3CNP

Crystal structure of fms1 in complex with S-N1-AcMeSpermidine

PDB DOI: https://doi.org/10.2210/pdb3CNP/pdb

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

Deposited: 2008-03-26 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: 0.267
R-Value Work: 0.216
R-Value Observed: 0.216

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal structure of fms1 in complex with S-N1-AcMeSpermidine

Huang, Q., Hao, Q.

To be published.

Macromolecule Content

Total Structure Weight: 119.95 kDa
Atom Count: 8,095
Modelled Residue Count: 992
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
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 3 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]
SP7 Query on SP7 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]	D [auth B], F [auth A]	N-{(1S)-3-[(4-aminobutyl)amino]-1-methylpropyl}acetamide C₁₀ H₂₃ N₃ O NCHUZACAGJBRLA-VIFPVBQESA-N		Interactions Focus chain D [auth B] Focus chain F [auth A] Interactions & Density Focus chain D [auth B] Focus chain F [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.267
R-Value Work: 0.216
R-Value Observed: 0.216
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.214	α = 90
b = 215.201	β = 90
c = 117.589	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
MOSFLM	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: Non-polymer description, 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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3CNP

Crystal structure of fms1 in complex with S-N1-AcMeSpermidine

Crystal structure of fms1 in complex with S-N1-AcMeSpermidine

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)