[English] 日本語
Yorodumi
- PDB-6vcj: Crystal structure of hsDHFR in complex with NADP+, DAP, and R-naproxen -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vcj
TitleCrystal structure of hsDHFR in complex with NADP+, DAP, and R-naproxen
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / NADP+ / 2 / 4-diaminopyridine / R-naproxen / inhibitor / complex
Function / homology
Function and homology information


regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / response to methotrexate / sequence-specific mRNA binding / axon regeneration / folic acid binding / dihydrofolate metabolic process / G1/S-Specific Transcription ...regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / response to methotrexate / sequence-specific mRNA binding / axon regeneration / folic acid binding / dihydrofolate metabolic process / G1/S-Specific Transcription / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / NADPH binding / tetrahydrofolate biosynthetic process / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / mRNA regulatory element binding translation repressor activity / positive regulation of nitric-oxide synthase activity / one-carbon metabolic process / NADP binding / negative regulation of translation / mRNA binding / mitochondrion / cytosol
Similarity search - Function
Dihydrofolate reductase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily
Similarity search - Domain/homology
FOLIC ACID / PYRIMIDINE-2,4-DIAMINE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / (2R)-2-(6-methoxynaphthalen-2-yl)propanoic acid / Dihydrofolate reductase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsPedersen, L.C. / London, R.E. / Gabel, S.A. / Krahn, J.M. / DeRose, E.F.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ZIA ES050111 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ZIA ES102645 United States
CitationJournal: J.Med.Chem. / Year: 2020
Title: The Structural Basis for Nonsteroidal Anti-Inflammatory Drug Inhibition of Human Dihydrofolate Reductase.
Authors: Duff Jr., M.R. / Gabel, S.A. / Pedersen, L.C. / DeRose, E.F. / Krahn, J.M. / Howell, E.E. / London, R.E.
History
DepositionDec 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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: Dihydrofolate reductase
B: Dihydrofolate reductase
C: Dihydrofolate reductase
D: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,25220
Polymers86,1514
Non-polymers6,10116
Water1,36976
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0635
Polymers21,5381
Non-polymers1,5254
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0635
Polymers21,5381
Non-polymers1,5254
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0635
Polymers21,5381
Non-polymers1,5254
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0635
Polymers21,5381
Non-polymers1,5254
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.397, 124.457, 84.614
Angle α, β, γ (deg.)90.000, 96.346, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Dihydrofolate reductase


Mass: 21537.775 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHFR / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P00374, dihydrofolate reductase

-
Non-polymers , 5 types, 92 molecules

#2: Chemical
ChemComp-LG3 / PYRIMIDINE-2,4-DIAMINE


Mass: 110.117 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6N4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NPX / (2R)-2-(6-methoxynaphthalen-2-yl)propanoic acid / (R)-Naproxen


Mass: 230.259 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H14O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#5: Chemical
ChemComp-FOL / FOLIC ACID


Mass: 441.397 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C19H19N7O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.33 Å3/Da / Density % sol: 47.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: Protein solution: 9mg/ml in 50mM NaCl, 10mM Tris, 5mM NADP+, 10mM 2,4-diaminopyrimidine, 20mM R-Naproxen Mother Liquor: 20% PEG 20,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.339→50 Å / Num. obs: 31414 / % possible obs: 94.6 % / Redundancy: 2.8 % / Biso Wilson estimate: 31.16 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.07 / Rrim(I) all: 0.122 / Rsym value: 0.1 / Net I/σ(I): 7.8
Reflection shellResolution: 2.339→2.39 Å / Mean I/σ(I) obs: 1.86 / Num. unique obs: 1495 / CC1/2: 0.61 / Rpim(I) all: 0.385 / Rsym value: 0.516

