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- PDB-7udh: Integrin alaphIIBbeta3 complex with BMS4-3 -

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Basic information

Entry
Database: PDB / ID: 7udh
TitleIntegrin alaphIIBbeta3 complex with BMS4-3
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 / blood coagulation, fibrin clot formation / negative regulation of lipid transport / vascular endothelial growth factor receptor 2 binding / negative regulation of low-density lipoprotein receptor activity / angiogenesis involved in wound healing / Elastic fibre formation / cell-substrate junction assembly / mesodermal cell differentiation / regulation of release of sequestered calcium ion into cytosol / alphav-beta3 integrin-IGF-1-IGF1R complex / platelet-derived growth factor receptor binding / filopodium membrane / extracellular matrix binding / positive regulation of fibroblast migration / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of vascular endothelial growth factor receptor signaling pathway / apolipoprotein A-I-mediated signaling pathway / regulation of bone resorption / apoptotic cell clearance / wound healing, spreading of epidermal cells / 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 / positive regulation of cell-matrix adhesion / smooth muscle cell migration / cell adhesion mediated by integrin / microvillus membrane / negative chemotaxis / Syndecan interactions / 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 activation / platelet aggregation / 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
alpha-D-mannopyranose / : / Chem-MWO / Integrin beta-3 / Integrin alpha-IIb
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99998841007 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 19, 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)302,77943
Polymers297,4068
Non-polymers5,37335
Water26,5541474
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)151,21320
Polymers148,7034
Non-polymers2,51016
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)151,56623
Polymers148,7034
Non-polymers2,86319
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)258.330, 144.670, 105.060
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 , 5 types, 7 molecules

#5: 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
#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)-[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
#11: 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
#13: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 1502 molecules

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


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#9: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#12: Chemical ChemComp-MWO / (4-{[(5S)-3-(piperidin-4-yl)-4,5-dihydro-1,2-oxazol-5-yl]methyl}piperazin-1-yl)acetic acid


Mass: 310.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H26N4O3 / Feature type: SUBJECT OF INVESTIGATION
#14: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#15: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1474 / 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: 3.3 Å3/Da / Density % sol: 62.73 %
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-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99998841007→50 Å / Num. obs: 258061 / % possible obs: 97.4 % / Redundancy: 1.4 % / Biso Wilson estimate: 46.1928588694 Å2 / CC1/2: 0.997 / Net I/σ(I): 8.34
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 15365 / CC1/2: 0.092

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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: 1.99998841007→48.9948312022 Å / SU ML: 0.433986322673 / Cross valid method: FREE R-VALUE / σ(F): 1.3260955489 / Phase error: 28.2397489827
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.213531650742 2000 0.77547633634 %
Rwork0.185043728716 255906 -
obs0.185262826011 257906 97.4060897218 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.5686845745 Å2
Refinement stepCycle: LAST / Resolution: 1.99998841007→48.9948312022 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20715 0 312 1474 22501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006745781525221713
X-RAY DIFFRACTIONf_angle_d0.63884041796629439
X-RAY DIFFRACTIONf_chiral_restr0.04587017259743271
X-RAY DIFFRACTIONf_plane_restr0.004069320029623803
X-RAY DIFFRACTIONf_dihedral_angle_d12.085250306212923
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.536716744241140.43596646081214589X-RAY DIFFRACTION78.5039243953
2.05-2.10540.3812930366591360.3878683203617460X-RAY DIFFRACTION93.6704817674
2.1054-2.16740.3157029300371420.3328705974618188X-RAY DIFFRACTION97.9690005345
2.1674-2.23730.3111992703331450.29750559498718509X-RAY DIFFRACTION99.2286823767
2.2373-2.31730.3124086787891440.27108425452818475X-RAY DIFFRACTION99.3649268865
2.3173-2.41010.266101751381450.25323277179418508X-RAY DIFFRACTION99.1126461211
2.4101-2.51980.2749910741881460.24070130770218598X-RAY DIFFRACTION99.6120529309
2.5198-2.65260.2206694786661450.21465270426718588X-RAY DIFFRACTION99.569469544
2.6526-2.81880.2693973612951450.20293525172818660X-RAY DIFFRACTION99.6713838978
2.8188-3.03640.2291249720941470.19524583181518662X-RAY DIFFRACTION99.5290506932
3.0364-3.34190.243873792881450.18060896707218753X-RAY DIFFRACTION99.746648369
3.3419-3.82530.1946470600071480.15830133805518818X-RAY DIFFRACTION99.6636889122
3.8253-4.81880.1493918839531480.13633124705618900X-RAY DIFFRACTION99.53493233
4.8188-48.99483120220.1787455227551500.15421949270419198X-RAY DIFFRACTION98.3130081301
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)
15.94369780444-2.03827772306-1.665835874373.472164696241.535114321993.832518703650.08292405338490.2442350758020.143243340466-0.326891178318-0.09077363819210.108592770486-0.0902823584146-0.4370221123020.0515317757520.347455648132-0.00620881643025-0.005800946230010.2525546301860.07055725905670.2284057238746.659172685690.662869166438.2840210751
21.255738805720.07272746234120.05171762658661.052308515010.144298246241.027491394510.022980587887-0.116713078634-0.03364384556770.25364636294-0.08901827438340.1691333810390.176468877101-0.1653414314830.0831712277980.390598653314-0.03589183278050.09388990243760.2506476252080.0121834260910.32504318921944.981767358893.374034530962.2513863494
31.359847966430.331788412920.2752671233112.059136053980.7173419043941.933251396820.00630693147604-0.034615899311-0.1789642478640.1469002025840.036062588081-0.1620676883090.2505472546540.0859057746402-0.04003522096460.3492720280120.04795461844720.06442259251690.2066795426870.03344938553830.29817929674764.426909065683.944897771247.2262611656
46.87460999851-3.78484802754-3.797163000243.894918811422.474432279044.40605874901-0.007199889675930.01819918744840.172259910660.03777840335130.48054575484-0.7964105356650.3946718917011.33541479674-0.3695720613450.4322130042460.121529712445-0.08675381158051.24985111485-0.1920428249310.791089621119113.457003155101.3775823843.754303704
51.100664619180.440705369150.07377338076521.934385874240.5777515366741.080175033440.0337636796595-0.07608651787290.205768114410.1147327059250.0277447390778-0.0488796759278-0.1828901907210.0515002052537-0.06069770074890.4136486034130.006233047803270.04144377492250.2390330001560.007658483723150.34925694041666.5539825512118.14788326563.4562422988
64.80669863944-3.62708387079-5.124861127443.386356804273.539393470616.30367569136-0.237636891521-0.0647896455525-0.1516657110040.2542134240460.156420290386-0.2283343299620.5466869782630.6911364585880.0517999206850.4364013964970.0449701680475-0.06183501058220.690595882295-0.1172070714970.63906454417696.6862714485106.64235728656.7976388705
73.527163342332.668589517271.38772786125.46362714679-2.530233591074.31188323124-0.1878637527860.592288740186-0.635863580752-0.8914213797520.608599464242-0.9025767325280.1504959673162.48591955113-0.4599007227020.7553111775130.2301858918670.1327869147031.98239495965-0.1046711570981.0043672294115.80754072889.887657942319.8375809478
85.995196182021.52832276658-2.836330241281.928306779960.003102337964743.94265806813-0.143783981448-0.370758284246-0.01741378846880.07946032215770.0198805631688-0.2551598725680.108177496380.7593063807540.1472692114280.299529000980.01525531328470.01429439670130.52971031039-0.05490564999910.34209591874787.674764874395.1603810894132.51065957
91.843060648460.2822886419450.2843717819821.11206095878-0.3058353660061.87644585572-0.1032450820850.296450273908-0.103901679936-0.310992297941-0.031688478505-0.2585549583720.2442863207170.584584557780.1457610137030.4469327757210.05503885579440.1491603371210.6796591201550.0001485740083350.40906506844490.776391021589.2722704251108.161774148
