5H7W

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

PDB DOI: https://doi.org/10.2210/pdb5H7W/pdb

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.

Macromolecule Content

Total Structure Weight: 118.27 kDa
Atom Count: 9,230
Modelled Residue Count: 1,057
Deposited Residue Count: 1,058
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
venom 5'-nucleotidase	A, B	529	Naja atra	Mutation(s): 0
UniProt
Find proteins for A0A2I4HXH5 (Naja atra) Explore A0A2I4HXH5 Go to UniProtKB: A0A2I4HXH5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2I4HXH5
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
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	C, D	3		N-Glycosylation	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B]	F [auth A], G [auth A], I [auth B], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B]	H [auth A], K [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Interactions & Density Focus chain H [auth A] Focus chain K [auth B]

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 = 53.089	α = 90
b = 68.149	β = 95.73
c = 139.815	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
HKL-2000	data scaling
Coot	model building
PHASER	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2017-11-22

Deposition Author(s):

Chang, C.

Lin, C.-C.

Wu, W.-G.

Funding Organization	Location	Grant Number
Ministry of Science and Technology	Taiwan	103-2311-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

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5H7W

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)