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- PDB-3czu: Crystal structure of the human ephrin A2- ephrin A1 complex -

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Basic information

Entry
Database: PDB / ID: 3czu
TitleCrystal structure of the human ephrin A2- ephrin A1 complex
Components
  • Ephrin type-A receptor 2
  • Ephrin-A1
KeywordsTRANSFERASE/SIGNALING PROTEIN / ATP-BINDING / KINASE / NUCLEOTIDE-BINDING / RECEPTOR / TRANSFERASE / PHOSPHORYLATION / TRANSMEMBRANE / TYROSINE-PROTEIN KINASE / GLYCOPROTEIN / STRUCTURAL GENOMICS CONSORTIUM / SGC / PHOSPHOPROTEIN / GPI-anchor / Lipoprotein / TRANSFERASE-SIGNALING PROTEIN COMPLEX
Function / homology
Function and homology information


endocardial cushion to mesenchymal transition involved in heart valve formation / negative regulation of dendritic spine morphogenesis / negative regulation of proteolysis involved in protein catabolic process / positive regulation of amyloid precursor protein catabolic process / notochord cell development / mitral valve morphogenesis / notochord formation / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / lens fiber cell morphogenesis / negative regulation of lymphangiogenesis ...endocardial cushion to mesenchymal transition involved in heart valve formation / negative regulation of dendritic spine morphogenesis / negative regulation of proteolysis involved in protein catabolic process / positive regulation of amyloid precursor protein catabolic process / notochord cell development / mitral valve morphogenesis / notochord formation / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / lens fiber cell morphogenesis / negative regulation of lymphangiogenesis / axial mesoderm formation / cAMP metabolic process / regulation of blood vessel endothelial cell migration / pericyte cell differentiation / leading edge membrane / negative regulation of chemokine production / response to growth factor / post-anal tail morphogenesis / activation of GTPase activity / bone remodeling / positive regulation of bicellular tight junction assembly / regulation of lamellipodium assembly / negative regulation of thymocyte apoptotic process / branching involved in mammary gland duct morphogenesis / EPH-Ephrin signaling / aortic valve morphogenesis / tight junction / RND1 GTPase cycle / RND2 GTPase cycle / neural tube development / RND3 GTPase cycle / regulation of peptidyl-tyrosine phosphorylation / positive regulation of peptidyl-tyrosine phosphorylation / mammary gland epithelial cell proliferation / negative regulation of epithelial to mesenchymal transition / positive regulation of amyloid-beta formation / regulation of axonogenesis / RHOV GTPase cycle / EPHA-mediated growth cone collapse / growth factor binding / regulation of cell adhesion mediated by integrin / positive regulation of intracellular signal transduction / RHOU GTPase cycle / lamellipodium membrane / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / placental growth factor receptor activity / hepatocyte growth factor receptor activity / boss receptor activity / stem cell factor receptor activity / platelet-derived growth factor beta-receptor activity / brain-derived neurotrophic factor receptor activity / platelet-derived growth factor alpha-receptor activity / epidermal growth factor receptor activity / macrophage colony-stimulating factor receptor activity / protein tyrosine kinase collagen receptor activity / RAC2 GTPase cycle / RAC3 GTPase cycle / regulation of angiogenesis / transmembrane-ephrin receptor activity / insulin-like growth factor receptor activity / ephrin receptor signaling pathway / vascular endothelial growth factor receptor activity / GPI-linked ephrin receptor activity / regulation of ERK1 and ERK2 cascade / vasculogenesis / fibroblast growth factor receptor activity / negative regulation of MAPK cascade / keratinocyte differentiation / side of membrane / insulin receptor activity / ephrin receptor binding / transmembrane receptor protein tyrosine kinase activity / RAC1 GTPase cycle / substrate adhesion-dependent cell spreading / axon guidance / osteoclast differentiation / cell surface receptor protein tyrosine kinase signaling pathway / negative regulation of angiogenesis / molecular function activator activity / skeletal system development / protein localization to plasma membrane / cell chemotaxis / positive regulation of protein localization to plasma membrane / cell motility / receptor protein-tyrosine kinase / ruffle membrane / neuron differentiation / intrinsic apoptotic signaling pathway in response to DNA damage / osteoblast differentiation / cell migration / cell-cell signaling / lamellipodium / virus receptor activity / angiogenesis / receptor complex / cell adhesion / positive regulation of MAPK cascade / defense response to Gram-positive bacterium / protein stabilization
Similarity search - Function
Ephrin-A ectodomain / Ephrin receptor-binding domain / Ephrin, conserved site / Ephrin / Ephrin / Ephrin receptor-binding (ephrin RBD) domain signature. / Ephrin receptor-binding (ephrin RBD) domain profile. / Ephrin type-A receptor 2, ligand binding domain / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain ...Ephrin-A ectodomain / Ephrin receptor-binding domain / Ephrin, conserved site / Ephrin / Ephrin / Ephrin receptor-binding (ephrin RBD) domain signature. / Ephrin receptor-binding (ephrin RBD) domain profile. / Ephrin type-A receptor 2, ligand binding domain / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / : / Ephrin receptor ligand binding domain / Ephrin type-A receptor 2 transmembrane domain / Receptor tyrosine kinase class V signature 1. / Receptor tyrosine kinase class V signature 2. / Eph receptor ligand-binding domain profile. / Ephrin receptor ligand binding domain / Putative ephrin-receptor like / SAM domain (Sterile alpha motif) / Galactose-binding domain-like / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Cupredoxins - blue copper proteins / Sterile alpha motif/pointed domain superfamily / Growth factor receptor cysteine-rich domain superfamily / Fibronectin type III domain / Cupredoxin / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Jelly Rolls / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ephrin-A1 / Ephrin type-A receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsWalker, J.R. / Yermekbayeva, L. / Seitova, A. / Butler-Cole, C. / Bountra, C. / Wikstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Architecture of Eph receptor clusters.
Authors: Himanen, J.P. / Yermekbayeva, L. / Janes, P.W. / Walker, J.R. / Xu, K. / Atapattu, L. / Rajashankar, K.R. / Mensinga, A. / Lackmann, M. / Nikolov, D.B. / Dhe-Paganon, S.
History
DepositionApr 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ephrin type-A receptor 2
B: Ephrin-A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6963
Polymers45,1092
Non-polymers5871
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-10.6 kcal/mol
Surface area15040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.431, 99.431, 204.879
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Ephrin type-A receptor 2 / Tyrosine-protein kinase receptor ECK / Epithelial cell kinase


