3OLD

Crystal structure of alpha-amylase in complex with acarviostatin I03

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 3.1 of the entry. See complete history. 



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pancreatic alpha-amylase496Homo sapiensMutation(s): 1 
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04746
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
B
2N/A
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-quinovopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
C
3N/A
Glycosylation Resources
GlyTouCan:  G31885RT
GlyCosmos:  G31885RT
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
D
3N/A
Glycosylation Resources
GlyTouCan:  G96370VA
GlyCosmos:  G96370VA
GlyGen:  G96370VA
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose
E
3N/A
Glycosylation Resources
GlyTouCan:  G00395FS
GlyCosmos:  G00395FS
GlyGen:  G00395FS
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
I [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
ACI
Query on ACI
Download Ideal Coordinates CCD File 
J [auth A]6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL
C7 H13 N O4
XPHOBMULWMGEBA-VZFHVOOUSA-N
PCA
Query on PCA
Download Ideal Coordinates CCD File 
K [auth A]PYROGLUTAMIC ACID
C5 H7 N O3
ODHCTXKNWHHXJC-VKHMYHEASA-N
MPD
Query on MPD
Download Ideal Coordinates CCD File 
L [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
SO4
Query on SO4
Download Ideal Coordinates CCD File 
H [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CA
Query on CA
Download Ideal Coordinates CCD File 
F [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
G [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.986α = 90
b = 67.76β = 90
c = 130.469γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASESphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-04
    Changes: Data collection
  • Version 2.0: 2017-10-25
    Changes: Advisory, Atomic model, Derived calculations, Structure summary
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 3.1: 2023-11-01
    Changes: Data collection, Database references, Refinement description, Structure summary