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- PDB-7ufh: Integrin alaphIIBbeta3 complex with fradafiban (Mn/Ca) -

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Basic information

Entry
Database: PDB / ID: 7ufh
TitleIntegrin alaphIIBbeta3 complex with fradafiban (Mn/Ca)
Components
  • 10E5 Fab heavy chain
  • 10E5 Fab light chain
  • Integrin alpha-IIb heavy chain
  • Isoform Beta-3C of Integrin beta-3
KeywordsCELL ADHESION/INHIBITOR / Complex / Inhibitor / BLOOD CLOTTING / CELL ADHESION / CELL ADHESION-INHIBITOR complex
Function / homology
Function and homology information


tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / maintenance of postsynaptic specialization structure / regulation of extracellular matrix organization / platelet alpha granule membrane ...tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / maintenance of postsynaptic specialization structure / regulation of extracellular matrix organization / platelet alpha granule membrane / positive regulation of glomerular mesangial cell proliferation / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / glycinergic synapse / alphav-beta3 integrin-HMGB1 complex / vascular endothelial growth factor receptor 2 binding / blood coagulation, fibrin clot formation / negative regulation of lipid transport / negative regulation of low-density lipoprotein receptor activity / Elastic fibre formation / regulation of release of sequestered calcium ion into cytosol / cell-substrate junction assembly / mesodermal cell differentiation / angiogenesis involved in wound healing / alphav-beta3 integrin-IGF-1-IGF1R complex / platelet-derived growth factor receptor binding / filopodium membrane / extracellular matrix binding / positive regulation of fibroblast migration / positive regulation of vascular endothelial growth factor receptor signaling pathway / regulation of postsynaptic neurotransmitter receptor internalization / apolipoprotein A-I-mediated signaling pathway / regulation of bone resorption / wound healing, spreading of epidermal cells / apoptotic cell clearance / heterotypic cell-cell adhesion / positive regulation of cell adhesion mediated by integrin / integrin complex / Molecules associated with elastic fibres / cellular response to insulin-like growth factor stimulus / positive regulation of leukocyte migration / cell adhesion mediated by integrin / positive regulation of cell-matrix adhesion / smooth muscle cell migration / microvillus membrane / Syndecan interactions / negative chemotaxis / p130Cas linkage to MAPK signaling for integrins / cellular response to platelet-derived growth factor stimulus / cell-substrate adhesion / protein disulfide isomerase activity / positive regulation of smooth muscle cell migration / activation of protein kinase activity / positive regulation of osteoblast proliferation / TGF-beta receptor signaling activates SMADs / PECAM1 interactions / lamellipodium membrane / GRB2:SOS provides linkage to MAPK signaling for Integrins / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / platelet-derived growth factor receptor signaling pathway / fibronectin binding / ECM proteoglycans / positive regulation of bone resorption / positive regulation of T cell migration / Integrin cell surface interactions / coreceptor activity / negative regulation of endothelial cell apoptotic process / positive regulation of substrate adhesion-dependent cell spreading / embryo implantation / positive regulation of endothelial cell proliferation / cell adhesion molecule binding / Integrin signaling / substrate adhesion-dependent cell spreading / cell-matrix adhesion / positive regulation of endothelial cell migration / protein kinase C binding / response to activity / Signal transduction by L1 / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / positive regulation of smooth muscle cell proliferation / Signaling by high-kinase activity BRAF mutants / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / MAP2K and MAPK activation / wound healing / cell-cell adhesion / platelet aggregation / platelet activation / ruffle membrane / VEGFA-VEGFR2 Pathway / cellular response to mechanical stimulus / positive regulation of angiogenesis / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / regulation of protein localization
Similarity search - Function
Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin alpha Ig-like domain 3 / Integrin beta tail domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily ...Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin alpha Ig-like domain 3 / Integrin beta tail domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain cysteine-rich domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin alpha cytoplasmic region / EGF-like domain, extracellular / EGF-like domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / : / Integrin alpha Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1.
Similarity search - Domain/homology
: / Fradafiban / Integrin beta-3 / Integrin alpha-IIb
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99768170407 Å
AuthorsLin, F.-Y. / Zhu, J. / Zhu, J. / Springer, T.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL-103526 United States
CitationJournal: Cell / Year: 2022
Title: A general chemical principle for creating closure-stabilizing integrin inhibitors.
Authors: Lin, F.Y. / Li, J. / Xie, Y. / Zhu, J. / Huong Nguyen, T.T. / Zhang, Y. / Zhu, J. / Springer, T.A.
History
DepositionMar 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrin alpha-IIb heavy chain
B: Isoform Beta-3C of Integrin beta-3
C: Integrin alpha-IIb heavy chain
D: Isoform Beta-3C of Integrin beta-3
E: 10E5 Fab heavy chain
F: 10E5 Fab light chain
H: 10E5 Fab heavy chain
L: 10E5 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)302,74443
Polymers297,4068
Non-polymers5,33835
Water4,720262
1
A: Integrin alpha-IIb heavy chain
B: Isoform Beta-3C of Integrin beta-3
H: 10E5 Fab heavy chain
L: 10E5 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,56022
Polymers148,7034
Non-polymers2,85718
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Integrin alpha-IIb heavy chain
D: Isoform Beta-3C of Integrin beta-3
E: 10E5 Fab heavy chain
F: 10E5 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,18421
Polymers148,7034
Non-polymers2,48117
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)258.581, 144.453, 104.764
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Integrin alpha-IIb heavy chain


