5Z2G | pdb_00005z2g

Crystal Structure of L-amino acid oxidase from venom of Naja atra

• PDB DOI: https://doi.org/10.2210/pdb5Z2G/pdb

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


• Deposited: 2018-01-02 Released: 2018-06-20 
• Deposition Author(s): Kumar, J.V., Chien, K.Y., Wu, W.G., Lin, C.C., Chiang, L.C., Lin, T.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free: 
  0.220 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of L-amino acid oxidase from naja atra (Taiwan Cobra)

Kumar, J.V., Chien, K.Y., Lin, C.C., Chiang, L.C., Lin, T.H., 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.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 118.54 kDa 
• Atom Count: 7,958 
• Modeled Residue Count: 954 
• Deposited Residue Count: 1,014 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-amino acid oxidase	A, B	507	Naja atra	Mutation(s): 0  EC: 1.4.3.2
UniProt
Find proteins for A8QL58 (Naja atra) Explore A8QL58  Go to UniProtKB:  A8QL58
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	F [auth A], H [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
NAG	C [auth A], D [auth A], E [auth A], G [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free:  0.220 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.836	α = 90
b = 104.836	β = 90
c = 214.27	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-06-20 
Deposition Author(s): Kumar, J.V., Chien, K.Y., Wu, W.G., Lin, C.C., Chiang, L.C., Lin, T.H.

Revision History  

• Version 1.0: 2018-06-20
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.3: 2024-10-23
  Changes: Structure summary