2z9a

Crystal Structure of Human Saposin C Dimer in Open Conformation

Method: X-RAY DIFFRACTION D_max: 63.0 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Proactivator polypeptide

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 311–389 Chain B； UniProt 311–389	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4；291 K；20 mM NaAcetate, 240 mM magnesium sulfate, 41% (v/v) pentaerythriol ethoxylate 15/4, pH 4.0, vapor diffusion, sitting drop, temperature 291K	Resolution 2.50 Å R-free 0.271

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 2Z9A	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1M12 NMR solution structure of human Saposin C Deposited 2002-06-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 311–390（80 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) ~10-20mM NaCl；Pressure ambient NMR sample composition U-15N \| 90% H20, 10% D20 NMR sample composition U-15N, U-13C \| 90% H20, 10% D20 NMR sample composition U-15N, U-13C \| 100% D20	Resolution not provided
1N69 Crystal structure of human saposin B Deposited 2002-11-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 195–273（79 aa） Chain B 195–273（79 aa）	Not recorded	3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；295 K；POLYETHYLENE GLYCOL 3350, MAGNESIUM ACETATE, SODIUM CACODYLATE, PH 5.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K. THE CRYSTAL WAS TREATED WITH A MOTHER LIQUOR SOLUTION CONTAINING 0.1% HYDROGEN PEROXIDE PRIOR TO FREEZING.	Resolution 2.20 Å R-free 0.262
1N69 Crystal structure of human saposin B Deposited 2002-11-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 195–273（79 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；295 K；POLYETHYLENE GLYCOL 3350, MAGNESIUM ACETATE, SODIUM CACODYLATE, PH 5.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K. THE CRYSTAL WAS TREATED WITH A MOTHER LIQUOR SOLUTION CONTAINING 0.1% HYDROGEN PEROXIDE PRIOR TO FREEZING.	Resolution 2.20 Å R-free 0.262
1SN6 NMR solution structure of human Saposin C in SDS micelles Deposited 2004-03-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 311–390（80 aa） Fragment：Saposin C	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 25mM sodium dodecyl sulfate U-2H; 0.01% sodium azide；Pressure ambient NMR measurement conditions pH 6.4；298 K；Ionic strength (raw mmCIF value) 25mM sodium dodecyl sulfate U-2H; 0.01% sodium azide；Pressure ambient NMR sample composition 1mM saposin C U-15N, U-13C; 25mM sodium dodecyl sulfate U-2H; 0.01% sodium azide; 90% H20, 10% D20 \| 90% H20, 10% D20 NMR sample composition 1mM saposin C U-15N; 25mM sodium dodecyl sulfate U-2H; 0.01% sodium azide; 90% H20, 10% D20 \| 90% H20, 10% D20 NMR sample composition 1mM saposin C U-15N, U-13C; 25mM sodium dodecyl sulfate U-2H; 0.01% sodium azide; 100% D20 \| 100% D20	Resolution not provided
2DOB Crystal Structure of Human Saposin A Deposited 2006-04-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 60–140（81 aa） Fragment：Saposin A, residues 60-140	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 8K, Calcium Acetate, MES buffer, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.267
2DOB Crystal Structure of Human Saposin A Deposited 2006-04-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 60–140（81 aa） Fragment：Saposin A, residues 60-140	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 8K, Calcium Acetate, MES buffer, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.267
2GTG Crystal Structure of Human Saposin C Deposited 2006-04-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 311–391（81 aa） Fragment：saposin C, residues 311-391	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG400, Calcium Chloride, Sodium Hepes, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.283
2QYP Orthorhombic Crystal Structure of Human Saposin C Dimer in Open Conformation Deposited 2007-08-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 311–392（82 aa） Fragment：Saposin-C Domain Chain B 311–392（82 aa） Fragment：Saposin-C Domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；291 K；20 mM NaAcetate, 200 mM ammonium sulfate, 30% (v/v) pentaerythriol ethoxylate 15/4, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.45 Å R-free 0.290
