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- PDB-6gfi: Structure of Human Mesotrypsin in complex with APPI variant T11V/... -

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Basic information

Entry
Database: PDB / ID: 6gfi
TitleStructure of Human Mesotrypsin in complex with APPI variant T11V/M17R/I18F/F34V
Components
  • Amyloid-beta A4 protein
  • PRSS3 protein
KeywordsPROTEIN BINDING / protein protein interactions / serine proteases / amyloid protein precursor inhibitor
Function / homology
Function and homology information


Uptake of dietary cobalamins into enterocytes / antimicrobial humoral response / Alpha-defensins / amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / growth cone filopodium / microglia development / collateral sprouting in absence of injury / Formyl peptide receptors bind formyl peptides and many other ligands ...Uptake of dietary cobalamins into enterocytes / antimicrobial humoral response / Alpha-defensins / amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / growth cone filopodium / microglia development / collateral sprouting in absence of injury / Formyl peptide receptors bind formyl peptides and many other ligands / regulation of synapse structure or activity / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / axo-dendritic transport / regulation of Wnt signaling pathway / zymogen activation / axon midline choice point recognition / astrocyte activation involved in immune response / NMDA selective glutamate receptor signaling pathway / regulation of spontaneous synaptic transmission / mating behavior / Antimicrobial peptides / growth factor receptor binding / peptidase activator activity / Golgi-associated vesicle / PTB domain binding / Lysosome Vesicle Biogenesis / positive regulation of amyloid fibril formation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / astrocyte projection / neuron remodeling / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / positive regulation of protein metabolic process / dendrite development / TRAF6 mediated NF-kB activation / modulation of excitatory postsynaptic potential / Advanced glycosylation endproduct receptor signaling / signaling receptor activator activity / The NLRP3 inflammasome / negative regulation of long-term synaptic potentiation / main axon / transition metal ion binding / regulation of multicellular organism growth / trypsin / intracellular copper ion homeostasis / regulation of presynapse assembly / ECM proteoglycans / positive regulation of T cell migration / endothelial cell migration / neuronal dense core vesicle / Purinergic signaling in leishmaniasis infection / positive regulation of chemokine production / digestion / cellular response to manganese ion / clathrin-coated pit / Notch signaling pathway / extracellular matrix organization / neuron projection maintenance / serine-type peptidase activity / Mitochondrial protein degradation / astrocyte activation / ionotropic glutamate receptor signaling pathway / axonogenesis / response to interleukin-1 / positive regulation of mitotic cell cycle / positive regulation of calcium-mediated signaling / protein serine/threonine kinase binding / cellular response to copper ion / platelet alpha granule lumen / cellular response to cAMP / positive regulation of glycolytic process / adult locomotory behavior / central nervous system development / positive regulation of long-term synaptic potentiation / positive regulation of interleukin-1 beta production / trans-Golgi network membrane / endosome lumen / dendritic shaft / TAK1-dependent IKK and NF-kappa-B activation / learning / positive regulation of JNK cascade / Post-translational protein phosphorylation / locomotory behavior / microglial cell activation / serine-type endopeptidase inhibitor activity / regulation of long-term neuronal synaptic plasticity / positive regulation of non-canonical NF-kappaB signal transduction / synapse organization / cellular response to nerve growth factor stimulus / visual learning / recycling endosome / response to lead ion / positive regulation of interleukin-6 production / Golgi lumen / cognition / endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of inflammatory response / cellular response to amyloid-beta / neuron projection development
Similarity search - Function
Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide ...Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site / Beta-amyloid precursor protein C-terminus / Amyloid precursor protein (APP) intracellular domain signature. / Amyloidogenic glycoprotein, extracellular / Amyloidogenic glycoprotein, heparin-binding / Amyloidogenic glycoprotein, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / Amyloid A4 N-terminal heparin-binding / E2 domain of amyloid precursor protein / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / amyloid A4 / Amyloidogenic glycoprotein / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / : / Few Secondary Structures / Irregular / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / PH-like domain superfamily / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Amyloid-beta precursor protein / Trypsin-3 / trypsin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsShahar, A. / Cohen, I. / Radisky, E. / Papo, N. / Naftaly, S.
Funding support Israel, 1items
OrganizationGrant numberCountry
2015134 Israel
CitationJournal: Nat Commun / Year: 2018
Title: Mapping protein selectivity landscapes using multi-target selective screening and next-generation sequencing of combinatorial libraries.
Authors: Naftaly, S. / Cohen, I. / Shahar, A. / Hockla, A. / Radisky, E.S. / Papo, N.
History
DepositionApr 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PRSS3 protein
E: Amyloid-beta A4 protein
B: PRSS3 protein
C: Amyloid-beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9475
Polymers66,8854
Non-polymers621
Water21612
1
A: PRSS3 protein
E: Amyloid-beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5053
Polymers33,4422
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-3 kcal/mol
Surface area12510 Å2
MethodPISA
2
B: PRSS3 protein
C: Amyloid-beta A4 protein


