9axg

Human saposin B in the presence of globotriaosylceramide-NBD

Method: X-RAY DIFFRACTION D_max: 48.8 Å Quality: GOOD

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

Saposin-B

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 195–273 Chain B； UniProt 195–273	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

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 9AXG	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 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
2Z9A Crystal Structure of Human Saposin C Dimer in Open Conformation 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 311–389（79 aa） Chain B 311–389（79 aa）	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
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 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
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 4–82； UniProt 195–273 Author chain B； PDBConstruct 4–82； UniProt 195–273

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	9axg
Deposition date deposition_date	2024-03-06
Structure title title	Human saposin B in the presence of globotriaosylceramide-NBD
Keywords keywords	;Saposin, Saposin B, SapB, Fabry disease, Lysosomal, Activator protein, Globotriaosylceramide, Gb3, Nitrobenzoxadiazole, NBD, LIPID BINDING PROTEIN ;; 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	17.13 Å
Radius of gyration Rg (electron density) rg_electron	15.81 Å
Forward intensity I(0) i0	6469260.00
Molecular weight molecular_weight	16876.0 kDa
Excluded volume excluded_volume	20477 Å³
Envelope volume envelope_volume	26467 Å³
Hydration-shell volume shell_volume	14437 Å³
Envelope diameter envelope_diameter	47.7 Å
Shell Rg shell_rg	21.43 Å
Envelope Rg envelope_rg	15.43 Å
Shape Rg shape_rg	15.85 Å
Total Rg total_rg	16.71 Å
Total atoms total_atoms	1163
Residues n_residues	159
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	48.8 Å
Rg (real space) rg_real	16.95 Å
Rg uncertainty (real space) rg_real_error	0.17 Å
I(0) (real space) i0_real	6.4690e+06
I(0) uncertainty (real space) i0_real_error	6.4710e+04
Rg (reciprocal space) rg_reciprocal	16.98 Å
I(0) (reciprocal space) i0_reciprocal	6469000.0000
Solution quality estimate total_estimate	0.8989
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.4 Å
Skewness Skewness skewness	-0.153
Kurtosis Kurtosis kurtosis	-0.499
Angular range angular_range	— – 0.4650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	451300.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.933

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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	Saposin-B
Molecular weight formula_weight	9097.5 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	1166

GASGDVCQDCIQMVTDIQTAVRTNSTFVQALVEHVKEECDRLGPGMADICKNYISQYSEIAIQMMMHMQPKEICALVGFCDE

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	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MALONATE ION
Molecular weight formula_weight	102.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	3

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8. Citations (1)

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Unit-cell length a length_a	66.908 Å
Unit-cell length b length_b	66.908 Å
Unit-cell length c length_c	87.181 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 64
Space-group number int_tables_number	172
Crystal system crystal_system	hexagonal

Resolution resolution	2.680 Å
Low-resolution limit resolution_low	34.830 Å
R factor r_factor	0.2478
R_work r_work	0.2436
R_free r_free	0.2868

fit	/app/data/saxs_computation/ax/9axg/9axg.fit
pddf	/app/data/pr_computation/ax/9axg/9axg.pr.out
profile	/app/data/saxs_computation/ax/9axg/9axg.dat