Mass: 49515.965 Da / Num. of mol.: 2 / Fragment: UNP Residues 32-488
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGA2B, GP2B, ITGAB / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P08514
#2: Protein Isoform Beta-3C of Integrin beta-3 / Platelet membrane glycoprotein IIIa / GPIIIa


Mass: 52087.902 Da / Num. of mol.: 2 / Fragment: UNP Residues 27-498
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB3, GP3A / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P05106

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Antibody , 2 types, 4 molecules EHFL

#3: Antibody 10E5 Fab heavy chain


Mass: 23766.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#4: Antibody 10E5 Fab light chain


Mass: 23332.686 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)

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Sugars , 4 types, 6 molecules

#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#12: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 7 types, 291 molecules

#8: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#10: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#11: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#13: Chemical ChemComp-MWX / Fradafiban / [(3S,5S)-5-{[(4'-carbamimidoyl[1,1'-biphenyl]-4-yl)oxy]methyl}-2-oxopyrrolidin-3-yl]acetic acid


Mass: 367.398 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H21N3O4 / Feature type: SUBJECT OF INVESTIGATION
#14: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#15: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.9
Details: 11% PEG 8000, 0.2 M ammonium sulfate, 0.1 M Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.99768170407→50 Å / Num. obs: 78933 / % possible obs: 99.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 86.888577151 Å2 / CC1/2: 0.992 / Net I/σ(I): 6.83
Reflection shellResolution: 3→3.08 Å / Num. unique obs: 5802 / CC1/2: 0.186

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T3P

3t3p


Resolution: 2.99768170407→42.0485237188 Å / SU ML: 0.446488327874 / Cross valid method: FREE R-VALUE / σ(F): 1.32571241517 / Phase error: 26.8695523535
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.245106875461 1992 2.53225703934 %
Rwork0.225492075435 76673 -
obs0.226004588301 78665 99.0044804672 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 104.27426029 Å2
Refinement stepCycle: LAST / Resolution: 2.99768170407→42.0485237188 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20715 0 313 262 21290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082107240927421720
X-RAY DIFFRACTIONf_angle_d0.56897432846729501
X-RAY DIFFRACTIONf_chiral_restr0.04332814242663281
X-RAY DIFFRACTIONf_plane_restr0.004041835254833821
X-RAY DIFFRACTIONf_dihedral_angle_d12.063727859812925
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9977-3.07260.3776987218991350.3667102006725218X-RAY DIFFRACTION95.5210563883
3.0726-3.15570.3395215431521390.3562271447515350X-RAY DIFFRACTION98.6875224739
3.1557-3.24850.3693593327411400.3453102279465423X-RAY DIFFRACTION99.2683797288
3.2485-3.35330.351953641131420.3145594559095452X-RAY DIFFRACTION99.5196584238
3.3533-3.47310.3055496059511420.2911446759025440X-RAY DIFFRACTION99.518630772
3.4731-3.61210.2860786144921420.2769517268165501X-RAY DIFFRACTION99.6644295302
3.6121-3.77640.3331791344291420.2733917908645449X-RAY DIFFRACTION99.6435572982
3.7764-3.97530.2584197507021430.2491496798125508X-RAY DIFFRACTION99.770480226
3.9753-4.22420.2602350260741430.2184937999575484X-RAY DIFFRACTION99.6987951807
4.2242-4.550.2221869319561440.1934350426085524X-RAY DIFFRACTION99.6483825598
4.55-5.00720.2003992402861430.1874856704655503X-RAY DIFFRACTION99.5065209729
5.0072-5.73020.2178796634991440.1937843254215546X-RAY DIFFRACTION99.3019197208
5.7302-7.21350.2420802304511450.2109754047325571X-RAY DIFFRACTION98.9269643475
7.2135-42.0480.1790419962641480.1715095713325704X-RAY DIFFRACTION97.4845910378
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)
11.930640729860.2321213989060.1412382680381.25649888615-0.2010420601672.029116886210.01102183939060.1591411163760.0335762378978-0.275047700663-0.01104816048640.328749168648-0.00208023289074-0.267589825924-0.0001396375379140.7488715514460.02928457144560.0675449871410.5082967858280.01811785459030.72854710210646.33340567489.979112645638.4647390213
22.27989740298-0.697937373131-0.314500762251.489955831950.3493833363740.8588471886370.13151294794-0.197549947280.02865787548620.34556236323-0.2121551962710.3157452151040.15081043486-0.269294623889.78753793525E-60.75515856041-0.05414027538340.1964106544850.474575331348-0.01319889748110.73862064317845.14571184392.781870216262.4822261026
31.698608784050.7020212992940.4018909487312.505113462190.3481722333923.10336480157-0.04765738302130.0306238954378-0.2634610959080.04459171422030.0760033288474-0.1502555938140.2268467110180.06111481284910.0003527548977540.6812074783350.1064065430370.1163907891070.3797465667930.0470669684520.67001180603264.333628037983.357063695647.2130780814
41.507130796460.5662557194650.04359467824840.313480032360.07087205264411.49722020296-0.06477877479170.09993834799210.09845642411550.2008868838470.343399668626-0.5619301212490.2165608777871.34935866095-2.72359442553E-50.8663121461190.1695049103850.006207525091851.64004006379-0.00254948150581.20762902102113.51041851100.35084097143.338283818
52.141964237371.021946350660.03708852180753.082810043040.6012594730991.612823429380.120776444279-0.2310528690670.2515144181660.187226672858-0.117587211813-0.00749326616917-0.2594492245840.047436553091-0.0002137618048110.7354312927890.007656960339850.1185657064620.390245219320.004059499444260.67544531246566.8834342135117.52688373463.349388624
