1TDK

L-amino acid oxidase from Agkistrodon halys in complex with suicide substrate L-vinylglycine

• PDB DOI: https://doi.org/10.2210/pdb1TDK/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Gloydius halys
• Mutation(s): No 


• Deposited: 2004-05-22 Released: 2004-06-22 
• Deposition Author(s): Zhang, H., Teng, M., Niu, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.221 
• R-Value Work: 0.192 
• R-Value Observed: 0.192 

Starting Model: experimental

Literature

Structures of L-amino acid oxidase in complexes with substrates and substrate analogue

Zhang, H., Teng, M., Niu, L.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 56.64 kDa 
• Atom Count: 4,004 
• Modelled Residue Count: 484 
• Deposited Residue Count: 486 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-amino acid oxidase	A	486	Gloydius halys	Mutation(s): 0  EC: 1.4.3.2
UniProt
Find proteins for Q6STF1 (Gloydius halys) Explore Q6STF1  Go to UniProtKB:  Q6STF1
Glycosylation
Glycosylation Sites: 2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	D [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
NAG	B [auth A], C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
LVG	E [auth A], F [auth A]	L-VINYLGLYCINE C4 H7 N O2 RQVLGLPAZTUBKX-VKHMYHEASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.221 
• R-Value Work: 0.192 
• R-Value Observed: 0.192 
• Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 169.36	α = 90
b = 169.36	β = 90
c = 169.36	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
AUTOMAR	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-06-22 
Deposition Author(s): Zhang, H., Teng, M., Niu, L.

Revision History  

• Version 1.0: 2004-06-22
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-10-25
  Changes: Data collection, Database references, Refinement description, Structure summary