PDB-9s8w: Human heparanase in complex with neutralizing antibody A54 Fab fr...

ID or keywords:

Entry

Database: PDB / ID: 9s8w

Title

Human heparanase in complex with neutralizing antibody A54 Fab fragment

Components

A54 Fab heavy chain
A54 Fab light chain
Heparanase
Heparanase 8 kDa subunit

Keywords

CARBOHYDRATE / Heparanase / Glycosaminoglycan / Hydrolase / Antibody / Fab

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 ...
Similarity search - Function

Biological species

Homo sapiens (human)

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.49 Å

Authors

Wu, L.

Funding support

United Kingdom, 1items

Citation

Journal: Cells / Year: 2025
Title: Heparanase-Neutralizing Monoclonal Antibody (mAb A54) Attenuates Tumor Growth and Metastasis.
Authors: Barash, U. / Farhoud, M. / Odeh, M. / Huberman, E. / Wu, L. / Vlodavsky, I.

History

Deposition	Aug 5, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 24, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9s8w.cif.gz	810 KB	Display	PDBx/mmCIF format
PDB format	pdb9s8w.ent.gz	592.7 KB	Display	PDB format
PDBx/mmJSON format	9s8w.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9s8w_validation.pdf.gz	783.4 KB	Display	wwPDB validaton report
Full document	9s8w_full_validation.pdf.gz	796.6 KB	Display
Data in XML	9s8w_validation.xml.gz	37.9 KB	Display
Data in CIF	9s8w_validation.cif.gz	49.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s8/9s8w ftp://data.pdbj.org/pub/pdb/validation_reports/s8/9s8w	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: Heparanase

B: Heparanase 8 kDa subunit

H: A54 Fab heavy chain

L: A54 Fab light chain

hetero molecules

101 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration, proteins elute in one peak on gel filtration

Unit cell

Length a, b, c (Å)	69.738, 69.738, 429.781
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	92
Space group name H-M	P4₁2₁2

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Protein , 2 types, 2 molecules AB

#1: Protein	Heparanase / Endo-glucoronidase / Heparanase-1 / Hpa1 Mass: 43464.074 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: Trichoplusia ni (cabbage looper) / References: UniProt: Q9Y251, heparanase
#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: Trichoplusia ni (cabbage looper) / References: UniProt: Q9Y251

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Antibody , 2 types, 2 molecules HL

#3: Antibody	A54 Fab heavy chain Mass: 23921.568 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#4: Antibody	A54 Fab light chain Mass: 24027.420 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)

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Sugars , 2 types, 4 molecules

#5: Polysaccharide

alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose

Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
LFucpa1-6DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}	LINUCS	PDB-CARE

#6: 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: obtained synthetically / Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

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Non-polymers , 1 types, 31 molecules

#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.62 Å³/Da / Density % sol: 53.07 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Sodium Nitrate 20% PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91589 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 24, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.91589 Å / Relative weight: 1
Reflection	Resolution: 3.49→107.44 Å / Num. obs: 9227 / % possible obs: 86.8 % / Redundancy: 15 % / CC_1/2: 0.999 / R_rim(I) all: 0.28 / Net I/σ(I): 9.2
Reflection shell	Resolution: 3.49→3.87 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 452 / CC_1/2: 0.95 / R_rim(I) all: 2.25

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
xia2		data reduction
STARANISO		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.49→107.44 Å / Cor.coef. F_o:F_c: 0.928 / Cor.coef. F_o:F_c free: 0.833 / SU B: 130.966 / SU ML: 0.9 / Cross valid method: FREE R-VALUE / ESU R Free: 1.2
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.323	465	5.04 %
R_work	0.2197	8762	-
all	0.224	-	-
obs	-	9227	63.446 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 143.262 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.237 Å²	0 Å²	0 Å²
2-	-	-0.237 Å²	0 Å²
3-	-	-	0.475 Å²

Refinement step

Cycle: LAST / Resolution: 3.49→107.44 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6983	0	66	31	7080

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	7230
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	6691
X-RAY DIFFRACTION	r_ext_dist_refined_b	0.079	0.1	93092
X-RAY DIFFRACTION	r_angle_refined_deg	1.813	1.821	9836
X-RAY DIFFRACTION	r_angle_other_deg	0.628	1.744	15485
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.65	5	891
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	3.139	5	31
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.776	10	1178
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.647	10	299
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	1105
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	8396
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1632
X-RAY DIFFRACTION	r_nbd_refined	0.21	0.2	1238
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.21	0.2	6121
X-RAY DIFFRACTION	r_nbtor_refined	0.184	0.2	3484
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.086	0.2	3803
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.136	0.2	132
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.019	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.235	0.2	27
X-RAY DIFFRACTION	r_nbd_other	0.27	0.2	81
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.219	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	2.76	6.816	3579
X-RAY DIFFRACTION	r_mcbond_other	2.76	6.816	3579
X-RAY DIFFRACTION	r_mcangle_it	4.764	12.262	4465
X-RAY DIFFRACTION	r_mcangle_other	4.763	12.262	4466
X-RAY DIFFRACTION	r_scbond_it	3.238	7.19	3651
X-RAY DIFFRACTION	r_scbond_other	3.238	7.19	3651
X-RAY DIFFRACTION	r_scangle_it	5.684	13.149	5371
X-RAY DIFFRACTION	r_scangle_other	5.684	13.148	5372
X-RAY DIFFRACTION	r_lrange_it	11.558	150.521	98933
X-RAY DIFFRACTION	r_lrange_other	11.557	150.529	98921