102.3975428749-0.362435700210.3191389742932.18552377258-0.0684949744423.28713242322-0.134082493469-0.12468003318-0.416939994159-0.05505877133720.0787795798055-0.07088670970310.6925021286650.09593925215450.01847209016760.4386846818520.02834238142580.1160745097780.3705800108410.04442471853110.3600354296274.149802491779.4981489427127.366814695
112.854403053941.27704147317-2.540304266062.06227176217-2.05096507386.39756391963-0.3690071532240.655043501087-0.261299930821-0.05523319116010.3886685153830.2981989789540.982971094305-1.92963459518-0.08960803195390.78277384703-0.432197795870.0485420306931.45631067854-0.01846823265160.74211945209220.528873146280.0423704375129.729976273
122.42601348076-0.06807513203810.4560534275920.971419995962-0.5123885229232.93828275938-0.0612529144450.3774584799310.305942400752-0.1680526785790.09449339156710.0681836566599-0.120471865731-0.386341377234-0.06283766490160.436378609769-0.0619226359520.02393821834590.5260649934040.07867836095330.32572153296860.9693966144102.613554167100.150216982
132.767093435951.66252338535-3.139802734881.70137359114-1.750031845623.64172974792-0.4272155249970.530626390864-0.346389519845-0.1708659389250.1449723406910.03471841332280.6804219783-0.9631502449550.3440480132360.618942580076-0.1969027972830.0008355854815110.9388235043930.03386281719970.53459295965335.317227207185.9857364048114.881625659
144.766804934385.31813038664.606109320015.978154122275.188643174324.91336436137-0.113277383067-0.379932770979-0.8506237878580.548398085144-0.3431591543590.06173232257011.39683138389-1.641484847810.2230716713210.905597021035-0.3086709088320.2532724012091.01836862435-0.1562515894011.0308856910321.865346891978.2602750232157.332681938
159.86933594565-1.18690559241-5.886248593033.355809886441.504943151053.73586963673-0.3313127737240.157219834696-0.913044594932-1.51212531543-0.515591751538-0.5560136803042.929756529481.968942414580.9682638391571.737990040720.06047836854370.3320997510921.04293775898-0.02070566268830.787422245747120.45052977783.058816590683.7120650354
166.88054614197-2.993749884653.471336064067.462462388931.9129322313.636626857880.928446785134-0.252271885738-0.832901681811-0.311204654735-0.281000994030.362130096942.2158564842-0.638768080437-1.045259281971.63713284477-0.4073314138750.1314160376581.02224936433.95090988141E-50.775797977438110.54760301583.052923683689.5542620751
175.16528312711-3.302559215013.657703636245.079492225241.80755241228.544095425310.2710991907990.3560557333270.89785229543-0.937238414645-0.107244202189-0.7327584781281.168426530090.267595751269-0.1338621894970.857968192831-0.09231084011740.3533414083910.943668173030.05824878432280.701668437292117.37113044795.821641749187.5205659505
182.44468490984-1.173046220811.98748243999.607775139442.627530392688.549496283890.8063497929681.255117562690.26156399302-1.45895503725-0.362360717537-0.2776272141950.925804285493-0.7570245258280.1160318656661.06596713346-0.1742061458880.1350830628861.169439244620.05640158973650.64764468627108.01201411796.798809563783.0409535992
198.05806674459-1.18202050464-3.399911120192.248967370160.7337101180486.643670229830.1277474809780.640282112943-0.0299815782732-1.08805515038-0.0827148697247-0.4446414568371.05160827239-0.2305287184870.2355966672411.17118100661-0.1677138791760.3152009555030.972212730486-0.03039038987020.703883542435114.41478103789.660050712488.0748807224
201.73348275345-0.285201935090.5398877411033.82901077962-2.500566718891.704350190131.707985171591.119038322130.326140876321-0.804325078807-0.708651865189-0.00729857854213-0.00931251986750.241921596025-0.7948462460471.782590328820.5208844834850.5580680775911.852692748470.08435258239780.942839303478131.3584155584.800900067472.5906271152
214.385019014772.062950334240.9338715807965.946964352693.661046406563.387356515550.2995767540671.74093314814-0.074308786386-0.2740624704840.133813268994-1.946157619350.2609686404661.28236641911-0.3065236896221.266800503170.4829681287180.1199669989011.935948176680.1868995074691.4291918668151.39562369882.984259134379.8612016079
221.361056859722.865741802741.002864402526.063995677042.132787336850.7528121552391.024552155631.60447718993-0.020936259881-0.16519751382-0.929819482157-1.229156039680.5463661330330.59592626411-0.02219918586131.208116117240.3442586094320.3169183899581.707638793760.2160612614751.48337200311147.65934368886.508404804387.3223642891
