[English] 日本語
Yorodumi
- PDB-9qrt: FSP1 (tetrapod ancestor; L323A mutant) bound to FAD and NAD+ and ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9qrt
TitleFSP1 (tetrapod ancestor; L323A mutant) bound to FAD and NAD+ and compound 2
ComponentsFSP1 (tetrapod ancestor; L323A mutant) bound to FAD and NAD+ and compound 2
KeywordsOXIDOREDUCTASE / Flavin / NAD / coenzyme Q / ferroptosis / myristoylation / inhibitor discovery
Function / homology: / FLAVIN-ADENINE DINUCLEOTIDE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Function and homology information
Biological speciesMammalia (mammals)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCecchini, D. / Mattevi, A.
Funding supportEuropean Union, Italy, 2items
OrganizationGrant numberCountry
European Research Council (ERC)101094471European Union
Italian Association for Cancer Research28754 Italy
CitationJournal: To Be Published
Title: Best-in-Class FSP1 Inhibitors Unraveled By AI-Enhanced Adaptive Screening Platform
Authors: Cecchini, D. / Mattevi, A.
History
DepositionApr 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FSP1 (tetrapod ancestor; L323A mutant) bound to FAD and NAD+ and compound 2
B: FSP1 (tetrapod ancestor; L323A mutant) bound to FAD and NAD+ and compound 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9168
Polymers79,5372
Non-polymers3,3806
Water2,900161
1
A: FSP1 (tetrapod ancestor; L323A mutant) bound to FAD and NAD+ and compound 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6995
Polymers39,7681
Non-polymers1,9314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FSP1 (tetrapod ancestor; L323A mutant) bound to FAD and NAD+ and compound 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2173
Polymers39,7681
Non-polymers1,4492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.454, 78.058, 115.075
Angle α, β, γ (deg.)90.00, 98.93, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein FSP1 (tetrapod ancestor; L323A mutant) bound to FAD and NAD+ and compound 2


Mass: 39768.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammalia (mammals) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 5 types, 167 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-A1I9W / ~{N}-[[2-[(3-phenyl-1,2-oxazol-5-yl)carbonyl]-1,3-dihydroisoindol-5-yl]methyl]cyclohept-4-ene-1-carboxamide


Mass: 441.522 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H27N3O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: -FSP1(L323A)-FAD-NAD+-2; 0.06 M MgCl2, 0.06 M CaCl2, 0.1 M HEPES/MOPS (acid) pH 7.5, 20% ethylene glycol, 20% PEG8000. Crystals were then soaked with 1 mM 2 added to the crystallisation drop.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 28, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.4→78.06 Å / Num. obs: 29339 / % possible obs: 96.1 % / Redundancy: 2.7 % / CC1/2: 0.973 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.104 / Rrim(I) all: 0.18 / Χ2: 1.03 / Net I/σ(I): 7.4 / Num. measured all: 80117
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.838 / Num. unique obs: 3164 / CC1/2: 0.361 / Rpim(I) all: 0.609 / Rrim(I) all: 1 / Χ2: 1.05

-
Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→64.43 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.875 / SU B: 11.5 / SU ML: 0.253 / Cross valid method: THROUGHOUT / ESU R: 0.639 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27865 1481 5.1 %RANDOM
Rwork0.21571 ---
obs0.21889 27840 95.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.277 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å2-0 Å2-0.73 Å2
2---1.63 Å20 Å2
3---1.33 Å2
Refinement stepCycle: 1 / Resolution: 2.4→64.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5528 0 228 161 5917
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125879
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165587
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.6437979
X-RAY DIFFRACTIONr_angle_other_deg0.4821.57712893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.675729
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.865526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.53101000
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0650.2907
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026683
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021237
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.613.0122919
X-RAY DIFFRACTIONr_mcbond_other2.613.0122919
X-RAY DIFFRACTIONr_mcangle_it4.1495.4043647
X-RAY DIFFRACTIONr_mcangle_other4.1485.4043648
X-RAY DIFFRACTIONr_scbond_it3.4613.3852960
X-RAY DIFFRACTIONr_scbond_other3.4613.3852961
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5096.0484333
X-RAY DIFFRACTIONr_long_range_B_refined7.7232.556698
X-RAY DIFFRACTIONr_long_range_B_other7.67331.346682
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 104 -
Rwork0.329 2125 -
obs--97.85 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more