7D0V

Crystal structure of Taiwan cobra 5'-nucleotidase

• PDB DOI: https://doi.org/10.2210/pdb7D0V/pdb

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


• Deposited: 2020-09-12 Released: 2021-09-15 
• Deposition Author(s): Tsai, M.-H., Lin, I.-J., Lin, C.-C., Wu, W.-G.
• Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 0.219 
• R-Value Observed: 0.177 

Starting Model: experimental

Literature

Crystal structure of Taiwan cobra 5'-nucleotidase

Tsai, M.-H., Lin, I.-J., Lin, C.-C., Wu, W.-G.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 118.95 kDa 
• Atom Count: 8,810 
• Modelled Residue Count: 1,052 
• Deposited Residue Count: 1,060 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Snake venom 5'-nucleotidase	A, B	530	Naja atra	Mutation(s): 0  EC: 3.1.3.5
UniProt
Find proteins for A0A2I4HXH5 (Naja atra) Explore A0A2I4HXH5  Go to UniProtKB:  A0A2I4HXH5
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC GlyCosmos:  G86851RC GlyGen:  G86851RC

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	I [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN (Subject of Investigation/LOI)	F [auth A], G [auth A], J [auth B], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	H [auth A], L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 0.219 
• R-Value Observed: 0.177 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.327	α = 90
b = 68.127	β = 95.17
c = 140.214	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-09-15 
Deposition Author(s): Tsai, M.-H., Lin, I.-J., Lin, C.-C., Wu, W.-G.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	--

Revision History  

• Version 1.0: 2021-09-15
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description