231.94052657367-0.094109040661-0.7583078137012.868221835722.298937022152.07754136740.2405106177570.772389639446-0.0592948895218-0.2344133046230.157899772747-0.9600050261470.8148538917671.79231959086-0.1233200987631.37306330330.8981188566240.3304832476032.55002293620.1867324917861.44040748529153.77556149484.416205281181.716446155
240.936243048836-1.12110503792-1.467657154732.270230544621.681163540882.34797355283-0.1614249819631.02283203296-0.288455464011-0.229717655492-0.24004300926-0.8923681244710.8785110643861.423282532880.1411616212041.697335577220.3733602189350.2582006578622.13072952467-0.2397111172661.71478962385151.10417128376.908764607876.171163271
255.51734972943-4.774360842525.527798511484.48211710016-4.333682936946.23493247964-0.0545324538044-0.2138213900621.02301725717-0.0967679268792-0.286665652568-1.28387614303-0.227611275390.9198284637590.1221422908140.508261444764-0.2244606063030.1649967501341.222264213090.07080706396751.34125962703131.37261397104.231767151100.956485973
264.96660997791-4.079785364941.777985742314.17463092564-2.114529439732.55602558237-0.2479760077080.06870143050061.27462810876-0.121614902873-0.348892112568-1.19149700158-0.1723799236040.5873383509650.6194467628030.494314079876-0.1403070372640.1170994076731.11348599484-0.0311117464671.15411673514121.604962407104.678074717101.255484392
272.87808132069-0.8727031947222.22215172033.77924295905-1.760960715443.82914388191-0.230514669733-0.2100804530210.401926823110.230307634649-0.226111699348-0.47041518410.06459361859930.4690643652480.3123509414740.574475120041-0.1090719035430.114345640451.1148558024-0.1250955862380.935842885781122.5420065797.0355761022105.899300544
283.64700608552-1.43810525022.5767438943.44492176228-2.281189243074.56749541655-0.1703926367240.3883069329330.569047076691-0.190726605709-0.280218098036-1.201703800310.1971597407550.7568836171720.4793318581620.511561255667-0.0875641436750.2634398783951.132088313030.01263628458481.04201140673124.70776431398.882255163799.3048738467
297.80837973328-0.7165474994960.1187404624070.0877368451248-0.007077013594310.00382017399662-0.226124148082-0.3583601988110.232700379921-0.416761896893-0.559836932227-0.627578517370.1897057036741.477326492660.6456301922690.4817262567480.08315233374450.2050170797521.977013114880.2749862164861.68642182307146.76272328798.8630640309100.150272691
304.888593690082.16976143247-1.503426342631.22903183337-1.135799650842.46197430355-1.02123218377-0.0201473759784-1.10824049288-0.8352771996240.705429816093-0.938848336370.4182715825371.590598720970.2962129034171.539763067190.4877859964150.7670941524881.950742638540.07292282214191.8292776896157.16788039889.871948565372.9274037105
312.663055385071.91311979629-0.01430248370931.888501062031.526687278074.59287571474-0.1021599568690.0375447832999-0.223274492946-0.692657935580.276745358348-0.627548074174-0.2408856681.72976700552-0.1401202389731.175929977690.132127712060.2956388712121.733667789130.4517176773811.64571680076151.38610122797.212123192787.5722583935
322.819104226592.62996430005-1.434173748392.6220322824-0.309204625818.57170199081-0.161404459340.1599098599570.131538814215-0.92774529140.303587999129-0.241255150734-0.7552406293441.4688291564-0.2399362940731.44937411454-0.1392192813150.7091124436071.569668378210.4750705073962.13922816151154.561721368106.39516654675.8467296313
336.877936645992.3983187341-1.83367719672.588474180080.5167434254587.24041268707-0.00184440853662-0.599392308524-0.257821897761-0.666570316107-0.4902186951-0.7669519398110.2243852624860.9865962551890.469495460740.7333540553710.1718197973240.3446668222851.481383794010.4852647044161.61418920496146.44167490995.234486047788.5488646249
346.518860615650.630260403934-3.817998309631.603375957070.662624499962.946769352780.2054327031430.0282555678598-0.0823663106694-0.9896037687030.34736365207-1.34179574765-0.4098159659441.81435380131-0.01487469037971.37033049932-0.009609933444470.5479703338891.909551176680.3956710663241.82582508819158.384838412100.2312408175.7815107609
357.22594636098-5.36987167695-6.055068902244.009855980894.496907586845.05557149924-1.1371197-0.937691142206-0.7773839206382.034027449060.2043643895890.9571043196741.684992587620.1520608648510.8742506468561.24260746590.05803342313460.3279808193520.9744241364980.03890550275120.70494982371815.27302193590.207991227689.1560777146
