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- PDB-5e9b: Crystal structure of human heparanase in complex with HepMer M09S05a -

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Basic information

Entry
Database: PDB / ID: 5e9b
TitleCrystal structure of human heparanase in complex with HepMer M09S05a
Components(Heparanase) x 2
KeywordsHYDROLASE / glycoside hydrolase / ligand 3 / protein / sugar
Function / homology
Function and homology information


heparanase / heparanase activity / regulation of hair follicle development / heparin metabolic process / proteoglycan metabolic process / heparan sulfate proteoglycan catabolic process / beta-glucuronidase activity / positive regulation of hair follicle development / HS-GAG degradation / protein transmembrane transport ...heparanase / heparanase activity / regulation of hair follicle development / heparin metabolic process / proteoglycan metabolic process / heparan sulfate proteoglycan catabolic process / beta-glucuronidase activity / positive regulation of hair follicle development / HS-GAG degradation / protein transmembrane transport / syndecan binding / vascular wound healing / angiogenesis involved in wound healing / establishment of endothelial barrier / positive regulation of osteoblast proliferation / positive regulation of vascular endothelial growth factor production / positive regulation of blood coagulation / lysosomal lumen / cell-matrix adhesion / : / extracellular matrix / specific granule lumen / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lysosome / membrane raft / lysosomal membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / extracellular space / extracellular region / nucleoplasm / nucleus
Similarity search - Function
Glycoside hydrolase, family 79 / Glycosyl hydrolase family 79, N-terminal domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsWu, L. / Davies, G.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Structural characterization of human heparanase reveals insights into substrate recognition.
Authors: Wu, L. / Viola, C.M. / Brzozowski, A.M. / Davies, G.J.
History
DepositionOct 14, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 1.2Dec 16, 2015Group: Database references
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 2.0Jul 15, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / atom_sites ...atom_site / atom_sites / atom_type / chem_comp / computing / diffrn / entity / pdbx_database_related / pdbx_database_status / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / pdbx_validate_torsion / pdbx_version / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns_shell / software / struct / struct_conf / struct_conn / struct_mon_prot_cis / struct_site / struct_site_gen
Item: _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] ..._atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] / _chem_comp.type / _diffrn.pdbx_serial_crystal_experiment / _entity.pdbx_number_of_molecules / _pdbx_database_status.deposit_site / _pdbx_struct_assembly.details / _pdbx_struct_assembly_prop.value / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_R_factor_obs / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _reflns_shell.d_res_low / _reflns_shell.number_unique_obs / _struct.pdbx_CASP_flag / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_mon_prot_cis.pdbx_omega_angle / _struct_site.pdbx_num_residues
Description: Ligand geometry / Provider: author / Type: Coordinate replacement
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Jan 10, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heparanase
B: Heparanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9087
Polymers52,2762
Non-polymers1,6325
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10690 Å2
ΔGint-44 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.990, 71.060, 78.290
Angle α, β, γ (deg.)90.000, 95.090, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Heparanase / Endo-glucoronidase / Heparanase-1 / Hpa1


Mass: 43733.324 Da / Num. of mol.: 1 / Fragment: residues 158-543
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPSE, HEP, HPA, HPA1, HPR1, HPSE1, HSE1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9Y251, heparanase
#2: Protein Heparanase / Endo-glucoronidase / Heparanase-1 / Hpa1


Mass: 8542.769 Da / Num. of mol.: 1 / Fragment: residues 36-109
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPSE, HEP, HPA, HPA1, HPR1, HPSE1, HSE1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9Y251, heparanase

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Sugars , 2 types, 4 molecules

#3: Polysaccharide 2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-6-O- ...2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid


Type: oligosaccharide / Mass: 932.764 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNSa1-4DGlcpAb1-4DGlcpNS[6S]a1-4DGlcpAb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122A-1b_1-5][a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a2122h-1a_1-5_2*NSO/3=O/3=O]/1-2-1-3/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpA]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][b-D-GlcpA]{[(4+1)][a-D-GlcpNSO3]{}}}}LINUCSPDB-CARE
#4: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
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 , 2 types, 202 molecules

