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- PDB-9o29: Heparanase P6 in complex with fragment J61 -

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Basic information

Entry
Database: PDB / ID: 9o29
TitleHeparanase P6 in complex with fragment J61
Components
  • Heparanase 50 kDa subunit
  • Heparanase 8 kDa subunit
KeywordsHYDROLASE / Heparanase / small molecule / cancer / complex / therapeutics
Function / homology
Function and homology information


heparanase / heparanase activity / regulation of hair follicle development / heparin proteoglycan metabolic process / heparan sulfate proteoglycan catabolic process / beta-glucuronidase activity / HS-GAG degradation / positive regulation of hair follicle development / syndecan binding / proteoglycan metabolic process ...heparanase / heparanase activity / regulation of hair follicle development / heparin proteoglycan metabolic process / heparan sulfate proteoglycan catabolic process / beta-glucuronidase activity / HS-GAG degradation / positive regulation of hair follicle development / 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 / lysosomal lumen / cell-matrix adhesion / extracellular matrix / specific granule lumen / lysosome / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / membrane raft / intracellular membrane-bounded organelle / lysosomal membrane / response to antibiotic / 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
NICOTINAMIDE / Heparanase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDavies, L.J. / Frkic, R.L. / Jackson, C.J.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)CE200100012 Australia
Australian Research Council (ARC)CE200100029 Australia
CitationJournal: Acs Med.Chem.Lett. / Year: 2026
Title: Fragment Screening and Structure-Guided Development of Heparanase Inhibitors Reveal Orthosteric and Allosteric Inhibition
Authors: Davies, L.J. / Whitefield, C. / Kim, H. / Nitsche, C. / Jackson, C.J. / Frkic, R.L.
History
DepositionApr 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)51,9589
Polymers51,2602
Non-polymers6997
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9410 Å2
ΔGint-130 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.540, 74.038, 124.999
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Heparanase 50 kDa subunit


Mass: 42986.309 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 (E. coli) / References: UniProt: Q9Y251
#2: Protein Heparanase 8 kDa subunit


Mass: 8273.514 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 (E. coli) / References: UniProt: Q9Y251
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NCA / NICOTINAMIDE


Mass: 122.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N2O / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
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: 2.69 Å3/Da / Density % sol: 54.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium sulfate, 0.1 M ammoniuma acetate, 25% 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: Feb 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→46.4 Å / Num. obs: 28829 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.991 / Rmerge(I) obs: 0.432 / Rpim(I) all: 0.12 / Rrim(I) all: 0.449 / Χ2: 0.97 / Net I/σ(I): 6 / Num. measured all: 392407
Reflection shellResolution: 2.2→2.27 Å / % possible obs: 100 % / Redundancy: 14.2 % / Rmerge(I) obs: 4.927 / Num. measured all: 34746 / Num. unique obs: 2450 / CC1/2: 0.312 / Rpim(I) all: 1.342 / Rrim(I) all: 5.109 / Χ2: 0.93 / Net I/σ(I) obs: 0.9

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→37.25 Å / SU ML: 0.28 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 26.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2404 1380 4.8 %
Rwork0.2026 --
obs0.2045 28743 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→37.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3620 0 39 159 3818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.874
X-RAY DIFFRACTIONf_dihedral_angle_d15.0711368
X-RAY DIFFRACTIONf_chiral_restr0.052554
X-RAY DIFFRACTIONf_plane_restr0.007646
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.280.34291500.31612664X-RAY DIFFRACTION100
2.28-2.370.35151290.28342704X-RAY DIFFRACTION100
2.37-2.480.321160.26562710X-RAY DIFFRACTION100
2.48-2.610.28981340.24532707X-RAY DIFFRACTION100
2.61-2.770.27511260.23542717X-RAY DIFFRACTION100
2.77-2.990.3051360.22692739X-RAY DIFFRACTION100
2.99-3.290.24491710.20472680X-RAY DIFFRACTION100
3.29-3.760.19391340.16712759X-RAY DIFFRACTION100
3.76-4.740.17241370.15182767X-RAY DIFFRACTION99
4.74-37.250.22651470.19052916X-RAY DIFFRACTION100

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