[English] 日本語
Yorodumi
- PDB-8im3: Crystal structure of human HPPD complexed with compound a10 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8im3
TitleCrystal structure of human HPPD complexed with compound a10
Components4-hydroxyphenylpyruvate dioxygenase
KeywordsOXIDOREDUCTASE / Complex / inhibitor
Function / homology
Function and homology information


Tyrosine catabolism / 4-hydroxyphenylpyruvate dioxygenase / 4-hydroxyphenylpyruvate dioxygenase activity / L-tyrosine catabolic process / L-phenylalanine catabolic process / Golgi membrane / endoplasmic reticulum membrane / protein homodimerization activity / extracellular exosome / metal ion binding / cytosol
Similarity search - Function
4-hydroxyphenylpyruvate dioxygenase / 4-hydroxyphenylpyruvate dioxygenase, C-terminal / 4-hydroxyphenylpyruvate dioxygenase, N-terminal / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Similarity search - Domain/homology
Chem-92U / : / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsDong, J. / Lin, H.-Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Structure / Year: 2023
Title: Structure-based discovery of pyrazole-benzothiadiazole hybrid as human HPPD inhibitors.
Authors: Dong, J. / Xiao, H. / Chen, J.N. / Zheng, B.F. / Xu, Y.L. / Chen, M.X. / Yang, W.C. / Lin, H.Y. / Yang, G.F.
History
DepositionMar 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 4-hydroxyphenylpyruvate dioxygenase
B: 4-hydroxyphenylpyruvate dioxygenase
C: 4-hydroxyphenylpyruvate dioxygenase
D: 4-hydroxyphenylpyruvate dioxygenase
E: 4-hydroxyphenylpyruvate dioxygenase
F: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)272,43318
Polymers269,9786
Non-polymers2,45612
Water2,684149
1
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

C: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,8116
Polymers89,9932
Non-polymers8194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area3790 Å2
ΔGint-13 kcal/mol
Surface area30160 Å2
MethodPISA
2
B: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

D: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,8116
Polymers89,9932
Non-polymers8194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area3880 Å2
ΔGint-12 kcal/mol
Surface area30020 Å2
MethodPISA
3
F: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

E: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,8116
Polymers89,9932
Non-polymers8194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area4020 Å2
ΔGint-27 kcal/mol
Surface area29340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.030, 88.895, 94.279
Angle α, β, γ (deg.)97.27, 110.71, 110.29
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
4-hydroxyphenylpyruvate dioxygenase / 4-hydroxyphenylpyruvic acid oxidase / 4HPPD / HPD / HPPDase


Mass: 44996.250 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPD, PPD
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P32754, 4-hydroxyphenylpyruvate dioxygenase
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-92U / [1,3-diethyl-2,2-bis(oxidanylidene)-2$l^{6},1,3-benzothiadiazol-5-yl]-(1-methyl-5-oxidanyl-pyrazol-4-yl)methanone


Mass: 350.393 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H18N4O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.03M CaCl2, 0.03M MgCl2, 0.05M Tris, 0.05M Bicine, pH8.5, 25% MPD, 25% PEG 1000, 25% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9875 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9875 Å / Relative weight: 1
ReflectionResolution: 2.78→50 Å / Num. obs: 53437 / % possible obs: 88.6 % / Redundancy: 1.4 % / CC1/2: 0.98 / Rmerge(I) obs: 0.095 / Net I/σ(I): 5.3
Reflection shellResolution: 2.78→2.83 Å / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2140 / CC1/2: 0.851

-
Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.78→48.19 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2474 2670 5 %
Rwork0.2167 --
obs0.2182 53437 95.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.78→48.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17591 0 150 149 17890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00318190
X-RAY DIFFRACTIONf_angle_d0.57824681
X-RAY DIFFRACTIONf_dihedral_angle_d23.1756593
X-RAY DIFFRACTIONf_chiral_restr0.0452637
X-RAY DIFFRACTIONf_plane_restr0.0043213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.78-2.830.35161110.32042140X-RAY DIFFRACTION78
2.83-2.880.3381450.30562757X-RAY DIFFRACTION97
2.88-2.940.34641420.30752688X-RAY DIFFRACTION97
2.94-30.30191380.32641X-RAY DIFFRACTION96
3-3.070.31311420.28652705X-RAY DIFFRACTION96
3.07-3.150.25491420.272703X-RAY DIFFRACTION96
3.15-3.240.28961400.25052655X-RAY DIFFRACTION94
3.24-3.330.27591400.23392653X-RAY DIFFRACTION97
3.33-3.440.27461450.23632748X-RAY DIFFRACTION98
3.44-3.560.27751430.2262736X-RAY DIFFRACTION97
3.56-3.70.25321440.2172722X-RAY DIFFRACTION97
3.7-3.870.22051400.20572687X-RAY DIFFRACTION97
3.87-4.080.23631410.19412673X-RAY DIFFRACTION96
4.08-4.330.23551420.18392690X-RAY DIFFRACTION96
4.33-4.670.19451420.17892693X-RAY DIFFRACTION96
4.67-5.140.20611410.17612695X-RAY DIFFRACTION97
5.14-5.880.23781450.20082748X-RAY DIFFRACTION98
5.88-7.40.23931440.20932729X-RAY DIFFRACTION97
7.4-48.190.19271430.16832704X-RAY DIFFRACTION97

+
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