Mass: 23639.592 Da / Num. of mol.: 1 / Fragment: Ligand binding domain: Residues 23-202
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA2, ECK / Plasmid: PFHMSP-LIC-N / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: P29317, receptor protein-tyrosine kinase
#2: Protein Ephrin-A1 / EPH-related receptor tyrosine kinase ligand 1 / LERK-1 / Immediate early response protein B61 / ...EPH-related receptor tyrosine kinase ligand 1 / LERK-1 / Immediate early response protein B61 / Tumor necrosis factor / alpha-induced protein 4


Mass: 21469.766 Da / Num. of mol.: 1 / Fragment: Residues 17-171
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EFNA1, EPLG1, LERK1, TNFAIP4 / Plasmid: PFHMSP-LIC-N / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P20827
#3: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAUTHORS STATE THAT THE CORRECT SEQUENCE IS PROVIDED IN GENBANK ENTRY NP_004422.

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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: 3.24 Å3/Da / Density % sol: 62.04 %
Crystal growTemperature: 290.9 K / pH: 5.6
Details: 14.9% PEG 4000, 0.1M Sodium citrate pH 5.6, 20% Isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 290.9K, pH 5.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 10, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.65→25 Å / Num. obs: 18122 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 20.8 % / Rsym value: 0.109 / Net I/σ(I): 35.74
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 21.2 % / Mean I/σ(I) obs: 5.509 / Rsym value: 0.714 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3C8X, 1SHW

