5H7W

Crystal structure of 5'-nucleotidase from venom of Naja atra

  • Classification: HYDROLASE
  • Organism(s): Naja atra
  • Mutation(s): No 

  • Deposited: 2016-11-21 Released: 2017-11-22 
  • Deposition Author(s): Chang, C., Lin, C.-C., Wu, W.-G.
  • Funding Organization(s): Ministry of Science and Technology

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Crystal strucuture of Taiwan cobra (Naja atra) venom 5'-nucleotidase at 1.9 Angstroms resolution.

Chang, C.Lin, C.-C.Wu, W.-G.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
venom 5'-nucleotidaseA, B529Naja atraMutation(s): 0 
EC: 3.1.3.5
UniProt
Find proteins for A0A2I4HXH5 (Naja atra)
Explore A0A2I4HXH5 
Go to UniProtKB:  A0A2I4HXH5
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC, D3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.089α = 90
b = 68.149β = 95.73
c = 139.815γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
Cootmodel building
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and TechnologyTaiwan103-2311-B007-011-MY3

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-22
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary