[English] 日本語
Yorodumi
- PDB-7u4r: Structure of MAP kinase phosphatase 5 in complex with 3,3-dimethy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7u4r
TitleStructure of MAP kinase phosphatase 5 in complex with 3,3-dimethyl-1-((9-propyl-5,6-dihydrothieno[2,3-h]quinazolin-2-yl)thio)butan-2-one, an allosteric inhibitor
ComponentsDual specificity protein phosphatase 10
KeywordsHYDROLASE/INHIBITOR / phosphatase / protein-tyrosine phosphatase / dual specificity phosphatase / phosphatase-inhibitor complex / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


negative regulation of epithelium regeneration / MAP kinase phosphatase activity / MAP kinase tyrosine phosphatase activity / protein tyrosine/threonine phosphatase activity / regulation of adaptive immune response / MAP kinase tyrosine/serine/threonine phosphatase activity / regulation of brown fat cell differentiation / negative regulation of p38MAPK cascade / negative regulation of epithelial cell migration / peptidyl-threonine dephosphorylation ...negative regulation of epithelium regeneration / MAP kinase phosphatase activity / MAP kinase tyrosine phosphatase activity / protein tyrosine/threonine phosphatase activity / regulation of adaptive immune response / MAP kinase tyrosine/serine/threonine phosphatase activity / regulation of brown fat cell differentiation / negative regulation of p38MAPK cascade / negative regulation of epithelial cell migration / peptidyl-threonine dephosphorylation / Signaling by MAPK mutants / negative regulation of oligodendrocyte differentiation / negative regulation of JUN kinase activity / RAF-independent MAPK1/3 activation / negative regulation of JNK cascade / JUN kinase binding / positive regulation of regulatory T cell differentiation / negative regulation of stress-activated MAPK cascade / myosin phosphatase activity / mitogen-activated protein kinase p38 binding / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / protein-serine/threonine phosphatase / oligodendrocyte differentiation / phosphatase activity / negative regulation of respiratory burst involved in inflammatory response / stress-activated MAPK cascade / dephosphorylation / negative regulation of cell migration / protein-tyrosine-phosphatase / negative regulation of ERK1 and ERK2 cascade / Negative regulation of MAPK pathway / negative regulation of epithelial cell proliferation / response to lipopolysaccharide / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Mitogen-activated protein (MAP) kinase phosphatase / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Rhodanese Homology Domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily ...Mitogen-activated protein (MAP) kinase phosphatase / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Rhodanese Homology Domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like
Similarity search - Domain/homology
Chem-L8R / Dual specificity protein phosphatase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.14 Å
AuthorsGannam, Z.T.K. / Jamali, H. / Gentzel, E. / Lolis, E. / Anderson, K.S. / Ellman, J.A. / Bennett, A.M.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)R01AR66003 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122473 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32AI055403 United States
National Institutes of Health/National Institute on Minority Health and Health Disparities (NIH/NIMHD)R35MD122473 United States
CitationJournal: Eur.J.Med.Chem. / Year: 2022
Title: Defining the structure-activity relationship for a novel class of allosteric MKP5 inhibitors.
Authors: Gannam, Z.T.K. / Jamali, H. / Kweon, O.S. / Herrington, J. / Shillingford, S.R. / Papini, C. / Gentzel, E. / Lolis, E. / Bennett, A.M. / Ellman, J.A. / Anderson, K.S.
History
DepositionFeb 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dual specificity protein phosphatase 10
B: Dual specificity protein phosphatase 10
C: Dual specificity protein phosphatase 10
D: Dual specificity protein phosphatase 10
E: Dual specificity protein phosphatase 10
F: Dual specificity protein phosphatase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,86312
Polymers104,7006
Non-polymers2,1636
Water00
1
A: Dual specificity protein phosphatase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8102
Polymers17,4501
Non-polymers3611
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dual specificity protein phosphatase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8102
Polymers17,4501
Non-polymers3611
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dual specificity protein phosphatase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8102
Polymers17,4501
Non-polymers3611
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Dual specificity protein phosphatase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8102
Polymers17,4501
Non-polymers3611
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Dual specificity protein phosphatase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8102
Polymers17,4501
Non-polymers3611
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Dual specificity protein phosphatase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8102
Polymers17,4501
Non-polymers3611
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.376, 129.505, 83.654
Angle α, β, γ (deg.)90.000, 91.819, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: 322 - 464 / Label seq-ID: 7 - 149

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and ((resid 322 and (name N or name...AA
22(chain 'B' and ((resid 322 and (name N or name...BB
33(chain 'C' and ((resid 322 and (name N or name...CC
44(chain 'D' and ((resid 322 and (name N or name...DD
55chain 'E'EE
66(chain 'F' and ((resid 322 and (name N or name...FF

-
Components

#1: Protein
Dual specificity protein phosphatase 10 / Mitogen-activated protein kinase phosphatase 5 / MKP-5


Mass: 17449.961 Da / Num. of mol.: 6 / Fragment: UNP residues 320-467
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP10, MKP5 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9Y6W6, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-L8R / 3,3-dimethyl-1-{[(9aM)-9-propyl-5,6-dihydrothieno[2,3-h]quinazolin-2-yl]sulfanyl}butan-2-one


Mass: 360.537 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C19H24N2OS2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.38 Å3/Da / Density % sol: 63.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM bis-Tris, pH 5.5, 200 mM ammonium acetate, 5% w/v PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9798 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 3.14→48.49 Å / Num. obs: 24364 / % possible obs: 84.66 % / Redundancy: 1.7 % / Biso Wilson estimate: 89.69 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.05884 / Rrim(I) all: 0.08216 / Net I/σ(I): 9.07
Reflection shellResolution: 3.14→3.252 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.5262 / Mean I/σ(I) obs: 1.62 / Num. unique obs: 3500 / CC1/2: 0.586 / Rrim(I) all: 0.7351 / % possible all: 86.03

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Cootmodel building
XDSdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6MC1

6mc1


Resolution: 3.14→48.49 Å / SU ML: 0.4592 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.4883
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2247 1985 9.62 %
Rwork0.1724 18649 -
obs0.1774 20634 84.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 95.84 Å2
Refinement stepCycle: LAST / Resolution: 3.14→48.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7058 0 144 0 7202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00317370
X-RAY DIFFRACTIONf_angle_d0.52429974
X-RAY DIFFRACTIONf_chiral_restr0.04111065
