3KVE

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free: 0.276
R-Value Work: 0.191
R-Value Observed: 0.195

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DI84
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D]	E [auth A], H [auth B], K [auth C], N [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain O [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain O [auth D]	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		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain P [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D]	G [auth A], J [auth B], M [auth C], P [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free: 0.276
R-Value Work: 0.191
R-Value Observed: 0.195
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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-10-13

Deposition Author(s):

Revision History (Full details and data files)

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

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Help and Resources

3KVE

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

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

Entity ID: 1

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)