 
• Deposited Residue Count: 496 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pancreatic alpha-amylase	A	496	Homo sapiens	Mutation(s): 0  Gene Names: AMY2A EC: 3.2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04746 (Homo sapiens) Explore P04746  Go to UniProtKB:  P04746
PHAROS:  P04746 GTEx:  ENSG00000243480

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QV4	E [auth A]	4,6-dideoxy-4-{[(1S,4R,5R,6S)-4-{[alpha-D-glucopyranosyl-(1->4)-alpha-D-glucopyranosyl-(1->4)-alpha-D-glucopyranosyl]oxy}-5,6-dihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose C31 H53 N O23 SPMGVWYYOZMEBD-NPPSNIQKSA-N
NAG	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
NO2	D [auth A]	NITRITE ION N O2 IOVCWXUNBOPUCH-UHFFFAOYSA-M
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 0.224 
• R-Value Work: 0.176 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.859	α = 90
b = 67.723	β = 90
c = 130.099	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MAR345dtb	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-25 
Deposition Author(s): Williams, L.K., Maurus, R., Brayer, G.D.

Revision History  

• Version 1.0: 2008-03-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2019-12-25
  Changes: Database references, Derived calculations, Polymer sequence
• Version 2.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Structure summary
• Version 2.2: 2020-11-11
  Changes: Structure summary
• Version 2.3: 2023-08-30
  Changes: Data collection, Database references, Refinement description