61.27250791511-0.173688685602-0.8021992781850.545317556315-0.1769825283270.851420615676-0.0645542469649-0.0645040455795-0.1586947086570.2256953409270.000216566240582-0.1086961734660.4293203785070.761959194587-1.51199073806E-50.8336078121980.084653855058-0.08324819732151.098117341990.007604187128751.0402666091996.8071744699105.71460986856.546486774
70.1067427419980.130308387755-0.03494403878880.262307233713-0.06185276252020.0104740537920.0306410624783-0.8045059570950.253526494828-0.39174580516-0.246044934358-0.6373213569990.4027417493340.108554333721-0.0001146748235261.219386601470.3080391115780.2775432022782.173249151690.1474281253991.50920621825115.61576556388.853202007619.4078165436
81.85486499837-0.0539163161962-0.7596174277651.341609295150.7571601584031.17432805748-0.0752596260577-0.252461951012-0.07560696127240.000394051202728-0.127756771612-0.3356833306040.1328163947380.710489899602-0.0001321482405280.7827800571180.06272079146760.06602066712840.852970661920.06749279728090.74757193820887.673800000794.4835684608131.877999507
93.213931483040.895742399407-0.7237229067521.00154334556-0.875164360762.22194738796-0.4559544793380.699817183205-0.20210135128-0.451091031010.0413728121519-0.2416321368690.607127480150.2901692859967.85694851421E-50.942892248098-0.06463375185970.2641456435350.976163012396-0.04335735558550.76499263971990.277044159888.7994683657107.655370637
103.0170943030.1220786895560.2137499716042.173372032940.774118154992.84271523656-0.425469058643-0.0463768171891-0.60909080851-0.0772413909140.101712611004-0.1502439559020.6930819838570.0217933519303-0.0008418862900950.94614493518-0.01709814540710.2812671467770.611637194427-0.003361339866340.77232549323973.678269533579.0089408285126.894101376
111.34378502456-0.798480634656-0.1928977049430.6885820851970.4954139974071.2056894563-0.5666722867660.839657096639-0.198177934997-0.08989475879650.2551717167490.349778399290.585504683155-1.24783985219-6.17416233853E-51.03831366671-0.4532263788260.01735820700981.61177929458-0.02875299330521.1928430756520.147641374380.1446856765129.795493172
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150.113786045786-0.000367548664002-0.04506823410690.007673329033040.04561933446350.07785798115770.1445359240120.783511223253-0.7570174842650.0369712395103-0.2460337847230.4767629715360.5233822258020.3007641577060.0003962493083741.455549645380.2491183530060.2061760809581.52639912069-0.1366960566641.20487969342119.90257352282.722765298482.9710504053
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170.03397114196040.08709949560080.03174949751480.06909115769980.07414540362370.03224365972220.1845385194430.2724843722680.816458333799-0.184657320441-0.0559616215995-0.450976555440.5033245020390.294880017779-0.0002748914434321.08506432803-0.1240831908730.2737097156911.583049459830.1207202513281.02152486986116.88384903995.518403247386.925698561
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200.04331807916880.08030119181140.01546554074650.1016304836610.06510905645330.09144935661140.3772492230230.7985264061320.0169855849775-0.0219332747116-0.155581951785-0.2939045495440.5567203506340.8862173499045.5707512988E-51.66492000880.5376846871940.3828877289272.116474225970.02075964911031.05045496078130.91753925684.569562386571.9194843513
210.0039057488739-0.0506876491587-0.008768652221390.2236883353340.2193744796650.119691991354-0.1085560045561.24339906662-0.339775565950.3638731314470.637778549507-0.6771947589180.2643288963490.478044971385-0.0002224583383681.878067290750.643001691050.06660234230492.26520248968-0.04056382645951.55601137286150.81876459182.359350124779.1774060678
220.0307468985257-0.00582093936386-0.0196433277510.0182817783184-0.001621244316860.03360351820680.04768467925680.08522329034770.287725498834-0.459971767485-0.3130727373630.00917187961955-0.490072294201-0.03627342682430.0004781896238961.491785197910.2912745955070.2269419289952.296943403030.3432928928681.46297046503147.0383435185.878839836386.6551427347