3c8x

1shw


Resolution: 2.65→24.86 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / SU B: 17.245 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.325 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.22533 938 5.2 %RANDOM
Rwork0.19343 ---
obs0.19507 17120 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.445 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20.09 Å20 Å2
2--0.19 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.65→24.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2473 0 39 72 2584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212606
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.9493542
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.595306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.8923.985133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.55715415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.661514
X-RAY DIFFRACTIONr_chiral_restr0.0870.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022008
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1910.2972
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21732
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1020.2110
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.221
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.00631565
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.70342466
X-RAY DIFFRACTIONr_scbond_it2.20651198
X-RAY DIFFRACTIONr_scangle_it3.5971076
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.721 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 62 -
Rwork0.249 1212 -
obs--99.53 %
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)
13.3913-6.5392-1.006812.71921.0797.04820.6961-0.3725-1.3543-0.50380.04841.21960.3602-0.5992-0.74450.2015-0.09150.06450.1889-0.0280.3155-58.1074-6.609812.2467
29.795-0.78840.633413.0796-1.38984.5110.28070.71980.3649-0.8784-0.0942-0.9349-0.01680.6224-0.18660.29630.0450.13080.2449-0.06470.1596-41.0256-1.08448.6363
313.173-7.6568-3.1975.65755.274410.4444-0.8329-0.3386-1.1570.37860.67140.77720.6939-0.63130.16150.2841-0.06170.06890.1342-0.0420.1587-44.8404-16.921718.66
43.2395-1.87542.48246.7864-3.93146.47020.06550.27690.61570.7532-0.1249-0.3638-0.57780.75530.05940.2541-0.06860.12140.1541-0.08630.2018-37.76611.405916.6161
52.6589-0.8529-0.29312.4419-0.4493.20060.11890.21560.17760.0225-0.08150.568-0.284-0.7301-0.03740.19820.03290.10430.2147-0.03360.272-54.51381.659615.1282
612.35814.634220.34310.763516.768542.743-1.3111.04061.8369-1.32460.2845-2.4803-2.40733.61131.02650.59-0.03880.01640.6596-0.07570.5702-30.15251.525930.7857
73.0808-1.66152.67853.0902-3.0411.2399-0.0735-0.09150.5740.23550.0943-0.0464-0.797-0.293-0.02080.2363-0.02990.10510.0067-0.08360.2551-47.51627.684215.3629
84.3884-0.88713.21137.3115-2.99610.1233-0.113-0.6685-0.40421.36720.0492-0.33310.30080.3730.06380.2895-0.06410.06250.1002-0.01880.1057-43.2074-9.494630.6354
96.2965-4.47190.28646.60671.34320.71030.3164-0.39210.21780.0650.55381.3658-1.7703-1.4517-0.87020.26280.10120.16860.2055-0.01470.3701-60.87769.110813.0299
104.2582-1.82070.45124.9406-0.94832.91590.1409-0.1205-0.00260.09990.090.4754-0.2401-0.5194-0.23090.22590.03770.12580.2002-0.0740.2058-53.22731.317115.5057
115.4551-0.27260.39899.66867.18257.8113-0.17910.63280.1007-0.85230.3557-0.6125-0.2390.4141-0.17660.1868-0.00260.18420.2668-0.06130.1518-29.0548-20.68084.4233
123.1405-0.3241.653124.279214.775210.08310.0195-0.0786-0.1378-0.84360.1714-1.69190.34861.154-0.1910.1627-0.05520.24220.3399-0.09230.2854-21.6639-25.66668.3968
132.01830.55321.13162.91271.51135.55990.20790.62150.5135-0.6241-0.0536-0.5588-0.23170.7008-0.15430.1832-0.06010.1160.1656-0.05680.2334-30.7129-14.46338.5813
1410.42664.25160.209510.84052.755315.39410.21451.0351-0.216-1.63270.09220.38290.5432-0.8853-0.30680.31730.0601-0.07060.1509-0.02870.102-41.9904-31.05281.0843
1512.1341-3.0962-3.505513.8983-0.68571.20320.0822-1.99920.16480.54960.0526-1.38720.2612-0.3032-0.13490.15030.0024-0.00130.2484-0.04160.1402-29.5248-25.474121.5982
164.0695-2.2309-1.226410.9653-2.7734.90570.1587-0.27920.02670.5904-0.0289-0.22250.06910.2817-0.12980.1612-0.06260.01310.1645-0.10360.1353-34.237-26.409420.5791
1710.634-1.097-0.70298.0814-7.85257.92860.19950.08071.0434-0.5520.05680.805-0.9114-0.1234-0.25630.37830.0356-0.02720.0345-0.03530.2437-45.0779-22.41132.9885
1810.95489.12425.148316.004611.384711.3982-0.1606-0.45970.7622-0.29140.0540.2411-0.3560.2640.10650.1690.02230.06290.1481-0.06130.2538-33.3563-12.523913.7938
1923.1796.3562-10.00351.8734-2.23456.3017-0.4075-0.9039-0.4803-0.33270.4891-0.5081-0.56010.3747-0.08150.2739-0.08420.00090.2103-0.11530.1863-35.6191-10.162524.1578
204.26342.1371-0.12368.62550.31261.7810.00120.11350.0052-0.08710.2285-0.8577-0.00920.5573-0.22970.13730.00110.04950.3179-0.03410.1896-28.2023-24.467115.2514
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA27 - 3932 - 44
2X-RAY DIFFRACTION2AA40 - 5445 - 59
3X-RAY DIFFRACTION3AA55 - 6460 - 69
4X-RAY DIFFRACTION4AA65 - 8170 - 86
5X-RAY DIFFRACTION5AA82 - 10587 - 110
6X-RAY DIFFRACTION6AA106 - 113111 - 118
7X-RAY DIFFRACTION7AA114 - 152119 - 157
8X-RAY DIFFRACTION8AA153 - 166158 - 171
9X-RAY DIFFRACTION9AA167 - 176172 - 181
10X-RAY DIFFRACTION10AA177 - 201182 - 206
11X-RAY DIFFRACTION11BB18 - 3029 - 41
12X-RAY DIFFRACTION12BB31 - 4042 - 51
13X-RAY DIFFRACTION13BB41 - 5352 - 64
14X-RAY DIFFRACTION14BB54 - 6865 - 79
15X-RAY DIFFRACTION15BB69 - 7680 - 87
16X-RAY DIFFRACTION16BB77 - 9188 - 102
17X-RAY DIFFRACTION17BB92 - 101103 - 112
18X-RAY DIFFRACTION18BB102 - 110113 - 121
19X-RAY DIFFRACTION19BB111 - 119122 - 130
20X-RAY DIFFRACTION20BB120 - 149131 - 160

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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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