[English] 日本語
Yorodumi
- PDB-9t27: Human fumarylacetoacetate hydrolase (FAH) in complex with S1.1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9t27
TitleHuman fumarylacetoacetate hydrolase (FAH) in complex with S1.1
ComponentsFumarylacetoacetase
KeywordsHYDROLASE / Chemical chaperone / Human fumarylacetoacetate hydrolase / tyrosinemia
Function / homology
Function and homology information


fumarylacetoacetase / fumarylacetoacetase activity / homogentisate catabolic process / Tyrosine catabolism / L-tyrosine catabolic process / L-phenylalanine catabolic process / L-arginine catabolic process / lipid metabolic process / extracellular exosome / metal ion binding / cytosol
Similarity search - Function
Fumarylacetoacetase / Fumarylacetoacetase, N-terminal / Fumarylacetoacetase, N-terminal domain superfamily / Fumarylacetoacetase N-terminal / Fumarylacetoacetase-like, C-terminal / Fumarylacetoacetate (FAA) hydrolase C-terminal / Fumarylacetoacetase-like, C-terminal domain superfamily
Similarity search - Domain/homology
: / Fumarylacetoacetase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.789 Å
AuthorsMillet, O. / Rojas, L.A. / Scarin, R.
Funding support Spain, European Union, 2items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)RTC2019-006826-1 Spain
H2020 Marie Curie Actions of the European Commission956758European Union
CitationJournal: J.Med.Chem. / Year: 2026
Title: Rational Design of Small-Molecule Stabilizers of Human Fumarylacetoacetate Hydrolase for the Treatment of Tyrosinemia Type I.
Authors: Scarin, R. / Rojas, A.L. / Gil-Martinez, J. / Gomez-Galan, M. / Torres-Mozas, A. / Lopitz-Otsoa, F. / Fernandez-Ramos, D. / Jimenez-Oses, G. / Mato, J.M. / Millet, O.
History
DepositionOct 22, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: Fumarylacetoacetase
F: Fumarylacetoacetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,69935
Polymers93,8132
Non-polymers1,88633
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11000 Å2
ΔGint-331 kcal/mol
Surface area30780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.93, 104.991, 75.931
Angle α, β, γ (deg.)90, 98.041, 90
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules EF

#1: Protein Fumarylacetoacetase / FAA / Beta-diketonase / Fumarylacetoacetate hydrolase


Mass: 46906.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAH / Production host: Escherichia coli (E. coli) / References: UniProt: P16930, fumarylacetoacetase

-
Non-polymers , 6 types, 366 molecules

#2: Chemical ChemComp-A1JS5 / 2-[4-(3-methanoyl-2,5-dimethyl-pyrrol-1-yl)phenoxy]ethanoic acid


Mass: 273.284 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H15NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.82 Å3/Da / Density % sol: 56.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris pH 5.5 and 7.0 at 25% to PEG 3350. / PH range: 5.5 - 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.789→61.128 Å / Num. obs: 96907 / % possible obs: 98.96 % / Redundancy: 6.85 % / CC1/2: 0.9983 / Net I/σ(I): 13.158
Reflection shellResolution: 1.789→1.82 Å / Num. unique obs: 4813 / CC1/2: 0.5705

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.105)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.789→61 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.571 / SU ML: 0.077 / Cross valid method: FREE R-VALUE / ESU R: 0.109 / ESU R Free: 0.104 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2078 4820 4.974 %
Rwork0.1819 92087 -
all0.183 --
obs-96907 98.957 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.907 Å2
Baniso -1Baniso -2Baniso -3
1-1.198 Å2-0 Å2-0.178 Å2
2---1.114 Å2-0 Å2
3----0.032 Å2
Refinement stepCycle: LAST / Resolution: 1.789→61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6544 0 96 333 6973
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0126799
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.8059229
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7645838
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.922536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.386101094
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.3110290
X-RAY DIFFRACTIONr_chiral_restr0.1090.2981
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025290
X-RAY DIFFRACTIONr_nbd_refined0.2140.23040
X-RAY DIFFRACTIONr_nbtor_refined0.3140.24635
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2407
X-RAY DIFFRACTIONr_metal_ion_refined0.1390.215
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1490.234
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1580.211
X-RAY DIFFRACTIONr_mcbond_it1.9882.623358
X-RAY DIFFRACTIONr_mcangle_it2.8934.6984194
X-RAY DIFFRACTIONr_scbond_it3.3152.9963441
X-RAY DIFFRACTIONr_scangle_it4.9885.3195035
X-RAY DIFFRACTIONr_lrange_it6.48929.3510192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.789-1.8350.2883400.2766754X-RAY DIFFRACTION98.024
1.835-1.8860.2873270.2426591X-RAY DIFFRACTION98.281
1.886-1.940.2443360.2186390X-RAY DIFFRACTION98.2615
1.94-20.2283530.2026212X-RAY DIFFRACTION98.6032
2-2.0650.2182900.1866027X-RAY DIFFRACTION98.5645
2.065-2.1380.1983150.1845826X-RAY DIFFRACTION98.714
2.138-2.2180.2253060.1845654X-RAY DIFFRACTION99.0198
2.218-2.3090.2112970.1735474X-RAY DIFFRACTION99.005
2.309-2.4110.2072690.1825188X-RAY DIFFRACTION99.1641
2.411-2.5290.212620.1855041X-RAY DIFFRACTION99.1957
2.529-2.6650.212480.1854768X-RAY DIFFRACTION99.3661
2.665-2.8270.2072260.184521X-RAY DIFFRACTION98.9577
2.827-3.0210.2162120.1744258X-RAY DIFFRACTION99.4438
3.021-3.2630.2142210.1793955X-RAY DIFFRACTION99.7849
3.263-3.5730.2092010.183638X-RAY DIFFRACTION99.5591
3.573-3.9930.2071540.1773345X-RAY DIFFRACTION99.8573
3.993-4.6080.1421570.1492922X-RAY DIFFRACTION99.7409
4.608-5.6350.2011460.1612488X-RAY DIFFRACTION99.7727
5.635-7.9360.1971090.1931930X-RAY DIFFRACTION99.902
7.936-610.235510.2021106X-RAY DIFFRACTION99.0582

+
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