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- PDB-9o2m: Heparanase P6 in complex with fragment C5A -

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Basic information

Entry
Database: PDB / ID: 9o2m
TitleHeparanase P6 in complex with fragment C5A
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
2-PHENYL-1H-IMIDAZOLE-4,5-DICARBOXYLIC ACID / Heparanase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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)51,4923
Polymers51,2602
Non-polymers2321
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8120 Å2
ΔGint-56 kcal/mol
Surface area18460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.561, 75.849, 124.868
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-4F8 / 2-PHENYL-1H-IMIDAZOLE-4,5-DICARBOXYLIC ACID


Mass: 232.192 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H8N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.75 Å3/Da / Density % sol: 55.29 %
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: Mar 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→48.2 Å / Num. obs: 48101 / % possible obs: 98.6 % / Redundancy: 13.2 % / CC1/2: 0.488 / Rmerge(I) obs: 2.151 / Rpim(I) all: 0.683 / Rrim(I) all: 2.273 / Χ2: 0.97 / Net I/σ(I): 4.8
Reflection shellResolution: 2→2.05 Å / Redundancy: 13.2 % / Num. unique obs: 2703 / CC1/2: 0.486 / Rpim(I) all: 6.666 / Rrim(I) all: 21.968 / Χ2: 0.94

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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→48.2 Å / SU ML: 0.19 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 20.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1987 1992 5.16 %
Rwork0.162 --
obs0.1638 38577 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3620 0 17 285 3922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_angle_d0.795
X-RAY DIFFRACTIONf_dihedral_angle_d13.9771404
X-RAY DIFFRACTIONf_chiral_restr0.049561
X-RAY DIFFRACTIONf_plane_restr0.006666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.27171380.20242424X-RAY DIFFRACTION93
2.05-2.110.24951420.17982545X-RAY DIFFRACTION100
2.11-2.170.20031490.16982578X-RAY DIFFRACTION100
2.17-2.240.23141340.162616X-RAY DIFFRACTION100
2.24-2.320.221310.16512583X-RAY DIFFRACTION100
2.32-2.410.18661400.17252598X-RAY DIFFRACTION100
2.41-2.520.25381580.17272598X-RAY DIFFRACTION100
2.52-2.660.21231510.16652595X-RAY DIFFRACTION100
2.66-2.820.1971440.16832622X-RAY DIFFRACTION100
2.82-3.040.18661480.16722613X-RAY DIFFRACTION100
3.04-3.350.19411380.17272637X-RAY DIFFRACTION100
3.35-3.830.20371340.1482667X-RAY DIFFRACTION100
3.83-4.830.15641170.13542716X-RAY DIFFRACTION100
4.83-48.20.19421680.17382793X-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)
14.05440.58850.54491.5762-0.14052.87560.02190.3190.0458-0.12590.02430.0639-0.00560.0878-0.03460.21710.02210.01540.1240.00320.17711.39549.41350.989
23.80390.3773-0.71041.4534-0.51263.00030.01830.0311-0.2467-0.13570.04780.08560.2155-0.0715-0.04280.2457-0.0065-0.04420.16870.01290.2483-5.39594.02733.6178
34.7771-0.02690.05884.25080.34424.9716-0.00530.1304-0.33960.18830.00940.09190.63880.00350.08820.2528-0.0073-0.00070.2060.04670.2518-3.1371.6312.0603
42.17540.46780.11651.0405-0.30681.52920.0337-0.2860.01510.0787-0.05150.1128-0.032-0.02360.01410.22040.03040.02070.20530.02640.21313.204810.638923.8109
51.89910.54521.42214.6482-0.82743.7294-0.0661-0.5971-0.47120.2959-0.0855-0.11820.12060.3240.22290.295-0.0426-0.04360.47070.16270.271915.77483.915335.8158
62.1406-0.1713-0.03351.0454-0.53792.82360.0417-0.5658-0.11640.2544-0.2274-0.1756-0.07780.6040.19180.3219-0.0811-0.0740.50130.09930.264221.531512.024335.6053
73.60930.91770.45292.67014.08576.52830.2168-0.7506-0.04291.1551-0.3008-0.0433-0.1964-0.25190.07060.6716-0.0683-0.04520.80570.15980.363113.40934.323847.1679
87.6062-1.87564.29345.6739-2.19797.23620.0711-1.0165-0.70660.80720.1167-0.18530.3382-0.1808-0.12980.37180.00630.02820.48130.22620.50778.7077-8.080434.522
92.25630.7668-0.10791.3598-0.98912.3351-0.04920.13270.0442-0.05520.0279-0.0617-0.05130.20720.04160.21340.02230.01020.22410.01460.231512.744412.558110.5883
105.6771-1.3806-3.99513.46830.8152.8850.07940.45770.2837-0.07750.1414-0.1766-0.0216-0.0212-0.32160.2136-0.0121-0.03110.27930.04710.2536-0.223214.7016-2.9986
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 160 through 201 )
2X-RAY DIFFRACTION2chain 'A' and (resid 202 through 254 )
3X-RAY DIFFRACTION3chain 'A' and (resid 255 through 276 )
4X-RAY DIFFRACTION4chain 'A' and (resid 277 through 423 )
5X-RAY DIFFRACTION5chain 'A' and (resid 424 through 449 )
6X-RAY DIFFRACTION6chain 'A' and (resid 450 through 543 )
7X-RAY DIFFRACTION7chain 'B' and (resid 36 through 45 )
8X-RAY DIFFRACTION8chain 'B' and (resid 46 through 50 )
9X-RAY DIFFRACTION9chain 'B' and (resid 51 through 96 )
10X-RAY DIFFRACTION10chain 'B' and (resid 97 through 109 )

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