#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M MES [5.5] 0.1 M MgCl2 17% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.85 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85 Å / Relative weight: 1
ReflectionResolution: 1.88→52.52 Å / Num. obs: 40880 / % possible obs: 99.8 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.1
Reflection shellResolution: 1.88→1.93 Å / Rmerge(I) obs: 1.01 / Num. unique obs: 3018

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5e8m

5e8m


Resolution: 1.88→52.52 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.505 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.133
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2172 2036 4.982 %taken from apo
Rwork0.1781 ---
all0.18 ---
obs-40866 99.715 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.236 Å2
Baniso -1Baniso -2Baniso -3
1-1.898 Å2-0 Å22.229 Å2
2---2.732 Å2-0 Å2
3---0.431 Å2
Refinement stepCycle: LAST / Resolution: 1.88→52.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3643 0 102 201 3946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133849
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173600
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.6835232
X-RAY DIFFRACTIONr_angle_other_deg1.2771.6048368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9875459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11421.868182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.30415649
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8071522
X-RAY DIFFRACTIONr_chiral_restr0.0710.2501
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024189
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02815
X-RAY DIFFRACTIONr_nbd_refined0.1980.2712
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.23268
X-RAY DIFFRACTIONr_nbtor_refined0.1670.21847
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21711
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2213
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0120.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2690.216
X-RAY DIFFRACTIONr_nbd_other0.2430.245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1170.29
X-RAY DIFFRACTIONr_mcbond_it3.1923.9561839
X-RAY DIFFRACTIONr_mcbond_other3.1923.9531838
X-RAY DIFFRACTIONr_mcangle_it4.485.9182297
X-RAY DIFFRACTIONr_mcangle_other4.4795.9222298
X-RAY DIFFRACTIONr_scbond_it3.874.5232010
X-RAY DIFFRACTIONr_scbond_other3.8734.5122002
X-RAY DIFFRACTIONr_scangle_it5.8826.5942935
X-RAY DIFFRACTIONr_scangle_other5.8816.5942936
X-RAY DIFFRACTIONr_lrange_it7.63547.2774212
X-RAY DIFFRACTIONr_lrange_other7.63447.2784213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.9290.3241660.3052847X-RAY DIFFRACTION99.6033
1.929-1.9820.3091270.2992792X-RAY DIFFRACTION99.6246
1.982-2.0390.2841390.2672713X-RAY DIFFRACTION99.9299
2.039-2.1020.2691210.2452655X-RAY DIFFRACTION99.7843
2.102-2.1710.26990.2242583X-RAY DIFFRACTION99.8511
2.171-2.2470.2531260.212463X-RAY DIFFRACTION99.6919
2.247-2.3310.2451250.2042376X-RAY DIFFRACTION99.96
2.331-2.4270.281350.1772311X-RAY DIFFRACTION99.7146
2.427-2.5340.2391240.1712181X-RAY DIFFRACTION99.6972
2.534-2.6580.228890.1712112X-RAY DIFFRACTION99.9092
2.658-2.8020.2371160.1742005X-RAY DIFFRACTION99.6711
2.802-2.9710.2331030.1761884X-RAY DIFFRACTION99.8994
2.971-3.1760.242890.1741795X-RAY DIFFRACTION99.894
3.176-3.430.2161080.1831654X-RAY DIFFRACTION99.83
3.43-3.7570.222900.1641526X-RAY DIFFRACTION99.6915
3.757-4.1990.169870.1341392X-RAY DIFFRACTION99.6631
4.199-4.8460.179570.1411232X-RAY DIFFRACTION99.7678
4.846-5.930.139560.1521047X-RAY DIFFRACTION99.6387
5.93-8.3610.186420.155807X-RAY DIFFRACTION98.951
8.361-52.520.2370.167455X-RAY DIFFRACTION98.5972

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