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M6J

4m6j


Resolution: 2.34→42.05 Å / SU ML: 0.2818 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.6832
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2382 1570 5 %
Rwork0.1916 29816 -
obs0.194 31386 94.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.18 Å2
Refinement stepCycle: LAST / Resolution: 2.34→42.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5734 0 420 76 6230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036346
X-RAY DIFFRACTIONf_angle_d0.56928652
X-RAY DIFFRACTIONf_chiral_restr0.0452921
X-RAY DIFFRACTIONf_plane_restr0.00241076
X-RAY DIFFRACTIONf_dihedral_angle_d14.11912223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.410.31791260.27332392X-RAY DIFFRACTION82.05
2.41-2.50.3331410.25522686X-RAY DIFFRACTION95.19
2.5-2.60.30391480.23752803X-RAY DIFFRACTION97.26
2.6-2.720.26351470.22412792X-RAY DIFFRACTION97.32
2.72-2.860.30241450.23532761X-RAY DIFFRACTION96.77
2.86-3.040.27381460.22042782X-RAY DIFFRACTION96.44
3.04-3.280.30851460.22382783X-RAY DIFFRACTION96.51
3.28-3.610.25651330.19382521X-RAY DIFFRACTION87.94
3.61-4.130.17651480.16272814X-RAY DIFFRACTION97.4
4.13-5.20.19021460.13982755X-RAY DIFFRACTION95.33
5.2-42.050.17451440.16022727X-RAY DIFFRACTION92.82
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)
10.3271469720930.0863436574256-0.02959808878170.874267970369-5.52267618977E-50.006179810569320.186101410692-0.0184460916719-0.0827591451868-0.163795112352-0.1307242161750.2020528116850.03962156360260.1956448541030.02721698752780.252009169790.09872743378090.01500019588940.2533716219240.0006853919329070.12627299298310.6925770254-1.7884676397833.0424311665
20.07121174855670.143007608940.1802273860560.5093331140460.5229820177730.577115230353-0.218233007885-0.2042076767060.06363602656250.004625195680520.02784129257070.125152952347-0.2662413290590.000503236927794-0.1633258742660.2615618419740.148953683485-0.03722387262260.220357194207-0.01636229891830.1117559025925.3742266392710.579172678443.3359258493
30.00222555640117-0.0161714653586-0.005669427919820.4976238460650.15492758340.04840881565260.128115568180.08662726623740.110620590643-0.248473363601-0.131335503195-0.067143618836-0.193750781920.383625958965-0.002531952468180.197804722695-0.004720705317640.03619179338660.3453186460840.03173620656560.17181105300817.85774092460.55905787340644.7033674468
40.388700284374-0.1742528289920.2089817370460.227375014606-0.1217719540890.1578542795420.01794447101050.01158708647920.158342936595-0.0442914067867-0.177285799477-0.0543884584348-0.2255383584690.166050557744-0.01258357255610.213705841525-0.003348589844340.03382391943990.228557585070.002090073562890.11593843064514.4299770844.3297563971849.0382076508
50.09384646372760.0448755879720.1245069729990.236203548223-0.006876431606680.184072244690.0494361713506-0.177431649101-0.0483649883370.383113309886-0.03242012060050.02836032956240.0507134511942-0.1739605627340.002083570434610.200825291140.04095076717180.006695809005250.2201695873330.02876555161120.1514711994929.71081094333-2.4054111931354.325076344
60.004773389816650.00493381742611-0.001963874098480.00575139527953-0.004063419477540.00554642031308-0.1133368290210.0143577269731-0.1688095091270.02848829033380.0901394356006-0.1878708550530.00846033874677-0.2046462735694.22771653129E-60.3089171192910.11231144322-0.01384043409860.2196248455280.006355718776820.2259059174914.54018202939-10.16265922942.6595846935
70.0287837446769-0.1287172222140.0456805813141.23687046937-0.1849079773150.1154518158160.1173196597260.172440076386-0.0398267682942-0.457727007411-0.06434169979010.268801837160.02634940741420.1243124390780.1166957852380.2584127623140.0882176815388-0.03834019168390.26504353441-0.0451695084720.1686240055570.981955648628-0.98597576558133.0424329155