230.03111653697840.03449573753090.001825600631280.06872231383710.00129973376430.06534876603310.256402273747-0.0158700894066-0.174387132877-0.1593359586840.0990006419809-0.04045858547040.3778771807120.314254631515-0.0007486846794341.823017292180.9232660554630.2204123772482.723173951460.2408649247041.47544161746153.17932518483.765607935481.0306992834
240.00200929945211-0.00593577756840.007590247189780.0395175406265-0.0281766717772-0.000353553086081-0.199399229146-0.0235854644220.6185226424340.1640618474660.169835890443-0.325074290730.31360222920.2197686359681.70343642267E-51.640382548480.660362998788-0.1974939329152.68484982107-0.4958792373621.72388591615150.54059221776.389128718375.3812577155
250.1188031267070.0358703246666-0.1375714513850.1999496296640.06437165536060.2005259259230.163295879187-0.3901405614640.139898986749-0.07229101030310.543761908149-0.288383110472-0.4601832807440.7444866024720.0001301246709990.981263513017-0.06813858845560.08107533132311.67139860950.1299040663811.44147969734131.008677021103.566317882100.498324163
260.04549126299990.03696760621780.1251388733780.3460927014610.05574338646340.322173438055-0.179668018070.3169399852071.50525025856-0.1729043586650.315217977343-0.5840871747170.4390875634370.5960681177670.001299960552190.576367884487-0.1037690573730.1625796648791.62419394630.1955089090791.38850053903121.152809937104.075965256100.85034642
270.303385197296-0.0416187256630.0491502239840.1363670375660.07544764832090.104379608918-0.584817556925-0.222782684490.4331097083340.5077867593650.392643032712-0.0287280345073-0.003700580468690.4707794180680.0001465009201050.955514516542-0.007963340040080.1346938447961.494172179020.02938589593671.16253274493122.03951054996.3367730942105.438303984
280.1820239890180.1249445748360.1570217030150.1778197261140.2675351777520.262922933423-0.1277798930310.2177897088810.1340549835480.04322357514750.122946544961-0.3885220069740.296619655440.521270411464-2.39442178175E-50.905970417852-0.06257591967970.274403982731.729820343610.1268397351651.09617140743124.24572504798.267374948598.7478171843
290.111011350472-0.01423125763740.1418236874950.1476474047940.02939991563210.183791738811-0.2793041897260.3430438197360.189654720182-0.455883107195-0.2699436619150.219603187426-0.2847430841860.961533297817-0.03295388969730.5851990308690.1569117007460.2868558142932.343378396360.2788821415831.37139688844146.39607822498.053161484499.5527236526
300.1114701051410.246325810860.03243993690620.5146225122710.07195120335020.0209815989816-0.06879268065030.3785645620910.0071014377571-0.453557261753-0.1812353312970.0873120471925-0.05386560174720.1027178415360.07174876797381.871295234271.172362925390.8005741920583.624401190380.3676530026721.60437073523156.4895855989.079090437672.1876707995
310.109549509044-0.04520921111880.01125550148470.0503730518639-0.03311594290220.04033709474580.3145408769150.977206426371-0.124161057758-0.57615930558-0.274418604475-0.203804586490.03001349596060.967270532122-0.000295323982261.477324728990.1319797160740.2656454880522.542653555190.4427065078091.35585649862150.8419213396.513138001386.8774849849
320.00942258732839-0.01969195691140.004129232267630.03597882787060.005934039858420.00254204255191-0.0969970101932-0.003395425392920.177877792949-0.5334792562810.450012050551-0.224527310218-0.0566590305774-0.0912804720257-0.0008976525621292.361753501060.02924281411070.8485926477241.837496795440.6108278006932.09641887408154.08234372105.8140137175.2925827663
33-0.02623401308460.0209305519283-0.01153711335050.0116669327067-0.07106097491320.0116668175443-0.03957824578920.252830178023-0.224059350526-0.6251128327960.1242881052780.145600212065-0.5000389410020.3031792817930.0002826186134491.3097982822-0.04474387704960.226203678072.167908214620.5047112433311.61110969359145.85895737794.480820761787.8702433862