X-RAY DIFFRACTIONf_plane_restr0.00371287
X-RAY DIFFRACTIONf_dihedral_angle_d9.6754388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.14-3.220.41721440.36581330X-RAY DIFFRACTION84.86
3.22-3.310.36581370.29381392X-RAY DIFFRACTION88.9
3.31-3.40.29711480.25231343X-RAY DIFFRACTION86.43
3.4-3.510.28851450.23071361X-RAY DIFFRACTION86.2
3.51-3.640.29751380.21331237X-RAY DIFFRACTION78.71
3.64-3.780.24411290.2081305X-RAY DIFFRACTION83.57
3.78-3.960.23371400.18671357X-RAY DIFFRACTION86.88
3.96-4.160.21341590.16071376X-RAY DIFFRACTION87.22
4.16-4.430.20341400.15791349X-RAY DIFFRACTION86.17
4.43-4.770.21141420.14181333X-RAY DIFFRACTION85.26
4.77-5.250.18961440.1471335X-RAY DIFFRACTION84.42
5.25-60.24481380.16741334X-RAY DIFFRACTION84.16
6-7.560.21121340.17431237X-RAY DIFFRACTION78.34
7.56-48.490.171470.12411360X-RAY DIFFRACTION84.81
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)
15.838109038062.474351310284.11237611935.976317412552.728578427247.43782019739-0.143764192217-0.2579933752130.02549885678530.720357572497-0.06906171548810.72304397880.0368767116956-0.4790012956810.2352331861260.673825542470.0242359203674-0.1117021901150.5683468991990.003776580075680.715275613174-33.1245965653.60928739475-17.733097993
28.918535161846.313944065031.583750772866.87645589275-2.592149275224.94569807947-0.364618806549-0.0110566963366-0.01172269133120.5248253681990.17222093732-0.333258634772-0.3464114682860.1984882460220.07519025095820.7191242458810.102233003634-0.1498137612490.6033069044050.008417968787810.734182542348-21.010207499810.0099282633-23.3360207528
33.97783919133-0.985508311014-1.062920844294.03919732423-1.476779038467.06502849669-0.1600870085910.547590156482-0.0664465275291-0.505142982736-0.1652209748650.366773863004-0.393016721441-0.2971628069760.3128771396160.8471154134890.0154552011739-0.1817993324020.569813024091-0.04300580416370.642031015468-30.928912111413.0439259741-29.4692797793
44.68871920765-2.73261248369-1.163694610756.36576355854.953789840945.136384600470.6957627133150.1902174322961.3323455226-1.167180374390.101242287938-1.40785915254-1.186637806041.46508370084-0.5885659959570.8660138119990.0613220974762-0.08765725809890.693590813904-0.04793840959940.807919887508-20.365829191820.5304918451-34.3891938889
52.39083584072-0.700128047089-2.421849817787.621375593854.602489301794.472266394641.35659383469-0.414574936822-0.9602889432020.355567713886-1.3407680942-1.057708496880.540409070741-0.207286245013-0.3742576272091.521113182580.209297562708-0.1930695967630.941037878698-0.1334721653090.866763733349-14.164204944814.538467244111.3572083915
68.460696470550.1368858007291.332241124296.32102743173-0.2926631191823.32864033967-0.0682548163542-0.8732993477460.6958634020121.32094598118-0.2297984644440.171479886099-0.576838690142-0.4569209673180.2868116903610.916412085560.0138775246259-0.1251596234630.698921565997-0.03127626280270.456600637465-21.597755410415.66464993226.12740933567
77.005455248180.4993070188540.1242281654325.040985347614.599822680334.071314218090.2040297978170.3563322217730.5252256682270.122425412147-0.3773289098550.511750215065-0.0725917322389-1.170108387990.2566958872961.024019126890.146583326417-0.2018741186070.6368560570.01351639484050.741795193018-24.979106691114.481395507-3.5614415089
87.91626010371-4.08395462684-1.032149747935.829326937676.419958671969.18476784912-0.006921873316630.2154117166930.180775267274-0.160464251639-0.426531126168-0.0165435686269-0.3941830191080.3241028705660.3291152452311.04683437869-0.0648592748637-0.1567900951510.7292148013840.1753840559070.749119755917-10.149663008211.4306256169-4.68717076329
96.23102141459-2.06664625155-1.193411372751.06018168625-1.058356018554.53523165833-0.691769239261-0.2382734370130.664386049751-0.4910424101860.5819149332580.535287378508-0.27205059169-0.0961154724058-0.05429001805191.169448687130.0937256486881-0.3086615633350.4960509248220.05359081670910.796383708603-11.333099402610.53724760513.13653106142
