[English] 日本語
Yorodumi
- PDB-1gth: DIHYDROPYRIMIDINE DEHYDROGENASE (DPD) FROM PIG, TERNARY COMPLEX W... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gth
TitleDIHYDROPYRIMIDINE DEHYDROGENASE (DPD) FROM PIG, TERNARY COMPLEX WITH NADPH AND 5-IODOURACIL
ComponentsDIHYDROPYRIMIDINE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / ELECTRON TRANSFER / FLAVIN / IRON-SULFUR CLUSTERS / PYRIMIDINE CATABOLISM / 5-FLUOROURACIL DEGRADATION
Function / homology
Function and homology information


dihydropyrimidine dehydrogenase (NADP+) / uracil binding / thymidine catabolic process / dihydropyrimidine dehydrogenase (NADP+) activity / beta-alanine biosynthetic process / uracil catabolic process / thymine catabolic process / FMN binding / NADP binding / flavin adenine dinucleotide binding ...dihydropyrimidine dehydrogenase (NADP+) / uracil binding / thymidine catabolic process / dihydropyrimidine dehydrogenase (NADP+) activity / beta-alanine biosynthetic process / uracil catabolic process / thymine catabolic process / FMN binding / NADP binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / protein homodimerization activity / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Dihydroprymidine dehydrogenase domain II / Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster / Alpha-helical ferredoxin / 4Fe-4S dicluster domain / Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 / Alpha-helical ferredoxin / Alpha-Beta Plaits - #20 / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / FAD/NAD(P)-binding domain ...Dihydroprymidine dehydrogenase domain II / Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster / Alpha-helical ferredoxin / 4Fe-4S dicluster domain / Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 / Alpha-helical ferredoxin / Alpha-Beta Plaits - #20 / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Aldolase class I / Aldolase-type TIM barrel / Alpha-Beta Plaits / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FLAVIN MONONUCLEOTIDE / (5S)-5-IODODIHYDRO-2,4(1H,3H)-PYRIMIDINEDIONE / 5-IODOURACIL / Chem-NDP / IRON/SULFUR CLUSTER / URACIL / Dihydropyrimidine dehydrogenase [NADP(+)]
Similarity search - Component
Biological speciesSUS SCROFA (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsDobritzsch, D. / Ricagno, S. / Schneider, G. / Schnackerz, K.D. / Lindqvist, Y.
Citation
Journal: J. Biol. Chem. / Year: 2002
Title: Crystal structure of the productive ternary complex of dihydropyrimidine dehydrogenase with NADPH and 5-iodouracil. Implications for mechanism of inhibition and electron transfer.
Authors: Dobritzsch, D. / Ricagno, S. / Schneider, G. / Schnackerz, K.D. / Lindqvist, Y.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallization and Preliminary X-Ray Study of Pig Liver Dihydropyrimidine Dehydrogenase
Authors: Dobritzsch, D. / Persson, K. / Schneider, G. / Lindqvist, Y.
History
DepositionJan 15, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 2.0Jan 23, 2019Group: Atomic model / Data collection / Category: atom_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z
Revision 2.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_unobs_or_zero_occ_atoms ...pdbx_entry_details / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AF", "BF", "CF" AND "DF" IN EACH CHAIN ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AF", "BF", "CF" AND "DF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL, THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DIHYDROPYRIMIDINE DEHYDROGENASE
B: DIHYDROPYRIMIDINE DEHYDROGENASE
C: DIHYDROPYRIMIDINE DEHYDROGENASE
D: DIHYDROPYRIMIDINE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)460,81936
Polymers446,4134
Non-polymers14,40632
Water55,3603073
1
A: DIHYDROPYRIMIDINE DEHYDROGENASE
B: DIHYDROPYRIMIDINE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,47418
Polymers223,2072
Non-polymers7,26816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: DIHYDROPYRIMIDINE DEHYDROGENASE
D: DIHYDROPYRIMIDINE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,34518
Polymers223,2072
Non-polymers7,13816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)82.210, 159.690, 167.590
Angle α, β, γ (deg.)90.00, 97.11, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-1, 0.0015, -0.004), (0.0019, -0.6979, -0.7162), (-0.0039, -0.7162, 0.6979)116.7223, 176.72121, 74.8225
2given(1, 0.0036, 0.0009), (-0.0023, 0.7927, -0.6096), (-0.003, 0.6096, 0.7927)-13.5323, 12.9793, -28.6192
3given(-1, -0.0036, -0.0049), (0.0043, -0.989, -0.148), (-0.0043, -0.148, 0.989)102.6084, 199.3446, -76.4262