34-0.0548629779096-0.06774413472610.0208053084860.0224933655034-0.05228851822540.0445219865572-0.0882968913670.5225429193730.142150445004-0.558659241591-0.044329168146-0.875531741914-0.3348705169230.9096683507990.0001498933517241.50791463063-0.06403051239550.5594342993622.452293301590.225970792961.86168193056157.89248919299.605319899575.1208158855
350.300889007657-0.04012414927020.04717644839040.0598813655634-0.09185156278870.126423194056-0.531471688612-0.6339849818730.3228602423080.5031235557160.224204122517-0.06690131147610.0926476685096-0.09454031285030.0001042929965321.246117588390.07894144394080.2981448283921.17604350886-0.02560474833511.0595841501914.948185976389.820324754689.3394288268
360.2293018486240.35648829260.02697767518750.739884686806-0.2297165411051.11109481176-0.185662368454-0.5259406516870.2222186748920.4362474144880.316658802972-0.01229668450980.1062663872880.3777541189742.84371682509E-50.7361550285960.05235895074210.1882339841871.13989286271-0.1596192120210.92627721482220.528778714897.030077360781.0923058648
370.1990136452180.1526590588190.05695165812750.1020612090830.059859786070.1038882190640.0860255110184-0.867643179565-0.1428407870850.5849800371680.285323244883-0.2632019269980.219593227030.279673028582-0.0002842086543851.104901930770.1657301634860.06444539154211.17020779204-0.1447257965180.99162941632422.187805367999.004223574787.2950369584
380.426304863869-0.21753643963-0.09487557191460.532224190189-0.2923320344240.1030169424720.247703178752-0.533773209595-0.141166382340.2581204462440.1965672019130.197259114685-0.03131702369710.0936196444843-0.0003025846968710.8558854242420.000853076662270.2590416351091.13006033323-0.07593323075621.0298502261312.626831824394.482642833684.3043887683
390.245028065536-0.23874767082-0.2353159645750.3242318749470.3272199497380.435190901067-0.0495866431552-0.41210871533-1.293458108470.8037416137190.2732694252210.3546552584051.131534681180.5000761377680.01057598692750.9636924275460.07812457792090.174580924281.129877898480.2944120532662.0800165668-15.326398391980.587174056892.3296706377
400.109762256828-0.07220266972310.0468764258080.123013679306-0.1112123523990.103566517923-0.596845218252-1.2998916091-0.797637791740.4022868504310.005530855978330.5025131875090.07633477493920.0252114447448-0.0004952539023881.047633219170.1081444356030.07338902093391.200789531740.07596786085441.4846130787-8.952357292189.768214543490.1309346602
410.02662945654660.0308112057785-0.04927568268560.03323223097470.03373645926880.290105819634-0.45418320982-0.255531318552-1.594723214130.1795368558990.207960781686-0.3031603187261.103613150130.4931057642180.002150602782521.20196014782-0.07487302561110.3757351096841.267834220770.408860798422.1617256418-16.01185740877.540928521894.6526760108
420.0763358195495-0.0629230768008-0.0662811936910.0606863601830.02600252507740.03896876346460.03483266640820.9373826704760.550196472351-0.12130656131-0.08143319154150.697356858019-0.269403309792-0.814563163357-0.0007723459223310.8042791162420.08408896923570.1257113578841.29199905859-0.30434298621.289609470410.14721993196797.792244419964.80284826
431.025811577560.3541446793190.5944445943320.3266394211850.3190354057480.356723135353-0.06455162210780.50147661626-0.0398662723493-0.273831648520.1050911140720.402191404941-0.0683200309774-0.8067940728051.801399172E-60.673698105774-0.05861088925470.09038492503051.11489385211-0.1511693411391.0599347852210.438819897495.304847911363.3290151706
440.1083206271950.05057970974060.01563920798970.06557802252560.05656673276470.0853934542219-0.38428085226-0.033130934962-0.578059912975-0.2419392709890.156189721850.2632577844130.140281707748-0.8742506870270.001053509988330.720202854343-0.1348656335130.1815174284691.37524971017-0.2127008407691.175837704543.7373661006689.81685865766.0383359272