2R0R Crystal Structure of Human Saposin D variant SapD K9E Deposited 2007-08-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 407–484（78 aa） Chain B 407–484（78 aa）	Mutation：K9E Mutation：K9E	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；291 K；100 mM BisTris, 2.3 M ammonium sulfate, 100 mM urea, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.50 Å R-free 0.287
2R1Q Crystal Structure of Iodinated Human Saposin D in Space Group C2221 Deposited 2007-08-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 407–484（78 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；291 K；100 mM BisTris, 2.3 M ammonium sulfate, 100 mM urea, pH 5.9, vapor diffusion, hanging drop, temperature 291K	Resolution 2.50 Å R-free 0.278
2RB3 Crystal Structure of Human Saposin D Deposited 2007-09-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 407–484（78 aa） Chain D 407–484（78 aa）	Not recorded	SO4 SULFATE ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；291 K；100 mM BisTris, 2.3 M ammonium sulfate, 100 mM urea, pH 5.9, vapor diffusion, hanging drop, temperature 291K	Resolution 2.10 Å R-free 0.274
2RB3 Crystal Structure of Human Saposin D Deposited 2007-09-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 407–484（78 aa） Chain C 407–484（78 aa）	Not recorded	SO4 SULFATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；291 K；100 mM BisTris, 2.3 M ammonium sulfate, 100 mM urea, pH 5.9, vapor diffusion, hanging drop, temperature 291K	Resolution 2.10 Å R-free 0.274
3BQP Crystal Structure of Human Saposin D (orthorhombic) Deposited 2007-12-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 405–484（80 aa） Fragment：SAPOSIN D, RESIDUES 405-484	Not recorded	MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；PEG 8K, MAGNESIUM CHLORIDE, TRIS.HCL BUFFER, PH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.30 Å R-free 0.234
3BQP Crystal Structure of Human Saposin D (orthorhombic) Deposited 2007-12-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 405–484（80 aa） Fragment：SAPOSIN D, RESIDUES 405-484	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；PEG 8K, MAGNESIUM CHLORIDE, TRIS.HCL BUFFER, PH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.30 Å R-free 0.234
3BQQ Crystal Structure of Human Saposin D (triclinic) Deposited 2007-12-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 405–484（80 aa） Fragment：SAPOSIN D, RESIDUES 405-484	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；PEG 4K, ZINC SULFATE, SODIUM ACETATE BUFFER, PH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.00 Å R-free 0.242
3BQQ Crystal Structure of Human Saposin D (triclinic) Deposited 2007-12-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 405–484（80 aa） Fragment：SAPOSIN D, RESIDUES 405-484	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；PEG 4K, ZINC SULFATE, SODIUM ACETATE BUFFER, PH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.00 Å R-free 0.242
3BQQ Crystal Structure of Human Saposin D (triclinic) Deposited 2007-12-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 405–484（80 aa） Fragment：SAPOSIN D, RESIDUES 405-484	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；PEG 4K, ZINC SULFATE, SODIUM ACETATE BUFFER, PH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.00 Å R-free 0.242
3BQQ Crystal Structure of Human Saposin D (triclinic) Deposited 2007-12-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 405–484（80 aa） Fragment：SAPOSIN D, RESIDUES 405-484	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；PEG 4K, ZINC SULFATE, SODIUM ACETATE BUFFER, PH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.00 Å R-free 0.242
4DDJ Crystal structure of saposin A in complex with lauryldimethylamine-N-oxide (LDAO) Deposited 2012-01-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 60–140（81 aa） Fragment：UNP residues 60-140	Not recorded	LDA LAURYL DIMETHYLAMINE-N-OXIDE × 40	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；300 K；1.6 M trisodium citrate, pH 6.5, VAPOR DIFFUSION, temperature 300K	Resolution 1.90 Å R-free 0.280