109.61434649943-2.04723149316-2.063275024233.55837936415-4.082885595947.263054673910.354979454496-0.491162038794-0.2101783099740.566943203336-0.41259461936-0.364553228527-0.2318300658480.7024863045670.1232421363740.942612726792-0.133922215028-0.2761625237560.8322276146990.0138546537730.965225018181-2.232500262587.1563633882910.7781092027
118.13428312623-0.910282348662-2.50455372297.950287546880.9232779250967.42929823360.05979164579120.5028537009-0.342091557677-0.654168701716-0.174689547409-0.5972492783850.1546062358620.4515734546540.1095857033150.9533144193830.0202489539824-0.1323309673490.7808271748060.01812314533530.620153270163-2.644978009091.574784080531.84739917651
128.43250321748-1.27942191548-4.994084913874.64815862551-2.927586288765.961327263260.0693555864727-0.8403597517110.1269954532980.4867981609131.109369200470.06406417193021.03196180743-0.333932915981-0.8150536075491.41047009816-0.0746230902391-0.02068397956250.545799087073-0.1267163355850.822960303283-41.0701343557-21.8622953288-35.9355225987
133.41085299105-4.80509257406-3.463455022159.314958207674.581498638784.034105435490.07274337065650.921756646574-0.28101069697-1.69650005701-0.2624460607481.5167938171-1.8307474649-1.180558675810.1019390214151.04434518569-0.0267402972472-0.2433880051350.8344196366390.07300588189031.07788466459-40.315875171-12.9790637382-39.9268472213
147.74899644051-4.5390291052-6.153335410437.712516470261.251504229235.809101863670.2720208779160.2812975740320.226774673428-0.2129806611280.003804965315890.339788521065-0.160840082435-0.375221770109-0.2909828975661.02671521701-0.154079613521-0.2019733848920.6126906724470.01659386785970.777163539236-31.5072397284-10.2704602418-39.0725984249
153.67054776621-3.16742586519-2.964631685824.608413510064.42029444955.553085070620.8540495761380.8454834194350.456864412992-1.29398072262-0.288675497203-1.37846944396-1.16512031796-0.475902807196-0.5832422860480.963495533432-0.111076585424-0.1088042345870.6434734471460.02868838523160.91750542139-23.7733917076-20.2288722822-45.6990229046
165.20545660623-4.89402119384-5.377962828096.507177799143.810051750456.097059745660.000346524087712-1.66806988937-0.008341512272262.506276989910.617143007083-0.639515756014-0.2647975678422.03508896971-0.2688054700971.67288066037-0.0435621992548-0.412186236150.9308153242190.08558829621720.894287385595-25.4481838139-23.2372836622-32.5540044433
176.43697239098-3.1031541366-0.1824305688047.77247939193.634567629425.077750296490.01427773922420.21545104011-0.5324468534470.448870906256-0.2138629720650.4117766568760.8055876436480.153997380279-0.008608266661050.884846130619-0.022234750443-0.2309048968840.427276275206-0.04046639994080.555614604648-32.3834406175-23.8824347411-40.0769341597
189.493018124134.10003387998-1.559671796337.679413175830.9674680677155.162993992110.314416965741-0.37319084096-0.2300207268350.721325043231-0.05366941475320.3873202051291.20226914564-0.158404991592-0.1597216663620.98908090450.0176864348232-0.1375691888980.5083575075230.06551075474690.714613543323-37.3922309059-32.6919606155-41.688316807
197.44700626962-2.86338724113.927415810428.91936549905-5.384238661386.577174395760.4096221411920.421030404854-1.10175331639-0.545182573676-0.602101595426-0.2716352825911.781631992152.34762743562-0.1804249355711.058998889270.0543898697986-0.136580465730.714312914021-0.06008887405650.960057882135-24.5007454277-36.8118235164-42.589933159
209.308248934175.3125296697-3.698845967097.20111697022-5.030665439463.5754062633-0.864149133405-0.3535301966110.0378397951820.9359858156510.515629150148-0.989646218961-0.07207385469030.3867154839960.3395316262441.370840070910.0117572316485-0.2210490440360.6405361794480.02765112413390.710224438394-10.94592739793.22119286876-56.7832157914
212.175538608253.29774893487-1.868005208677.875195095090.08839987756778.959756082310.4388220776760.870514566815-0.366014725448-1.586679536520.7307790527420.49916077202-0.716610134246-2.43745273504-1.283663798650.9749738356810.112902149544-0.1996133661091.055025666530.07441979404950.774886291569-22.48549425351.74757296486-59.5158708402