80.07228494810470.007341648832330.00387537904440.2092797035780.06163191992270.01912758457930.08793783768190.100784649722-0.244967809439-0.254901678251-0.307769547980.3324971555150.0227598693327-0.0515228660914-0.02219580485410.2436920839720.0427781075874-0.03394588059020.241430266742-0.07006119722650.283045135699-1.799409013071.0146178254133.3478600643
90.0697306319119-0.0744252710451-0.03858291917860.2697611408990.1586604935230.0921807997970.0755567643432-0.2870300394530.08649014524920.04945826442430.0511029019387-0.0353362729251-0.2638182706310.06262492530810.01417911104440.1531053363790.03120329201850.0518675082280.2971746458760.04859111304170.1354278076128.77859722136-4.2460415671490.3261681782
100.01024008456320.005885455377830.01034983804320.00313032003540.007391789942490.014593126082-0.121701800223-0.1549354235720.1162616574060.0742796489215-0.0942235544422-0.0377081933835-0.161865616104-0.0139348622922-1.86661389389E-70.282701446127-0.04701441614260.01783701352870.259097098162-0.1056087295450.29637212154411.72648483377.5340172266387.395361645
110.103546161692-0.07175614076850.2397923515630.054210942385-0.1682073704630.5532571123550.0414554751873-0.1715508346690.02199493743160.0650419020305-0.06197143371190.100975880554-0.416327417869-0.202740187438-0.02787382480490.25748612397-2.32450444718E-50.08835232978450.182863479005-0.03774877096980.2382922939546.577358148253.921222256777.4243070765
120.452864349308-0.07714596109250.02744496767070.0192542750104-0.005738027806330.0009470480980470.09491564520090.350176270922-0.249842900412-0.0717837463067-0.0671068007811-0.02211870674220.162248575406-0.04692760396640.004312049333490.2473379197220.04480555296720.0352232388650.159172937334-0.01533895109830.1560734662285.92698180293-5.45470511169.5252303948
130.0346236280356-0.002526006612870.0134174655220.0007037333158980.002574615020710.01577486814280.05835611394150.00709140578611-0.0153345209145-0.05271267912410.04459560615320.0575863162078-0.2255159732150.0569930108304-1.17061640645E-60.202772834099-0.0579286533320.03701091166850.1955754808250.02368857944250.1651393622315.84801399441.5921834379570.4385864563
140.05117332041560.0682993758346-0.004288527500250.1302020437770.01154088229550.081199311543-0.0503279301176-0.142196654139-0.3214589128740.1496214454540.15269748174-0.1676018721810.1101282074230.1493669942730.01422925214850.191117728932-0.01899838648850.02037402522960.3118406293660.05378800743720.28525003088517.807023563-7.5035864638983.0186793527
15-0.000225856504168-2.9108943841E-5-0.0006741397713690.0005001462431490.0002210014443210.0002091347888680.0613060891723-0.204141753968-0.03613238224030.264612128317-0.01905342701830.0785654846718-0.116098079037-0.09233233298150.08991484755070.42019193577-0.02252699273480.1100979460790.5606441852020.1750331514320.1994980853847.11258161038-9.1448687127796.2080284255
160.5742397016690.428010990738-0.549389499211.00616646313-0.4491562848880.551241737581-0.119128846846-0.674232791638-0.1334034766510.343028605195-0.129003389288-0.386527800012-0.2572166864460.25857665659-0.1415609844770.278536168163-0.0149450805368-0.06672178474150.484958310152-0.04130752240870.31702363647721.2272452696-1.3450924304892.1212431871
170.1052900058680.1168488228210.05221174365270.2595165545-0.07919514600640.174635268687-0.247615970420.0428920033208-0.23052537144-0.0896006648899-0.1147722671260.3826829957580.05377590645740.139671579588-0.06597363093130.2508623368750.01505330022150.03855955683940.290375339617-0.1081137702940.27172010786411.518492596633.410030973967.5823959827