450.140516126672-0.00309671580119-0.1652229970590.01784571734370.09372628206950.140126686078-0.264901685340.4800902210170.224303452614-0.177668413542-0.02709217985860.530772153195-0.228694874516-0.6450894610540.0002404232299240.698124149722-0.03807868889390.100335872511.17456730953-0.2376568531591.277646214550.63819593740396.348451116669.7455247328
460.8953742108240.09221199818260.3252373261780.7150149126520.02053254664310.44733027516-0.230935856651-0.106837374273-1.258789673440.3619758051910.1561325322180.4871364532030.311378852837-0.0880975363278-0.0001732221069420.836148911650.08936942122850.3164263844111.183777081080.2570141693391.5023189194-21.870829517592.761044956488.3295629847
470.983087353303-0.396948016790.556263964531.39600786999-0.5819170228551.06466619224-0.0187704731982-0.270567204137-1.151872014290.480713658485-0.09393634049090.2699942120360.0500168337634-0.5797690694950.0001978486656570.703263240651-0.03654918366630.2031839297351.183644907530.07566926125371.47468182735-22.477254298893.668341877287.001980071
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 67 )
2X-RAY DIFFRACTION2chain 'A' and (resid 68 through 313 )
3X-RAY DIFFRACTION3chain 'A' and (resid 314 through 454 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 111 )
5X-RAY DIFFRACTION5chain 'B' and (resid 112 through 339 )
6X-RAY DIFFRACTION6chain 'B' and (resid 340 through 431 )
7X-RAY DIFFRACTION7chain 'B' and (resid 432 through 466 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 67 )
9X-RAY DIFFRACTION9chain 'C' and (resid 68 through 291 )
10X-RAY DIFFRACTION10chain 'C' and (resid 292 through 453 )
11X-RAY DIFFRACTION11chain 'D' and (resid 1 through 105 )
12X-RAY DIFFRACTION12chain 'D' and (resid 106 through 339 )
13X-RAY DIFFRACTION13chain 'D' and (resid 340 through 438 )
14X-RAY DIFFRACTION14chain 'D' and (resid 439 through 471 )
15X-RAY DIFFRACTION15chain 'E' and (resid 1 through 16 )
16X-RAY DIFFRACTION16chain 'E' and (resid 17 through 32 )
17X-RAY DIFFRACTION17chain 'E' and (resid 33 through 52 )
18X-RAY DIFFRACTION18chain 'E' and (resid 53 through 67 )
19X-RAY DIFFRACTION19chain 'E' and (resid 68 through 112 )
20X-RAY DIFFRACTION20chain 'E' and (resid 113 through 125 )
21X-RAY DIFFRACTION21chain 'E' and (resid 126 through 165 )
22X-RAY DIFFRACTION22chain 'E' and (resid 166 through 175 )
23X-RAY DIFFRACTION23chain 'E' and (resid 176 through 199 )
24X-RAY DIFFRACTION24chain 'E' and (resid 200 through 219 )
25X-RAY DIFFRACTION25chain 'F' and (resid 1 through 18 )
26X-RAY DIFFRACTION26chain 'F' and (resid 19 through 38 )
27X-RAY DIFFRACTION27chain 'F' and (resid 39 through 75 )
28X-RAY DIFFRACTION28chain 'F' and (resid 76 through 102 )
29X-RAY DIFFRACTION29chain 'F' and (resid 103 through 113 )
30X-RAY DIFFRACTION30chain 'F' and (resid 114 through 129 )
31X-RAY DIFFRACTION31chain 'F' and (resid 130 through 144 )
32X-RAY DIFFRACTION32chain 'F' and (resid 145 through 155 )
33X-RAY DIFFRACTION33chain 'F' and (resid 156 through 174 )
34X-RAY DIFFRACTION34chain 'F' and (resid 175 through 214 )
35X-RAY DIFFRACTION35chain 'H' and (resid 1 through 17 )
36X-RAY DIFFRACTION36chain 'H' and (resid 18 through 60 )
37X-RAY DIFFRACTION37chain 'H' and (resid 61 through 83 )
38X-RAY DIFFRACTION38chain 'H' and (resid 84 through 125 )
39X-RAY DIFFRACTION39chain 'H' and (resid 126 through 168 )
40X-RAY DIFFRACTION40chain 'H' and (resid 169 through 179 )
41X-RAY DIFFRACTION41chain 'H' and (resid 180 through 219 )
42X-RAY DIFFRACTION42chain 'L' and (resid 1 through 18 )
43X-RAY DIFFRACTION43chain 'L' and (resid 19 through 75 )
44X-RAY DIFFRACTION44chain 'L' and (resid 76 through 90 )
45X-RAY DIFFRACTION45chain 'L' and (resid 91 through 113 )
46X-RAY DIFFRACTION46chain 'L' and (resid 114 through 155 )
47X-RAY DIFFRACTION47chain 'L' and (resid 156 through 214 )

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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

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