5H7W

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

  • Classification: HYDROLASE

  • 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: 1.9 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
venom 5'-nucleotidase
A, B
529N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BMA
Query on BMA

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Download CCD File 
A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.155 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 53.089α = 90.00
b = 68.149β = 95.73
c = 139.815γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
HKL-2000data collection
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2017-11-22
    Type: Initial release