3CND

Crystal structure of fms1 in complex with N1-AcSpermine

PDB DOI: https://doi.org/10.2210/pdb3CND/pdb

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

Deposited: 2008-03-25 Released: 2008-04-22
Deposition Author(s): Huang, Q., Hao, Q.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.277
R-Value Work: 0.227
R-Value Observed: 0.227

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of fms1 in complex with N1-AcSpermine

Huang, Q., Hao, Q.

To be published.

Macromolecule Content

Total Structure Weight: 119.7 kDa
Atom Count: 7,906
Modelled Residue Count: 993
Deposited Residue Count: 1,032
Unique protein chains: 1

Macromolecules

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(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 EC: 1.5.3.11
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]	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]
SP5 Query on SP5 Download Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B]	D [auth B]	N-[3-({4-[(3-aminopropyl)amino]butyl}amino)propyl]acetamide C₁₂ H₂₈ N₄ O GUNURVWAJRRUAV-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.277
R-Value Work: 0.227
R-Value Observed: 0.227
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.579	α = 90
b = 215.853	β = 90
c = 118.904	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
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-04-22

Deposition Author(s):

Huang, Q.

Hao, Q.

Revision History (Full details and data files)

Version 1.0: 2008-04-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2019-07-24
Changes: Data collection, Refinement description
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

3CND

Crystal structure of fms1 in complex with N1-AcSpermine

Crystal structure of fms1 in complex with N1-AcSpermine

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)