1B5Q

A 30 ANGSTROM U-SHAPED CATALYTIC TUNNEL IN THE CRYSTAL STRUCTURE OF POLYAMINE OXIDASE

PDB DOI: https://doi.org/10.2210/pdb1B5Q/pdb

Classification: OXIDOREDUCTASE
Organism(s): Zea mays
Mutation(s): No

Deposited: 1999-01-07 Released: 2000-01-07
Deposition Author(s): Binda, C., Coda, A., Angelini, R., Federico, R., Ascenzi, P., Mattevi, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

A 30-angstrom-long U-shaped catalytic tunnel in the crystal structure of polyamine oxidase.

Binda, C., Coda, A., Angelini, R., Federico, R., Ascenzi, P., Mattevi, A.

(1999) Structure 7: 265-276

PubMed: 10368296 Search on PubMed
DOI: https://doi.org/10.1016/s0969-2126(99)80037-9
Primary Citation of Related Structures:
1B37, 1B5Q

PubMed Abstract:
Polyamines are essential for cell growth and differentiation; compounds interfering with their metabolism are potential anticancer agents. Polyamine oxidase (PAO) plays a central role in polyamine homeostasis. The enzyme utilises an FAD cofactor to catalyse the oxidation of the secondary amino groups of spermine and spermidine.

Organizational Affiliation

Dipartimento di Genetica e Microbiologia, Università di Pavia, Via Abbiategrasso 207, I-27100 Pavia, Italy.

Macromolecule Content

Total Structure Weight: 165.77 kDa
Atom Count: 12,059
Modelled Residue Count: 1,383
Deposited Residue Count: 1,416
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (POLYAMINE OXIDASE)	A, B, C	472	Zea mays	Mutation(s): 0
UniProt
Find proteins for O64411 (Zea mays) Explore O64411 Go to UniProtKB: O64411
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O64411
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E	2		N-Glycosylation	Interactions Focus chain D Focus chain E Interactions & Density Focus chain D Focus chain E
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-D-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose	F	5		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G04100CE GlyCosmos: G04100CE

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth C] SDF format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B]	G [auth A], I [auth B], K [auth C]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C]
MD2 Query on MD2 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C]	H [auth A], J [auth B], L [auth C]	N,N'-BIS(2,3-BUTADIENYL)-1,4-BUTANE-DIAMINE C₁₂ H₂₀ N₂ IKSQCMLJDHRWOA-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
MD2	Binding MOAD: 1B5Q	Ki: 550 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 184.6	α = 90
b = 184.6	β = 90
c = 281.5	γ = 120

Software Package:

Software Name	Purpose
CCP4	model building
TNT	refinement
CCP4	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2000-01-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2000-01-07
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-12-27
Changes: Advisory, Data collection, Database references, Structure summary