180.1705954067630.134198728158-0.1202623955870.106612864876-0.09776722593410.0912953202652-0.0409164061889-0.024812373381-0.002748499880230.15213327836-0.0256395025279-0.04699019016060.062371170578-0.0140791756648-0.09756497782250.3985015741810.02199044291050.09088403877490.09833275088790.07972897535070.27330040490219.955009606624.141824973970.5779708095
190.0844501837530.02630759770430.02268367849150.02189950210370.01847245423460.047535293126-0.08410651438220.0133090935924-0.07366505984050.236440036463-0.0766536419379-0.200195661606-0.1131908851880.184296904501-0.000375894991390.211734169099-0.0179541291880.0082026104590.1959369777240.006318812109820.21623229754426.598140333932.015415270663.0428925076
200.170835501983-0.0782246065358-0.01076548334770.08332480122790.06929706462880.0777957480048-0.2329069067090.0909195803251-0.0449123560316-0.02440537557830.151688658774-0.10653278347-0.1033646756970.2365685185610.0004088022644950.336236321085-0.0442894177911-0.0366606282780.2209097506820.043268872350.20421403527828.739159790839.272603765761.8784168322
211.11040240815-0.1388558460740.5675055380980.393451925344-0.2174994178130.359371719083-0.2616451711820.325872945235-0.00432558921202-0.0181342701242-0.04926205548730.0552113164567-0.02735964517320.00262109709993-0.5033582776250.199894163613-0.003389178644560.03057240122680.16993881773-0.07523681591630.16988491311916.403777699931.781177681358.9832535006
220.652193652044-0.32222418615-0.01777379993510.504487673314-0.08244860838010.0251195676874-0.2427063912350.1090529171930.140954957679-0.0654877718695-0.01808119527290.00576886719308-0.0553876396685-0.0925541107379-0.0976098868060.4053381447250.0229449713836-0.06630399609240.531509409206-0.2084368137150.3178598582546.4454278136427.689515201152.477684975
230.35826364983-0.2479551326930.04126986400140.181744085615-0.05000615151290.0822948136803-0.155149483546-0.0316604051016-0.3429439991830.0171223293279-0.104136388470.2683615255470.340602769914-0.2531837041830.0871575965160.361257154346-0.09067540447320.218457754780.272663624879-0.07179108948860.34743476169310.041244663320.432422201464.9041104861
240.1438610954430.0373818447624-0.046060039290.1971970445510.08017640654060.0714599606526-0.00587777526879-0.01055236996550.05368551036050.255448647895-0.1542188241490.3475941824590.298916600705-0.1228767467390.00715181441680.25743765955-0.0501502369154-0.02573753714150.1737602171020.004043067709210.295967346797-2.59829428503-27.159597911670.2984030635
250.09605180800060.0949560096745-0.09248307800660.105741041781-0.09848527730660.09261807185310.0699389091777-0.1234195144320.03162215781140.0733975525512-0.1218617854150.0831449332681-0.0289360454749-0.000751917930256-0.1122663901040.113584415064-0.1007251674120.04050643479610.207201942904-0.04711909141650.514195936219-10.6163287203-35.234757744365.5237560102
260.2807776298950.293176436946-0.2724800084210.333284836307-0.3488532683020.428432403715-0.130159728649-0.00869242584385-0.120233207394-0.09103239299530.0702324333157-0.01376112426220.2915176247310.133432072967-0.07306406588950.2102103669180.054589403045-0.07369660399810.204715094663-0.03896038075560.404424998162-0.0446666345733-38.870135802159.9833224845
270.07291705619640.08397103314010.01962686215350.1114822218920.02937754959840.04798778647160.0336828488441-0.0419199324144-0.1121673792830.0633890610240.0328738808973-0.01241519179280.05493727282880.04315375059180.1116267275640.0997931755611-0.130235423089-0.03448489190210.145731043215-0.06439921504940.5535567677996.12527823733-42.267652261264.1776834012
280.003041217894120.00474819343583-0.00511051262090.00794316965573-0.006495096116640.006495555409370.1816471592240.2597143701610.0979641079081-0.1871261027350.162225677883-0.1833976669460.004938274543560.120951285322-1.96161911494E-60.302284444745-0.09650652887370.03120225747780.392381741443-0.06876126694540.44697057519.93689340768-36.283760723152.8879001621
