[English] 日本語
Yorodumi
- PDB-7ljs: Porcine Dihydropyrimidine dehydrogenase (DPD) complexed with 5-Et... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ljs
TitlePorcine Dihydropyrimidine dehydrogenase (DPD) complexed with 5-Ethynyluracil (5EU) - Open Form
ComponentsDihydropyrimidine dehydrogenase [NADP(+)]
KeywordsFLAVOPROTEIN / Dihydropyrimidine dehydrogenase / DPD / dehydrogenase / 5-Ethynyluracil / 5EU / inhibitor / inactivator
Function / homology
Function and homology information


dihydropyrimidine dehydrogenase (NADP+) / uracil binding / thymidine catabolic process / dihydropyrimidine dehydrogenase (NADP+) activity / beta-alanine biosynthetic process / thymine catabolic process / uracil catabolic process / FMN binding / flavin adenine dinucleotide binding / NADP binding ...dihydropyrimidine dehydrogenase (NADP+) / uracil binding / thymidine catabolic process / dihydropyrimidine dehydrogenase (NADP+) activity / beta-alanine biosynthetic process / thymine catabolic process / uracil catabolic process / FMN binding / flavin adenine dinucleotide binding / NADP binding / 4 iron, 4 sulfur cluster binding / protein homodimerization activity / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Dihydroprymidine dehydrogenase domain II / Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster / 4Fe-4S dicluster domain / Alpha-helical ferredoxin / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. ...Dihydroprymidine dehydrogenase domain II / Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster / 4Fe-4S dicluster domain / Alpha-helical ferredoxin / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / 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 / FAD/NAD(P)-binding domain superfamily / Aldolase-type TIM barrel
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FLAVIN MONONUCLEOTIDE / IRON/SULFUR CLUSTER / 5-ethynylpyrimidine-2,4(1H,3H)-dione / Dihydropyrimidine dehydrogenase [NADP(+)]
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsButrin, A. / Forouzesh, D. / Beaupre, B. / Wawrzak, Z. / Liu, D. / Moran, G.
CitationJournal: Biochemistry / Year: 2021
Title: The Interaction of Porcine Dihydropyrimidine Dehydrogenase with the Chemotherapy Sensitizer: 5-Ethynyluracil.
Authors: Forouzesh, D.C. / Beaupre, B.A. / Butrin, A. / Wawrzak, Z. / Liu, D. / Moran, G.R.
History
DepositionJan 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dihydropyrimidine dehydrogenase [NADP(+)]
B: Dihydropyrimidine dehydrogenase [NADP(+)]
C: Dihydropyrimidine dehydrogenase [NADP(+)]
D: Dihydropyrimidine dehydrogenase [NADP(+)]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)457,55232
Polymers446,4134
Non-polymers11,13828
Water39,1112171
1
A: Dihydropyrimidine dehydrogenase [NADP(+)]
B: Dihydropyrimidine dehydrogenase [NADP(+)]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,77616
Polymers223,2072
Non-polymers5,56914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30350 Å2
ΔGint-284 kcal/mol
Surface area68810 Å2
MethodPISA
2
C: Dihydropyrimidine dehydrogenase [NADP(+)]
D: Dihydropyrimidine dehydrogenase [NADP(+)]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,77616
Polymers223,2072
Non-polymers5,56914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30240 Å2
ΔGint-281 kcal/mol
Surface area69800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.031, 160.046, 164.074
Angle α, β, γ (deg.)90.000, 95.950, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Dihydropyrimidine dehydrogenase [NADP(+)] / DPD / Dihydrothymine dehydrogenase / Dihydrouracil dehydrogenase


Mass: 111603.344 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: DPYD / Production host: Escherichia coli (E. coli)
References: UniProt: Q28943, dihydropyrimidine dehydrogenase (NADP+)

-
Non-polymers , 5 types, 2199 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#5: Chemical
ChemComp-Y3G / 5-ethynylpyrimidine-2,4(1H,3H)-dione


Mass: 136.108 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H4N2O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2171 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Drops were formed by mixing 3 uL of 39 uM of DPD, 1 mM 5EU, 1 mM NADPH in 25 mM HEPES, 10 mM DTT, 10% glycerol pH 7.5 with 3 uL of well solution (1 mL) containing 50-200 mM NaCl, 19% PEG 6000, 1 mM DTT pH 4.8

