3KVE | pdb_00003kve

Structure of native L-amino acid oxidase from Vipera ammodytes ammodytes: stabilization of the quaternary structure by divalent ions and structural changes in the dynamic active site

• PDB DOI: https://doi.org/10.2210/pdb3KVE/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Vipera ammodytes ammodytes
• Mutation(s): No 


• Deposited: 2009-11-30 Released: 2010-10-13 
• Deposition Author(s): Gergiova, D., Murakami, M.T., Perbandt, M., Arni, R.K., Betzel, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free: 
  0.276 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Structure of native L-amino acid oxidase from Vipera ammodytes ammodytes: stabilization of the quaternary structure by divalent ions and structural changes in the dynamic active site

Gergiova, D., Murakami, M.T., Perbandt, M., Arni, R.K., Betzel, C.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 224.31 kDa 
• Atom Count: 16,288 
• Modeled Residue Count: 1,936 
• Deposited Residue Count: 1,944 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-amino acid oxidase	A, B, C, D	486	Vipera ammodytes ammodytes	Mutation(s): 0  EC: 1.4.3.2
UniProt
Find proteins for P0DI84 (Vipera ammodytes ammodytes) Explore P0DI84  Go to UniProtKB:  P0DI84
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	E [auth A], H [auth B], K [auth C], N [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
NAG	F [auth A], I [auth B], L [auth C], O [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN	G [auth A], J [auth B], M [auth C], P [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free:  0.276 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 196.978	α = 90
b = 95.839	β = 92.53
c = 108.442	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-10-13 
Deposition Author(s): Gergiova, D., Murakami, M.T., Perbandt, M., Arni, R.K., Betzel, C.

Revision History  

• Version 1.0: 2010-10-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Structure summary
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.4: 2024-11-06
  Changes: Structure summary