228.132062613291.99021100636-2.351238455843.06478172393.687983374057.722551771220.6351091863280.7002074258350.2800317532980.304013746838-0.4251384238690.1229691388420.0840282228136-0.795861288422-0.1614668111191.119542644140.104931080701-0.2154238253460.5131667801850.05630975569350.703052394868-20.8729682291-6.69289845584-54.9501716747
234.837312756450.9566850093321.163534770614.00655633926-1.68111982298.145331673230.175593189294-0.17013634219-0.05444894004170.430644125049-0.174132852111-0.4941011175960.7127957116210.1171302129280.007767617548450.9799479274050.0789080473698-0.1284242744270.4109344376880.03701496304910.70032507252-9.99240781081-8.0974946083-46.7160628336
246.666435151773.725141491023.217098091563.876106731552.033671861256.612166348790.1403865923370.4556098505530.202052833813-0.5502697995610.145957444944-0.0878574891217-0.06441858422010.696864937558-0.2874178408120.8771132813030.0715465037875-0.05108937781890.4734039123530.07549804209910.649213564599-6.71243376833.35582722637-49.1021726071
256.76101708764-5.81514773683-6.533220467445.12428306525.235678318036.72468473728-0.785802178111-1.723177829541.077714926050.5845582620680.805873269656-1.39800443940.455236393932.422238952490.05325777615351.101022445930.0993865137315-0.1137964702861.272741775810.03013216700021.002920940510.722236860209-1.21672468996-38.4430939171
263.65795135419-1.87554447527-3.115079473969.55346696216-2.921565151994.98892329606-0.0053710189153-0.420175075428-0.4285086208820.62851518360.1322186527550.2448140531240.06411635915550.248265468884-0.1096463879470.874480810014-0.160389797746-0.1694332131210.843957062996-0.03930775321690.831529109745-14.248172492239.1443323418-4.66167655968
278.669106822131.72530116863-7.799261905544.00108272237-1.764347758417.61144518856-0.438010737812-0.7259459115260.8111152767-0.6697577361930.3776601891330.2882507383880.4011553742-0.01100278667020.1062362135460.853807912311-0.0695960384298-0.3506672492220.655086516102-0.09807979558420.817019486435-10.335654346832.9641277898-12.0432693538
285.13389452424-0.239926087268-3.796608510325.675646078830.06424604364972.7763870483-0.1138960515360.845396792601-0.327657403034-0.4099083980680.437327364469-0.0877759242735-0.3490904823320.0366654885931-0.4147620176021.00019240573-0.0395093613367-0.1837090153090.849897424134-0.1436926094860.606686754101-6.1160201937344.1832952666-18.6342291727
297.363754773434.059105920283.466360640997.169303369163.962789344277.788506947490.102532207955-0.2213905356510.6425897469330.363377957857-0.1823774862770.374616553438-0.229102716894-0.1067941804990.1197998352410.758104392959-0.0446268992452-0.1368869764620.668947931143-0.02223868919240.710304870421-8.4224288147250.8243100067-8.82258815067
304.37115854246-4.416893026873.564706910366.83657428091-3.53203701068.25446044054-0.2377044399590.8231664752271.57799464970.0637625786123-0.0487030798425-1.32588999403-1.11244670790.1843322265330.1871708390851.01440182168-0.119811396931-0.1893268764290.731260475026-0.02058970203971.09380239002-1.0194263531558.6840479301-17.2910663289
314.81599022111-5.10336161605-4.46440336285.429428691014.41306807924.93349103876-0.234751203207-0.7870215644121.408140465530.2942543647990.49927506399-0.6437653829060.7001044027210.368497699613-0.1953904318370.64497540510.101809149358-0.231728269270.741249822679-0.05380781199891.1552085375912.000107842415.1421784035-21.0201969336
324.3903847284-5.53661042851-3.045131136278.259712356821.016953288268.60155432391-0.368550508531-1.422757034240.2830801606040.2879303175510.337803921217-0.498611273552-0.1419037478161.27937878287-0.1203167355770.758927169858-0.0380746829736-0.2217113686670.7858663385230.02121376122371.100180850958.4888283232123.666529501-12.7542828573