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1.127 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 255614 / % possible obs: 90.2 % / Redundancy: 2.9 % / CC1/2: 0.992 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.121 / Rrim(I) all: 0.211 / Net I/σ(I): 5.6
Reflection shellResolution: 1.99→2.02 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.869 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 9241 / CC1/2: 0.377 / Rpim(I) all: 0.665 / % possible all: 66

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
xia2data scaling
PHASERphasing
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H7X

1h7x


Resolution: 2→45.62 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2286 10691 4.88 %
Rwork0.1721 208462 -
obs0.1749 219153 77.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.14 Å2 / Biso mean: 30.5255 Å2 / Biso min: 13.98 Å2
Refinement stepCycle: final / Resolution: 2→45.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30769 0 504 2171 33444
Biso mean--22.72 37.5 -
Num. residues----4033
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.020.31861340.22872797293131
2.02-2.040.2941700.2253416358638
2.04-2.070.32142100.2184088429846
2.07-2.090.28132280.22564611483951
2.09-2.120.29472550.22195116537157
2.12-2.150.25642830.20745378566160
2.15-2.180.28572930.20415667596063
2.18-2.210.25153020.19535725602763
2.21-2.250.29673320.18755856618865
2.25-2.290.27082850.18955884616965
2.29-2.330.2712770.19055989626666
2.33-2.370.26023260.20045997632367
2.37-2.410.24333330.20076165649868
2.41-2.460.26492950.19126369666471
2.46-2.520.27093210.19356542686373
2.52-2.570.27532990.19266917721676
2.57-2.640.25883900.20477274766481
2.64-2.710.24813930.20788123851690
2.71-2.790.25244230.19888663908696
2.79-2.880.2684320.20078792922497
2.88-2.980.26714500.19118850930098
2.98-3.10.25715000.19238804930498
3.1-3.240.22865280.18038816934499
3.24-3.410.22064750.1738895937098
3.41-3.630.22354510.1678893934499
3.63-3.910.20834220.15448967938998
3.91-4.30.19684670.14398884935199
4.3-4.920.18364690.13558882935199
4.92-6.20.21164940.15239011950599
6.2-45.620.17724540.14369091954599
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7563-0.03530.38420.5152-0.07180.1212-0.0472-0.07730.01410.09280.0309-0.0151-0.03210.06830.00070.2741-0.0137-0.00460.28560.03360.231194.2365.624280.1748
20.4413-0.1733-0.29650.59030.31380.43910.02540.09160.0103-0.007-0.03790.0515-0.0511-0.0434-0.00590.2026-0.004-0.00930.20740.00720.217356.424672.715279.1162
31.1348-0.12580.69290.20050.19960.9874-0.0151-0.1032-0.03440.06750.0351-0.02160.0112-0.0063-0.00350.28160.00940.02420.27630.00050.252460.864180.3386102.0456
40.2361-0.0649-0.06340.47610.25610.59020.00430.0188-0.0531-0.022-0.03120.07860.0723-0.03720.00190.1893-0.0276-0.01120.25150.00250.240951.624852.703458.1052
50.5982-0.10170.06480.1792-0.29130.55650.01950.0648-0.0016-0.0246-0.0066-0.0139-0.00530.0393-0.00950.2126-0.01960.00090.25530.01510.213968.370956.050651.3286
60.9164-0.13340.1730.1353-0.01770.48360.04390.08880.2065-0.09620.013-0.0324-0.24210.03220.0050.338-0.01170.00930.2910.05130.299187.91474.237163.1411
70.6761-0.0004-0.25320.3142-0.16250.2032-0.0233-0.10610.04460.06610.03940.0745-0.0013-0.0382-0.00610.2601-0.01530.02140.3039-0.0050.273861.295351.051984.7477
80.8236-0.07860.22390.2014-0.09550.82380.0132-0.0803-0.07980.04470.0245-0.02440.07880.1109-0.00050.22980.0054-0.00040.23560.0080.2168100.459543.090393.4068
