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- PDB-8e07: Crystal structure of HPSE P6 in complex with triose pentosan inhibitor -

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Basic information

Entry
Database: PDB / ID: 80000000
TitleCrystal structure of HPSE P6 in complex with triose pentosan inhibitor
Components
  • Heparanase 50 kDa subunit
  • Heparanase 8 kDa subunit
KeywordsHYDROLASE / Heparanase / Heparan Sulfate / Pentosan Polysulfate Sodium
Function / homology
Function and homology information


heparanase / heparanase activity / regulation of hair follicle development / heparin proteoglycan metabolic process / heparan sulfate proteoglycan catabolic process / positive regulation of hair follicle development / HS-GAG degradation / beta-glucuronidase activity / syndecan binding / proteoglycan metabolic process ...heparanase / heparanase activity / regulation of hair follicle development / heparin proteoglycan metabolic process / heparan sulfate proteoglycan catabolic process / positive regulation of hair follicle development / HS-GAG degradation / beta-glucuronidase activity / syndecan binding / proteoglycan metabolic process / vascular wound healing / protein transmembrane transport / establishment of endothelial barrier / angiogenesis involved in wound healing / positive regulation of osteoblast proliferation / positive regulation of vascular endothelial growth factor production / positive regulation of blood coagulation / extracellular matrix / lysosomal lumen / cell-matrix adhesion / specific granule lumen / lysosome / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / membrane raft / lysosomal membrane / response to antibiotic / 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 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / AMMONIUM ION / Heparanase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWhitefield, C. / Jackson, C.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)LP160101552 Australia
CitationJournal: Biochemistry / Year: 2023
Title: Complex Inhibitory Mechanism of Glycomimetics with Heparanase.
Authors: Whitefield, C. / Vo, Y. / Schwartz, B.D. / Hepburn, C. / Ahmed, F.H. / Onagi, H. / Banwell, M.G. / Nelms, K. / Malins, L.R. / Jackson, C.J.
History
DepositionAug 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Oct 25, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 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

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Assembly

Deposited unit
A: Heparanase 50 kDa subunit
B: Heparanase 8 kDa subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,15011
Polymers53,6432
Non-polymers2,5079
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10690 Å2
ΔGint-206 kcal/mol
Surface area18750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.536, 76.195, 124.965
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Heparanase 50 kDa subunit


Mass: 43375.863 Da / Num. of mol.: 1
Mutation: N178K, A195S, L197G, S212A, S219D, L230R, D234G, E244K, Q248H, R273G, S292A, R307L, I318T, S322Q, F327L, L354G, S426Q, K427D, K477Q, L483H, H486D, L498Q, M512K, E513P, S530A, A540P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPSE, HEP, HPA, HPA1, HPR1, HPSE1, HSE1 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q9Y251
#2: Protein Heparanase 8 kDa subunit


Mass: 10267.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPSE, HEP, HPA, HPA1, HPR1, HPSE1, HSE1 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q9Y251

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Sugars , 1 types, 2 molecules

#3: Polysaccharide 2,3,4-tri-O-sulfo-beta-D-xylopyranose-(1-4)-2,3-di-O-sulfo-beta-D-xylopyranose-(1-4)-2,3-di-O-sulfo- ...2,3,4-tri-O-sulfo-beta-D-xylopyranose-(1-4)-2,3-di-O-sulfo-beta-D-xylopyranose-(1-4)-2,3-di-O-sulfo-beta-D-xylopyranose


Type: oligosaccharide / Mass: 974.802 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
[][b-D-Xylp2SO33SO3]{[(4+1)][b-D-Xylp2SO33SO3]{[(4+1)][b-D-Xylp2SO33SO34SO3]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 375 molecules

#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.64 Å3/Da / Density % sol: 53.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2M Ammonium Sulfate, Sodium Acetate pH 5.5, 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→46.91 Å / Num. obs: 53337 / % possible obs: 99.6 % / Redundancy: 10.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.029 / Rrim(I) all: 0.097 / Χ2: 0.85 / Net I/σ(I): 14.8 / Num. measured all: 560186
Reflection shellResolution: 1.8→1.84 Å / % possible obs: 97.1 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.944 / Num. measured all: 32591 / Num. unique obs: 3029 / CC1/2: 0.92 / Rpim(I) all: 0.299 / Rrim(I) all: 0.992 / Χ2: 0.47 / Net I/σ(I) obs: 3.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RG8

7rg8


Resolution: 1.8→46.91 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2033 2713 5.1 %
Rwork0.1718 --
obs0.1734 53145 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→46.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3629 0 142 368 4139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063912
X-RAY DIFFRACTIONf_angle_d0.8465336
X-RAY DIFFRACTIONf_dihedral_angle_d13.1741424
X-RAY DIFFRACTIONf_chiral_restr0.057586
X-RAY DIFFRACTIONf_plane_restr0.006658
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.27421470.21112581X-RAY DIFFRACTION99
1.83-1.870.21961290.19832606X-RAY DIFFRACTION98
1.87-1.910.2391330.21232640X-RAY DIFFRACTION100
1.91-1.950.27411510.22712541X-RAY DIFFRACTION98
1.95-1.990.22641580.19792600X-RAY DIFFRACTION99
1.99-2.040.19971360.18682641X-RAY DIFFRACTION100
2.04-2.10.21681320.18572638X-RAY DIFFRACTION99
2.1-2.160.19861380.18472605X-RAY DIFFRACTION99
2.16-2.230.20851350.18282645X-RAY DIFFRACTION100
2.23-2.310.24781380.20292636X-RAY DIFFRACTION99
2.31-2.40.2341370.18062648X-RAY DIFFRACTION100
2.4-2.510.2331290.18992658X-RAY DIFFRACTION100
2.51-2.640.20661430.1782651X-RAY DIFFRACTION100
2.64-2.810.21481330.18122688X-RAY DIFFRACTION100
2.81-3.030.21531590.17932670X-RAY DIFFRACTION100
3.03-3.330.22661620.17532683X-RAY DIFFRACTION100
3.33-3.810.19251570.15032684X-RAY DIFFRACTION100
3.81-4.80.16411400.13412756X-RAY DIFFRACTION100
4.8-46.910.16721560.16712861X-RAY DIFFRACTION100

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