4UEX Structure of human Saposin A at lysosomal pH Deposited 2014-12-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 60–142（83 aa） Fragment：RESIDUES 60-142	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.8；SITTING-DROP VAPOUR DIFFUSION: 400 NL DROP (200 NL PROTEIN AT 19.6 MG/ML IN 150 MM NACL, 50 MM TRIS PH 7.4 MIXED WITH 200 NL RESERVOIR SOLUTION) WAS EQUILIBRATED AGAINST A 80 UL RESERVOIR OF 0.2 M LITHIUM SULPHATE, 0.1 M SODIUM ACETATE PH 4.8 AND 25% W/V POLYETHYLENE GLYCOL 4000	Resolution 1.80 Å R-free 0.210
4UEX Structure of human Saposin A at lysosomal pH Deposited 2014-12-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 60–142（83 aa） Fragment：RESIDUES 60-142	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.8；SITTING-DROP VAPOUR DIFFUSION: 400 NL DROP (200 NL PROTEIN AT 19.6 MG/ML IN 150 MM NACL, 50 MM TRIS PH 7.4 MIXED WITH 200 NL RESERVOIR SOLUTION) WAS EQUILIBRATED AGAINST A 80 UL RESERVOIR OF 0.2 M LITHIUM SULPHATE, 0.1 M SODIUM ACETATE PH 4.8 AND 25% W/V POLYETHYLENE GLYCOL 4000	Resolution 1.80 Å R-free 0.210
4V2O Structure of saposin B in complex with chloroquine Deposited 2014-10-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 195–273（79 aa） Chain C 195–273（79 aa）	Not recorded	CLQ N4-(7-CHLORO-QUINOLIN-4-YL)-N1,N1-DIETHYL-PENTANE-1,4-DIAMINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.1M MES, PH 6.0, 30% PEG6000	Resolution 2.13 Å R-free 0.254
4V2O Structure of saposin B in complex with chloroquine Deposited 2014-10-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 195–273（79 aa）	Not recorded	CLQ N4-(7-CHLORO-QUINOLIN-4-YL)-N1,N1-DIETHYL-PENTANE-1,4-DIAMINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.1M MES, PH 6.0, 30% PEG6000	Resolution 2.13 Å R-free 0.254
6SLR Structure of saposin B in complex with atovaquone Deposited 2019-08-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 195–272（78 aa） Chain C 195–272（78 aa）	Not recorded	GOL GLYCEROL × 1 AOQ 2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M MES, 30% PEG6000	Resolution 2.38 Å R-free 0.278
6SLR Structure of saposin B in complex with atovaquone Deposited 2019-08-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 195–272（78 aa）	Not recorded	GOL GLYCEROL × 4 AOQ 2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M MES, 30% PEG6000	Resolution 2.38 Å R-free 0.278
8EQU Structure of SARS-CoV-2 Orf3a in late endosome/lysosome-like environment, Saposin A nanodisc Deposited 2022-10-09	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain C 60–140（81 aa） Chain F 60–140（81 aa）	Not recorded	PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
9AVS Human alpha-galactosidase A in complex with saposin B Deposited 2024-03-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 195–273（79 aa）	Not recorded	SO4 SULFATE ION × 8 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；500 nL of protein (0.1 mM GLA plus 0.22 mM SapB) was mixed with 500 nL of reservoir solution (0.1 M Tris pH 8.0, 1 M Ammonium sulfate) and equilibrated against 70 uL reservoirs at 20 C.	Resolution 3.53 Å R-free 0.265
9AXG Human saposin B in the presence of globotriaosylceramide-NBD Deposited 2024-03-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 195–273（79 aa） Chain B 195–273（79 aa）	Not recorded	MLI MALONATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；500 nL of protein-lipid complex (0.82 mM SapB plus 0.87 mM Gb3-NBD) was mixed with 250 nL of reservoir solution (3.1-3.3 M malonate pH 5) and equilibrated against 70 uL reservoirs at 20 C.	Resolution 2.68 Å R-free 0.287
9EKO A chimeric hybrid protein fused with the FGFR3 Transmembrane Domain Deposited 2024-12-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 79–139（61 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.90 Å R-free 0.287
9I63 Synthetic Human Saposin D glycoprotein Deposited 2025-01-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 405–486（82 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.4 M (NH4)2SO4, 0.2 M NH4OAc, 20 mM Tris pH 7.5	Resolution 1.65 Å R-free 0.201
9I63 Synthetic Human Saposin D glycoprotein Deposited 2025-01-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 405–486（82 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.4 M (NH4)2SO4, 0.2 M NH4OAc, 20 mM Tris pH 7.5	Resolution 1.65 Å R-free 0.201