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.49-3.58	0.24	3	0.388	24	X-RAY DIFFRACTION	2.6812
3.58-3.678	0.403	1	0.29	74	X-RAY DIFFRACTION	7.2254
3.678-3.785	0.376	10	0.291	158	X-RAY DIFFRACTION	17.1429
3.785-3.901	0.397	13	0.297	196	X-RAY DIFFRACTION	21.48
3.901-4.029	0.453	12	0.289	340	X-RAY DIFFRACTION	38.7239
4.029-4.17	0.296	28	0.254	441	X-RAY DIFFRACTION	51.2568
4.17-4.327	0.205	33	0.238	584	X-RAY DIFFRACTION	68.7848
4.327-4.504	0.398	41	0.218	636	X-RAY DIFFRACTION	80.8841
4.504-4.704	0.292	30	0.205	670	X-RAY DIFFRACTION	85.1581
4.704-4.933	0.326	38	0.219	674	X-RAY DIFFRACTION	90.0126
4.933-5.199	0.322	40	0.184	649	X-RAY DIFFRACTION	93.4871
5.199-5.513	0.254	31	0.208	631	X-RAY DIFFRACTION	92.4581
5.513-5.893	0.284	33	0.22	597	X-RAY DIFFRACTION	93.75
5.893-6.364	0.488	30	0.251	602	X-RAY DIFFRACTION	98.5959
6.364-6.969	0.202	28	0.258	563	X-RAY DIFFRACTION	100
6.969-7.787	0.537	33	0.229	508	X-RAY DIFFRACTION	100
7.787-8.984	0.228	15	0.187	466	X-RAY DIFFRACTION	100
8.984-10.984	0.213	15	0.15	406	X-RAY DIFFRACTION	100
10.984-15.453	0.325	20	0.176	326	X-RAY DIFFRACTION	100
15.453-107.44	0.444	11	0.336	216	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	4.1636	2.3357	-0.5632	5.6003	-1.9848	3.7303	0.4588	-0.2634	-0.3389	-0.0671	-0.2893	0.9955	-0.3915	-0.8224	-0.1695	0.1523	0.2087	-0.1928	1.3572	-0.2867	0.6275	-10.1943	7.71	34.231
2	2.566	-0.8382	1.7547	5.3471	-1.7035	4.3165	0.0907	-0.6129	-0.0802	0.3887	-0.4978	0.1889	-0.3002	-0.2874	0.4071	0.0882	-0.0499	0.0197	1.3193	-0.0596	0.2275	7.9266	5.2888	48.426
3	2.4912	-0.1797	0.9848	5.6993	1.0632	3.2796	0.0399	-1.181	-0.1541	1.5284	-0.1614	0.0963	0.1748	-0.3539	0.1215	0.4271	-0.1719	-0.0031	1.731	0.1385	0.1991	12.938	-1.7755	66.1639
4	5.457	1.1368	3.0041	3.5495	0.1882	4.5623	0.2094	-0.2426	-0.2803	-0.0874	0.086	-0.1698	-0.5139	-0.6638	-0.2954	0.2017	0.0609	0.1257	1.4536	0.0566	0.2543	4.2237	3.8319	52.6271
5	3.8253	-2.9816	0.788	2.3473	-0.6953	0.6433	0.0704	-0.1724	-0.7048	-0.1548	0.0826	0.5678	0.5034	-0.3845	-0.1531	0.4988	-0.3288	-0.0604	1.3778	0.144	0.6727	-10.0452	-3.4532	41.9071
6	3.7497	-0.9967	-2.4587	4.6042	0.7704	7.4895	-0.5755	-0.0176	-0.5729	-0.5814	-0.4178	-0.4564	0.4977	0.5315	0.9933	0.2273	0.0073	0.196	0.6551	0.1347	0.6005	29.1393	-0.4364	15.6612
7	2.1573	-2.5101	1.4464	12.7237	3.4758	6.2561	-0.3386	0.8813	0.0237	-0.5454	-0.3074	-1.9534	0.2267	1.7103	0.646	1.0608	0.1401	0.7538	1.4228	0.4614	1.4415	47.2246	-3.4962	-1.4641
8	7.9824	0.0025	-4.1361	4.3962	-0.3165	10.0803	0.5818	-0.5797	0.6262	-0.5623	-0.3258	-0.2849	-1.8733	0.3135	-0.256	0.6598	-0.0764	-0.1392	0.5554	0.0497	0.3614	27.5751	21.1231	15.1442
9	4.676	0.6137	-2.166	5.9081	0.6714	5.5419	-0.0893	0.8582	-0.7821	-2.1909	-0.3426	-0.3994	0.3125	0.1359	0.4319	1.4921	0.1717	0.3582	1.0445	0.221	0.7029	42.7977	5.198	-16.1631

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	Ap	159 - 273
2	X-RAY DIFFRACTION	2	ALL	Ap	274 - 447
3	X-RAY DIFFRACTION	3	ALL	Ap	448 - 543

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