Theoretical massNumber of molelcules
Total (without water)33,4422
Polymers33,4422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-7 kcal/mol
Surface area12380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.215, 53.215, 237.163
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein PRSS3 protein


Mass: 24257.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRSS3
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q8N2U3, UniProt: P35030*PLUS
#2: Protein Amyloid-beta A4 protein / ABPP / APPI / APP / Alzheimer disease amyloid protein / Amyloid precursor protein / Amyloid-beta ...ABPP / APPI / APP / Alzheimer disease amyloid protein / Amyloid precursor protein / Amyloid-beta precursor protein / Cerebral vascular amyloid peptide / CVAP / PreA4 / Protease nexin-II / PN-II


Mass: 9185.026 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APP, A4, AD1 / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: P05067
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.9 Å3/Da / Density % sol: 57.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Sodium Chloride, 0.1M Bis-Tris pH 6.8 , 1.42M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.3→46.09 Å / Num. obs: 33309 / % possible obs: 99.7 % / Redundancy: 8.3 % / Rpim(I) all: 0.033 / Net I/σ(I): 10.9
Reflection shellResolution: 2.3→2.38 Å / Rpim(I) all: 0.269

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C67

5c67


Resolution: 2.3→46.086 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 37.89
RfactorNum. reflection% reflection
Rfree0.3012 3935 5.95 %
Rwork0.2454 --
obs0.2488 33190 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→46.086 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4251 0 4 12 4267
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134375
X-RAY DIFFRACTIONf_angle_d1.2765950
X-RAY DIFFRACTIONf_dihedral_angle_d8.4122939
X-RAY DIFFRACTIONf_chiral_restr0.075637
X-RAY DIFFRACTIONf_plane_restr0.007776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2985-2.32650.4587970.41011764X-RAY DIFFRACTION79
2.3265-2.35590.37191400.36922208X-RAY DIFFRACTION100
2.3559-2.38690.39921400.35952252X-RAY DIFFRACTION100
2.3869-2.41960.42271440.36762331X-RAY DIFFRACTION100
2.4196-2.45420.43451280.32752138X-RAY DIFFRACTION99
2.4542-2.49080.36121420.34252259X-RAY DIFFRACTION100
2.4908-2.52980.3291600.30222257X-RAY DIFFRACTION100
2.5298-2.57120.35121320.3042152X-RAY DIFFRACTION99
2.5712-2.61560.34261560.28742248X-RAY DIFFRACTION100
2.6156-2.66310.35371390.31822274X-RAY DIFFRACTION99
2.6631-2.71430.36691480.30852176X-RAY DIFFRACTION100
2.7143-2.76970.39911320.31482303X-RAY DIFFRACTION100
2.7697-2.82990.35971600.32292260X-RAY DIFFRACTION100
2.8299-2.89580.36881250.30622168X-RAY DIFFRACTION100
2.8958-2.96820.36171400.28212332X-RAY DIFFRACTION100
2.9682-3.04840.32351420.26732154X-RAY DIFFRACTION100
3.0484-3.13810.34351400.29042306X-RAY DIFFRACTION100
3.1381-3.23940.33081400.29072170X-RAY DIFFRACTION100
3.2394-3.35510.33991640.27652271X-RAY DIFFRACTION100
3.3551-3.48940.33281370.25312226X-RAY DIFFRACTION100
3.4894-3.64810.30331440.23542195X-RAY DIFFRACTION100