290.00584665558845-0.00313831657893-0.00335704251070.00934057987248-0.003840929459230.00474493320077-0.1269580351430.178617840976-0.0516359741241-0.1767390004860.107868826749-0.09405388468030.007145267818860.04911057969271.26064423477E-50.437778977422-0.161797154759-0.08497442557440.462308927016-0.004608570563060.413278496067-0.128526411628-41.154160432648.000790507
300.0245267153208-0.00916303143444-0.04701876929880.003551850483410.01868817460180.0902343535473-0.0548472794958-0.003955639884920.0399094309713-0.1084598894950.111616800583-0.00429408527736-0.1846883310720.247775266771-0.027246572180.1860243723-0.0913871805641-0.06548836809330.1695809912760.02171284638730.3169542314973.05686138268-27.421020434559.8213928067
311.06372321252-0.218758332994-0.413231980430.2136455239720.2089375712310.2564250097410.04940226335040.3125136513970.263479706802-0.240568166251-0.2570968491280.468386084955-0.04929290024980.0693513379842-0.0116003658680.3599338128010.0386400444008-0.06289418838960.273868412745-0.01401083112520.335805042232-4.47188302232-24.148080512258.0256525643
320.132083598301-0.0911473056319-0.02324935451580.2742003183250.2356201212190.214532969011-0.102139064176-0.1510200736310.4942886796630.0241079084017-0.2353700473550.522163316982-0.16180576301-0.240936811212-0.008574916395280.36244552444-0.075607703309-0.05906332318090.324487754945-0.08096771334450.547393088185-7.82859114525-21.403075179366.4121239815
330.0231846775381-0.0141740345992-0.01430965586450.07608671525750.002785167159110.0173766223637-0.2061830673390.02145546166560.175488618513-0.115605461147-0.1235633366380.548601772363-0.12796213359-0.0739949153741-0.004695837300730.32335212241-0.0466505417385-0.04115670210130.381398986831-0.01573148088620.476630435741-9.51627820373-22.061145292161.5686860454
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 27 )
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 48 )
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 64 )
4X-RAY DIFFRACTION4chain 'A' and (resid 65 through 75 )
5X-RAY DIFFRACTION5chain 'A' and (resid 76 through 117 )
6X-RAY DIFFRACTION6chain 'A' and (resid 118 through 126 )
7X-RAY DIFFRACTION7chain 'A' and (resid 127 through 174 )
8X-RAY DIFFRACTION8chain 'A' and (resid 175 through 186 )
9X-RAY DIFFRACTION9chain 'B' and (resid 2 through 27 )
10X-RAY DIFFRACTION10chain 'B' and (resid 28 through 39 )
11X-RAY DIFFRACTION11chain 'B' and (resid 40 through 70 )
12X-RAY DIFFRACTION12chain 'B' and (resid 71 through 100 )
13X-RAY DIFFRACTION13chain 'B' and (resid 101 through 117 )
14X-RAY DIFFRACTION14chain 'B' and (resid 118 through 138 )
15X-RAY DIFFRACTION15chain 'B' and (resid 139 through 148 )
16X-RAY DIFFRACTION16chain 'B' and (resid 149 through 185 )
17X-RAY DIFFRACTION17chain 'C' and (resid 2 through 27 )
18X-RAY DIFFRACTION18chain 'C' and (resid 28 through 39 )
19X-RAY DIFFRACTION19chain 'C' and (resid 40 through 59 )
20X-RAY DIFFRACTION20chain 'C' and (resid 60 through 101 )
21X-RAY DIFFRACTION21chain 'C' and (resid 102 through 148 )
22X-RAY DIFFRACTION22chain 'C' and (resid 149 through 158 )
23X-RAY DIFFRACTION23chain 'C' and (resid 159 through 186 )
24X-RAY DIFFRACTION24chain 'D' and (resid 2 through 27 )
25X-RAY DIFFRACTION25chain 'D' and (resid 28 through 39 )
26X-RAY DIFFRACTION26chain 'D' and (resid 40 through 59 )
27X-RAY DIFFRACTION27chain 'D' and (resid 60 through 87 )
28X-RAY DIFFRACTION28chain 'D' and (resid 88 through 101 )
29X-RAY DIFFRACTION29chain 'D' and (resid 102 through 111 )
30X-RAY DIFFRACTION30chain 'D' and (resid 112 through 126 )
31X-RAY DIFFRACTION31chain 'D' and (resid 127 through 138 )
32X-RAY DIFFRACTION32chain 'D' and (resid 139 through 174 )
33X-RAY DIFFRACTION33chain 'D' and (resid 175 through 186 )

+
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