3BNM

Crystal structure of polyamine oxidase FMS1 from Saccharomyces cerevisiae in complex with bis-(3R,3'R)-methylated spermine

PDB DOI: https://doi.org/10.2210/pdb3BNM/pdb

Classification: OXIDOREDUCTASE
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-12-14 Released: 2008-01-29
Deposition Author(s): Huang, Q., Hao, Q.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.274
R-Value Work: 0.226
R-Value Observed: 0.226

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural basis of the substrate stereospecificity of FMS1.

Huang, Q., Hao, Q.

To be published.

Macromolecule Content

Total Structure Weight: 119.92 kDa
Atom Count: 8,104
Modelled Residue Count: 996
Deposited Residue Count: 1,032
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyamine oxidase FMS1	A [auth B], B [auth A]	516	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: FMS1, YMR020W, YM9711.09 EC: 1.5.3.11 (PDB Primary Data), 1.5.3.17 (UniProt)
UniProt
Find proteins for P50264 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P50264 Go to UniProtKB: P50264
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P50264
Sequence Annotations Expand
Reference Sequence

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 C [auth B] SDF format, chain E [auth A] MOL2 format, chain C [auth B] MOL2 format, chain E [auth A] mmCIF format, chain C [auth B] mmCIF format, chain E [auth A]	C [auth B], E [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth B] Focus chain E [auth A] Interactions & Density Focus chain C [auth B] Focus chain E [auth A]
SPJ Query on SPJ Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain F [auth A] MOL2 format, chain D [auth B] MOL2 format, chain F [auth A] mmCIF format, chain D [auth B] mmCIF format, chain F [auth A]	D [auth B], F [auth A]	(3R,3'R)-N~1~,N~1~'-butane-1,4-diyldibutane-1,3-diamine C₁₂ H₃₀ N₄ LXKFTCVCBKNJNM-VXGBXAGGSA-N		Interactions Focus chain D [auth B] Focus chain F [auth A] Interactions & Density Focus chain D [auth B] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.274
R-Value Work: 0.226
R-Value Observed: 0.226
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162.237	α = 90
b = 103.969	β = 94.9
c = 77.583	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-01-29

Deposition Author(s):

Huang, Q.

Hao, Q.

Revision History (Full details and data files)

Version 1.0: 2008-01-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

3BNM

Crystal structure of polyamine oxidase FMS1 from Saccharomyces cerevisiae in complex with bis-(3R,3'R)-methylated spermine

Structural basis of the substrate stereospecificity of FMS1.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)