3.6481-3.84040.26251250.23552314X-RAY DIFFRACTION99
3.8404-4.08090.26471360.23432246X-RAY DIFFRACTION100
4.0809-4.39570.26641520.21482255X-RAY DIFFRACTION100
4.3957-4.83760.28591480.19672270X-RAY DIFFRACTION100
4.8376-5.53670.28721360.20772171X-RAY DIFFRACTION100
5.5367-6.97170.27881440.22892226X-RAY DIFFRACTION100
6.9717-46.09480.24621440.20742268X-RAY DIFFRACTION100
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)
12.996-2.047-0.54853.4642-1.0461.6-0.6016-0.7040.57760.65130.36090.2419-0.88810.7120.04990.8201-0.01840.08340.7511-0.0810.4642-41.441820.4391-1.8341
22.31331.13430.61431.6464-1.71266.76210.36260.2594-0.06630.207-0.2211-0.3086-0.22681.4918-0.24280.90830.07620.08571.0236-0.15790.5322-37.359510.7718-7.8977
34.4191-0.6412-0.36294.9942-2.09122.5057-0.39520.10750.4436-0.7886-0.28450.05741.67270.9879-0.63290.9033-0.0466-0.03550.72290.10420.5071-53.2152-2.0204-3.9699
41.72491.5231-0.38891.4403-0.23053.34320.47130.571-0.0571-1.0489-0.41830.1888-0.86071.481-0.16640.32650.36930.02881.0951-0.21460.4795-32.62829.79020.0548
54.76620.21291.14026.7416-4.83056.43850.8-0.2886-0.19240.8964-0.6474-0.5761-0.8313-0.2031-0.29720.75870.0318-0.09120.8483-0.00620.5359-49.30313.10110.5411
66.6703-1.11130.17062.74640.9894.1301-0.36051.28190.82440.4710.09760.1189-2.13660.968-0.19080.63640.01410.05570.8944-0.0670.5231-50.297623.833-9.3283
74.68951.4679-1.99092.32-0.34623.927-0.2581-2.7547-0.7041.0977-0.30860.1614-0.5052-0.24670.22950.65950.09950.31321.45090.17190.6315-58.066514.51356.9118
82.1184-1.5653-0.51692.7161.49542.9220.2338-0.21420.21020.2256-0.19790.00160.3263-0.2296-0.00930.71210.02150.03870.61360.00570.418-52.3659.00522.2854
92.87110.3319-3.08477.224-1.5256.5199-0.18061.1785-0.8435-1.96090.2834-0.0487-0.2924-0.9450.40361.4980.4496-0.09981.0351-0.24340.7724-66.24974.551-27.3344
107.0523-4.5042-1.52724.9998-2.47725.9424-0.0014-0.0317-0.89740.33130.77650.2231-0.78371.2956-0.57110.7617-0.00670.07670.6236-0.09750.3998-58.315911.6189-14.0079
112.22850.71980.1687.611-0.66645.22950.04961.1371-0.8214-0.20630.0714-0.8868-1.75890.4821-0.05950.63570.12760.17990.4122-0.08270.6416-55.281511.7017-23.989
127.5089-3.53752.52146.34-2.08171.99431.28880.87070.4025-2.4096-0.0192-0.5425-0.6346-0.0673-0.84381.04630.19030.14650.866-0.15980.68-58.490514.6003-26.2461
137.702-4.5826-6.29824.02083.03471.99620.1352-0.33020.14-0.20530.18760.3853-2.17471.263-0.2090.65370.28650.00880.86310.1010.5612-56.83145.835-20.463
147.4681-0.51016.19888.0326-0.90615.14261.3988-0.37180.0784-0.32860.20821.0383-0.8712-0.4557-0.12070.94440.19550.25980.7522-0.1460.3962-55.80256.7595-32.4461
151.4207-0.15361.8311.47590.45993.4303-0.0781-0.52920.9895-0.63220.26310.33410.1404-2.399-0.2460.63350.09360.13240.5790.37290.2307-50.0569.100235.2629
164.41160.59440.09995.76050.75795.79160.6225-0.2702-0.71731.03920.10860.03390.6978-0.3899-0.83040.8716-0.1919-0.19940.6740.1480.5892-40.15170.925940.4129
172.14171.4876-1.78053.9999-0.71551.42540.72670.4044-0.035-0.089-0.48180.70640.6784-0.1688-0.07480.988-0.0709-0.06670.64310.22650.4133-48.64040.372141.9489