332.14523211080.5083921995641.679152571826.392698474495.425168318965.27234903172-0.433619455665-0.842753645486-0.840574933389-0.437148967051-0.1127087897220.236643444014-0.982840591674-1.613338648480.5232131739580.888133291728-0.0812075712144-0.2226759381340.699931880804-0.03461549092091.05936898461-1.2430460279126.7466582247-25.0705354123
344.95765550222-6.295928826474.906632922768.49581275791-6.079507867358.341255019741.121906826320.2817059899130.413060192892-1.24323538588-0.428649311906-0.2505862916990.1120660430740.539445155112-0.6150695685540.744971375613-0.101216283725-0.005073481671320.8378068231430.08744607143141.1860603218611.043326176927.4951553838-29.8059652575
352.09382523665-0.9630916713970.5816060315894.352015658954.096177126877.375898187060.1520879136960.4951542973470.1667155311870.362777932875-0.222700478529-0.1704140573170.23615843487-0.242076985560.174444003540.719070724521-0.116208796875-0.2256064471370.4389877269630.1240577296410.9002367580957.3613324492719.5932061276-25.6211575825
366.74879136615-0.176364085374-1.67725850184.22988717491.814163307362.30859021246-0.6067712952290.774484303248-0.4605023421580.0736195110437-0.0600735818436-0.8145539239680.389573424358-0.4177565693220.8460480551860.873269943572-0.05918533055840.02071105124830.6626994013660.05325275579250.8036685035866.7764777512310.477667524-30.9985391929
377.408176811954.13877097627-6.591804575613.603429918-4.877865444338.07145098062-0.7800927801672.879588831030.256286431119-0.8808757195740.2735832541410.2350775039740.113294672189-1.39167524350.4502886341310.875581145145-0.164622736452-0.2030871198151.075689377-0.04462352653540.9909336322911.6928359334219.2306242567-40.2432181224
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 320 through 368 )
2X-RAY DIFFRACTION2chain 'A' and (resid 369 through 399 )
3X-RAY DIFFRACTION3chain 'A' and (resid 400 through 448 )
4X-RAY DIFFRACTION4chain 'A' and (resid 449 through 466 )
5X-RAY DIFFRACTION5chain 'B' and (resid 320 through 328 )
6X-RAY DIFFRACTION6chain 'B' and (resid 329 through 353 )
7X-RAY DIFFRACTION7chain 'B' and (resid 354 through 368 )
8X-RAY DIFFRACTION8chain 'B' and (resid 369 through 399 )
9X-RAY DIFFRACTION9chain 'B' and (resid 400 through 425 )
10X-RAY DIFFRACTION10chain 'B' and (resid 426 through 441 )
11X-RAY DIFFRACTION11chain 'B' and (resid 442 through 465 )
12X-RAY DIFFRACTION12chain 'C' and (resid 320 through 328 )
13X-RAY DIFFRACTION13chain 'C' and (resid 329 through 345 )
14X-RAY DIFFRACTION14chain 'C' and (resid 346 through 368 )
15X-RAY DIFFRACTION15chain 'C' and (resid 369 through 383 )
16X-RAY DIFFRACTION16chain 'C' and (resid 384 through 400 )
17X-RAY DIFFRACTION17chain 'C' and (resid 401 through 425 )
18X-RAY DIFFRACTION18chain 'C' and (resid 426 through 448 )
19X-RAY DIFFRACTION19chain 'C' and (resid 449 through 465 )
20X-RAY DIFFRACTION20chain 'D' and (resid 321 through 333 )
21X-RAY DIFFRACTION21chain 'D' and (resid 334 through 345 )
22X-RAY DIFFRACTION22chain 'D' and (resid 346 through 368 )
23X-RAY DIFFRACTION23chain 'D' and (resid 369 through 399 )
24X-RAY DIFFRACTION24chain 'D' and (resid 400 through 448 )
25X-RAY DIFFRACTION25chain 'D' and (resid 449 through 465 )
26X-RAY DIFFRACTION26chain 'E' and (resid 322 through 345 )
27X-RAY DIFFRACTION27chain 'E' and (resid 346 through 368 )
28X-RAY DIFFRACTION28chain 'E' and (resid 369 through 399 )
29X-RAY DIFFRACTION29chain 'E' and (resid 400 through 448 )
30X-RAY DIFFRACTION30chain 'E' and (resid 449 through 465 )
31X-RAY DIFFRACTION31chain 'F' and (resid 321 through 333 )
32X-RAY DIFFRACTION32chain 'F' and (resid 334 through 368 )
33X-RAY DIFFRACTION33chain 'F' and (resid 369 through 383 )
34X-RAY DIFFRACTION34chain 'F' and (resid 384 through 399 )
35X-RAY DIFFRACTION35chain 'F' and (resid 400 through 425 )
36X-RAY DIFFRACTION36chain 'F' and (resid 426 through 448 )
37X-RAY DIFFRACTION37chain 'F' and (resid 449 through 465 )

+
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://pdbjlvh1.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