90.9968-0.0706-0.03370.87830.17171.1576-0.0368-0.0002-0.14210.091-0.02550.0150.13170.02730.00120.28540.05660.00260.39410.03030.211284.188648.4499110.7623
100.6929-0.6235-0.14730.45060.11140.5538-0.0109-0.03640.2378-0.01430.0174-0.0741-0.13450.0026-0.00030.3911-0.012-0.01750.39480.00950.294690.208659.4708116.0584
110.23990.00040.15850.224-0.20770.8673-0.00640.02490.01840.02830.0224-0.0002-0.09950.120.0120.1996-0.00740.00990.2052-0.00440.2046104.948550.531469.0755
120.58330.3267-0.02330.69960.20031.03830.03590.22320.1519-0.27020.01530.0973-0.0592-0.0259-0.00340.28730.01430.01150.3342-0.00430.242899.341846.348536.7523
130.4439-0.32150.42340.6669-0.09680.49090.0225-0.0041-0.0380.02840.06050.07760.0101-0.0478-0.00640.2184-0.01290.00880.2731-0.00090.226187.873943.627255.5822
140.5996-0.0595-0.2540.19370.19980.0929-0.0414-0.1695-0.23020.12310.01560.06570.1996-0.0291-0.01330.3078-0.01820.01270.23490.03180.290567.204634.656776.5266
150.85550.0668-0.14940.1027-0.04030.38260.0050.06440.03-0.01280.00510.0059-0.0105-0.00990.00350.18980.0061-0.00590.164-0.00150.187160.66295.3249-9.3114
160.24190.09010.11690.10050.13380.8021-0.01720.0981-0.02-0.04750.00650.00330.0725-0.00750.00330.2263-0.00170.00950.2286-0.00650.216372.526891.5591-22.3337
170.68010.14290.09810.39680.16750.09470.018-0.10040.02520.0553-0.0109-0.005-0.003-0.03170.00990.1862-0.00160.00970.205-0.01460.189965.090998.174124.2098
180.65840.05790.28890.35060.09520.3061-0.03030.13780.0962-0.09650.03140.0095-0.12640.0663-0.00110.24330.00220.00230.17170.00880.230643.0273108.60720.5063
190.90320.14160.18310.24430.06930.24730.0593-0.0271-0.05090.0059-0.0361-0.00120.030.0308-0.00080.19040.00630.00520.1625-0.00860.185847.296175.09620.5479
201.34380.078-0.75610.19170.22310.9681-0.00080.1345-0.0432-0.06790.00330.01540.011-0.0285-0.01240.24-0.0033-0.01560.2158-0.01270.233132.958561.1492-18.9982
210.731-0.0896-0.10050.1940.00490.33480.0026-0.0686-0.06280.045-0.0077-0.00280.0555-0.0059-0.00180.195-0.019-0.01080.19790.00870.182444.190185.358622.9508
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 78 )A2 - 78
2X-RAY DIFFRACTION2chain 'A' and (resid 79 through 237 )A79 - 237
3X-RAY DIFFRACTION3chain 'A' and (resid 238 through 488 )A238 - 488
4X-RAY DIFFRACTION4chain 'A' and (resid 489 through 660 )A489 - 660
5X-RAY DIFFRACTION5chain 'A' and (resid 661 through 879 )A661 - 879
6X-RAY DIFFRACTION6chain 'A' and (resid 880 through 1017 )A880 - 1017
7X-RAY DIFFRACTION7chain 'B' and (resid 3 through 78 )B3 - 78
8X-RAY DIFFRACTION8chain 'B' and (resid 79 through 302 )B79 - 302
9X-RAY DIFFRACTION9chain 'B' and (resid 303 through 373 )B303 - 373
10X-RAY DIFFRACTION10chain 'B' and (resid 374 through 461 )B374 - 461
11X-RAY DIFFRACTION11chain 'B' and (resid 462 through 631 )B462 - 631
12X-RAY DIFFRACTION12chain 'B' and (resid 632 through 701 )B632 - 701
13X-RAY DIFFRACTION13chain 'B' and (resid 702 through 861 )B702 - 861
14X-RAY DIFFRACTION14chain 'B' and (resid 862 through 1018 )B862 - 1018
15X-RAY DIFFRACTION15chain 'C' and (resid 2 through 237 )C2 - 237
16X-RAY DIFFRACTION16chain 'C' and (resid 238 through 581 )C238 - 581
17X-RAY DIFFRACTION17chain 'C' and (resid 582 through 879 )C582 - 879
18X-RAY DIFFRACTION18chain 'C' and (resid 880 through 1017 )C880 - 1017
19X-RAY DIFFRACTION19chain 'D' and (resid 2 through 196 )D2 - 196
20X-RAY DIFFRACTION20chain 'D' and (resid 197 through 511 )D197 - 511
21X-RAY DIFFRACTION21chain 'D' and (resid 512 through 1019 )D512 - 1019

+
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