184.13892.38190.01712.311-1.06321.87770.31240.2373-0.0988-0.86720.5874-0.2507-0.51070.1671-0.27010.68410.26110.09360.7351-0.11460.727-24.88617.819137.4292
197.23843.80010.11754.886-0.28185.2713-0.00410.93430.1187-0.69280.13910.31361.2255-0.4751-0.62630.8541-0.0091-0.15040.61890.07710.4742-45.2938-3.850933.3585
202.0109-1.9151-1.05083.8924-1.54885.45830.60130.6208-0.5808-2.2588-0.23270.13750.2112-0.2885-0.15510.9886-0.09140.03650.91410.09180.4734-40.208512.266622.6961
212.6878-0.0228-0.34813.3985-0.44446.7623-0.27450.35070.2773-0.05680.3584-0.104-0.4354-0.1609-0.13960.9164-0.10780.02240.62670.08530.4942-39.259217.488332.5228
222.19540.86231.29488.8711.43575.37580.21210.7660.0184-0.58690.0598-0.981-0.30990.8753-0.57880.6464-0.0850.06910.86240.02150.493-32.72858.786831.0068
238.3323-6.08940.466.3272-0.24540.37280.41460.30052.03070.37420.9667-0.8609-2.33061.9388-1.70471.9143-0.01640.07161.034-0.21850.774-24.339423.468160.414
243.42842.40594.73017.87543.80666.5890.60631.56580.2113-0.18140.0877-0.3607-0.03481.0869-0.62440.4484-0.03280.01860.74540.16130.3624-34.126319.301847.4112
254.6709-1.02290.63964.09873.13772.78420.16670.6463-0.0471-0.5138-0.7460.17080.0186-0.07980.24090.6079-0.0167-0.0240.39820.04990.4488-36.163418.876358.453
267.66071.0177-2.93019.5605-4.87393.19080.0259-0.81570.27220.25130.937-0.1081-0.2921-1.186-0.8330.76790.0897-0.03530.605-0.03290.5831-30.588414.874559.5606
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 90 )
3X-RAY DIFFRACTION3chain 'A' and (resid 91 through 103 )
4X-RAY DIFFRACTION4chain 'A' and (resid 104 through 123 )
5X-RAY DIFFRACTION5chain 'A' and (resid 124 through 140 )
6X-RAY DIFFRACTION6chain 'A' and (resid 141 through 155 )
7X-RAY DIFFRACTION7chain 'A' and (resid 156 through 171 )
8X-RAY DIFFRACTION8chain 'A' and (resid 172 through 246 )
9X-RAY DIFFRACTION9chain 'E' and (resid 2 through 6 )
10X-RAY DIFFRACTION10chain 'E' and (resid 7 through 17 )
11X-RAY DIFFRACTION11chain 'E' and (resid 18 through 24 )
12X-RAY DIFFRACTION12chain 'E' and (resid 25 through 35 )
13X-RAY DIFFRACTION13chain 'E' and (resid 36 through 47 )
14X-RAY DIFFRACTION14chain 'E' and (resid 48 through 57 )
15X-RAY DIFFRACTION15chain 'B' and (resid 16 through 38 )
16X-RAY DIFFRACTION16chain 'B' and (resid 39 through 67 )
17X-RAY DIFFRACTION17chain 'B' and (resid 69 through 90 )
18X-RAY DIFFRACTION18chain 'B' and (resid 91 through 103 )
19X-RAY DIFFRACTION19chain 'B' and (resid 104 through 123 )
20X-RAY DIFFRACTION20chain 'B' and (resid 124 through 140 )
21X-RAY DIFFRACTION21chain 'B' and (resid 141 through 215 )
22X-RAY DIFFRACTION22chain 'B' and (resid 216 through 246 )
23X-RAY DIFFRACTION23chain 'C' and (resid 2 through 6 )
24X-RAY DIFFRACTION24chain 'C' and (resid 7 through 17 )
25X-RAY DIFFRACTION25chain 'C' and (resid 18 through 35 )
26X-RAY DIFFRACTION26chain 'C' and (resid 36 through 57 )

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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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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