363.548045635181.267541599150.06462131279165.833603383640.465676694326.421266343950.124384596983-0.5131120024760.091382863871.056655210640.04754872161420.1624909371910.3012411517270.11554342508-0.2171951436870.6048714384820.02747884681730.07160789519890.651661514466-0.113690793890.46615443163120.571478293697.380397643880.7224555537
375.388102988620.12263887209-1.975335479925.34317113505-2.541087759339.8311917493-0.158515086713-1.343329438590.2954044313481.58008272920.512679316432-0.0175488603952-0.192502828750.50128734017-0.1115779013650.855360137316-0.01029289980750.03327601687460.804890997639-0.1900401232520.46300659140222.284988374499.397552842486.830485165
385.703176209060.926218906068-3.580615658390.959916403202-1.894419370393.52060309597-0.0423651177486-0.7490048782810.164351155790.7237778972290.3011907597090.47890808496-0.0177656050304-0.107262004555-0.2668627112390.7934205224630.04445525689630.2645679565930.837961923374-0.03201321028320.70418953302512.864383909194.70821322484.0699263234
396.764787848233.061883154194.807150088555.262581213913.421734072937.75092628097-0.231207330503-0.862926033935-2.25869127710.333461557480.08964780761910.006502441220590.9588305985530.09010680828570.3170802127650.7378385457220.1339759988260.4078306821880.9158852324990.35622315231.73638881924-14.723638669680.445187718192.8180409872
405.555702607615.82553496985.567763742796.168626909465.734752678095.5982849771-1.09509618628-0.294113479022-0.5602636057570.1843918258490.03923062666711.796504743030.06293470935450.2581659793381.181770536490.5558436330350.08647883403510.1172047226740.9453151099820.1852538361951.4034284877-8.5109750974189.743794633390.3874640049
415.044132791930.2262602031722.312660687172.463411094521.678745072766.96181585037-0.120434303907-0.59467363751-1.948174833420.537302337499-0.1718328971010.08364485067521.820511188140.006978232312740.2070280627560.9864858809430.110197603330.4874931383591.024236070570.4452594116422.01344702447-15.312678042777.414809096995.1962092963
424.909775342482.894579864010.5804377659864.514863578120.8675813680450.915768990259-0.001057430035990.6052213200650.5365988770240.124765843785-0.2730768638271.390338569620.087390944938-0.9759134473160.2468320408410.464887630646-0.04622262624930.09321363838481.10857160685-0.3044858163741.07220651089-0.03301133153297.419665108464.8086541379
436.852904370840.561066934185-0.06524614663314.219918593320.8177847846562.97373987498-0.03448864091350.579549060037-0.310251827301-0.185568008928-0.2164851476140.7865470693430.23037448782-0.6547707034720.239907181530.3425673387540.01469636029510.07263545490510.758540434123-0.1251223150620.64362123198410.258855555695.248032661963.2082576183
443.619988532325.435677746090.7563501897138.520592450072.077624538284.152718412310.1523835362960.256240284697-0.7524058764160.396700013749-0.5701733308470.7793208874160.751926368164-0.9715721521910.3925429185040.483342274926-0.07280114711130.1621176781220.981612903142-0.2861169244951.093565960423.807996877189.657398231866.0798352289
456.442650335321.2902672374-1.951428003860.287743502711-0.4097108522620.672608859535-0.07225900671040.554386543414-0.3208931531620.0072756360974-0.302735201720.826304460487-0.0423353239902-0.7614043414670.09274904592780.382572838196-0.07501225671230.2133288673110.985976113328-0.3384515407681.093469671610.57487100901896.149229097469.7328638381
464.45133181835-0.396377566859-0.09383754898322.38050974111.176211403344.14149254042-0.606600823406-0.237768556502-1.442451908260.1867251982220.2187419705520.5203030346290.150441697032-0.1603106969820.3600597617740.4751672359790.08081005454570.3014503402810.8835647007050.1459199984671.26007383375-21.486402778292.416367572788.7773900366
475.34550022436-0.947743327173-2.869681047752.453910356921.950727925993.05349160364-0.4570517913760.185581291262-1.290948093270.169182930754-0.08670544151510.3132739854250.122135299902-0.4116472625390.5521755377690.4744440948870.0484679621390.1808751416830.9137356477340.06428368497641.14099703176-22.14848404593.269630733687.4366206584
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 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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