20 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SAP_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–81； UniProt 311–389 Author chain B； PDBConstruct 3–81； UniProt 311–389

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2z9a
Deposition date deposition_date	2007-09-18
Structure title title	Crystal Structure of Human Saposin C Dimer in Open Conformation
Keywords keywords	;lipid binding protein, saposin, activator protein, sap, Disease mutation, Gaucher disease, Glycoprotein, GM2-gangliosidosis, Lipid metabolism, Lysosome, Metachromatic leukodystrophy, Sphingolipid metabolism ;; LIPID BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	18.38 Å
Radius of gyration Rg (electron density) rg_electron	17.45 Å
Forward intensity I(0) i0	5794040.00
Molecular weight molecular_weight	17657.0 kDa
Excluded volume excluded_volume	22186 Å³
Envelope volume envelope_volume	26119 Å³
Hydration-shell volume shell_volume	13489 Å³
Envelope diameter envelope_diameter	64.6 Å
Shell Rg shell_rg	22.12 Å
Envelope Rg envelope_rg	17.79 Å
Shape Rg shape_rg	17.47 Å
Total Rg total_rg	18.23 Å
Total atoms total_atoms	1224
Residues n_residues	155
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	63.0 Å
Rg (real space) rg_real	18.47 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	5.7940e+06
I(0) uncertainty (real space) i0_real_error	7.2460e+04
Rg (reciprocal space) rg_reciprocal	18.46 Å
I(0) (reciprocal space) i0_reciprocal	5794000.0000
Solution quality estimate total_estimate	0.7767
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	18.7 Å
Skewness Skewness skewness	0.475
Kurtosis Kurtosis kurtosis	-0.225
Angular range angular_range	— – 0.4350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1147000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.729; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.908; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Proactivator polypeptide
Molecular weight formula_weight	10149.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1253

YVSDVYCEVCEFLVKEVTKLIDNNKTEKEILDAFDKMCSKLPKSLSEECQEVVDTYGSSILSILLEEVSPELVCSMLHLCSRHHHHHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Pichia pastoris

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	29

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2z9aa_
Class class	a — All alpha proteins
Fold Fold fold	a.64 — Saposin-like
Superfamily Superfamily superfamily	a.64.1 — Saposin
Family Family family	a.64.1.1 — NKL-like

Domain ID domain_id	d2z9ab_
Class class	a — All alpha proteins
Fold Fold fold	a.64 — Saposin-like
Superfamily Superfamily superfamily	a.64.1 — Saposin
Family Family family	a.64.1.1 — NKL-like

CATH v4.4 (2 domains)

Domain ID domain_id	2z9aA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	225 — NK-Lysin
Homologous superfamily homologous superfamily	10 — Saposin-like

Domain ID domain_id	2z9aB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	225 — NK-Lysin
Homologous superfamily homologous superfamily	10 — Saposin-like

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8. Citations (1)

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Unit-cell length a length_a	48.990 Å
Unit-cell length b length_b	48.990 Å
Unit-cell length c length_c	155.570 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.2400
R_work r_work	0.2390
R_free r_free	0.2710

fit	/app/data/saxs_computation/z9/2z9a/2z9a.fit
pddf	/app/data/pr_computation/z9/2z9a/2z9a.pr.out
profile	/app/data/saxs_computation/z9/2z9a/2z9a.dat