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
DIHYDROPYRIMIDINE DEHYDROGENASE / DPD / DHPDHASE / DIHYDROURACIL DEHYDROGENASE / DIHYDROTHYMINE DEHYDROGENASE


Mass: 111603.344 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SUS SCROFA (pig) / Organ: LIVER / Plasmid: PSE420 / Production host: Escherichia coli DH5[alpha] (bacteria)
References: UniProt: Q28943, dihydropyrimidine dehydrogenase (NADP+)

-
Non-polymers , 8 types, 3105 molecules

#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#6: Chemical ChemComp-IDH / (5S)-5-IODODIHYDRO-2,4(1H,3H)-PYRIMIDINEDIONE


Mass: 239.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H5IN2O2
#7: Chemical ChemComp-IUR / 5-IODOURACIL


Mass: 237.983 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3IN2O2
#8: Chemical ChemComp-URA / URACIL


Mass: 112.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4N2O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3073 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationN
Sequence detailsRESIDUE 671 IS S-(HEXAHYDRO-2,4-DIOXO-5-PYRIMIDINYL) CYSTEINE, WHICH ORIGINATES FROM ALKYLATION OF ...RESIDUE 671 IS S-(HEXAHYDRO-2,4-DIOXO-5-PYRIMIDINYL) CYSTEINE, WHICH ORIGINATES FROM ALKYLATION OF CYSTEINE BY 5-IODO-5,6-DIHYDROURACIL

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 41 %
Crystal growpH: 7.5
Details: 100 MM SODIUM CITRATE PH 4.7, 16-20 % POLYETHYLENE GLYCOL 6000, 1 MM DTT, 5 MM 5-IODOURACIL, 5 MM NADPH
Crystal grow
*PLUS
Temperature: 293 K / pH: 4.7 / Method: vapor diffusion / Details: Dobritzsch, D., (2001) Acta Crystallogr., 57, 153.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
117-22 %(w/v)PEG60001reservoir
210 mMdithiothreitol1reservoir
3100 mMsodium citrate1reservoirpH4.7
44.5 mg/mlDPD1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.9311
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 9, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9311 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 200114 / % possible obs: 98.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 14.3
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 5.2 / % possible all: 97.4
Reflection
*PLUS
Num. obs: 199249
Reflection shell
*PLUS
% possible obs: 97.4 % / Rmerge(I) obs: 0.25

-
Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DIHYDROPYRIMIDINE DEHYDROGENASE, UNCOMPLEXED

Resolution: 2.25→25 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3543123 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE 5 C-TERMINAL RESIDUES AND A FEW LOOP-RESIDUES WERE NOT SEEN IN THE DENSITY DUE TO DISORDER
RfactorNum. reflection% reflectionSelection details
Rfree0.209 3984 2 %RANDOM
Rwork0.177 ---
obs0.177 199143 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.445 Å2 / ksol: 0.342276 e/Å3
Displacement parametersBiso mean: 33.3 Å2
Baniso -1Baniso -2Baniso -3
1--8.16 Å20 Å20.91 Å2
2--9.51 Å20 Å2
3----1.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.25→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30999 0 690 3073 34762
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d3.11
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.25→2.35 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.244 478 2 %
Rwork0.215 24026 -
obs--97.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PG2.PARWATER.TOP
X-RAY DIFFRACTION3CIS_PEPTIDE.PARAMPG2.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMNEWSUB.TOP
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.37
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg3.11
LS refinement shell
*PLUS
Rfactor obs: 0.215

+
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