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1m12

NMR solution structure of human Saposin C

Method: SOLUTION NMR Dmax: 37.1 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

SAPOSIN C

Homo sapiens

UniProt P07602

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 311–390 Not recorded No other associated polymer 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

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 1M12 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1N69 Crystal structure of human saposin B Deposited 2002-11-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different experimental method 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 experimental conditions 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 ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 experimental method 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 mutation/modification Different oligomeric state Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 experimental method 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 experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 mutation/modification 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 oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different experimental method 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 experimental method 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 ligand/ion Different experimental method 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 1–80； UniProt 311–390

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

SAXS profile for 1m12

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1m12
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1m12
Deposition date deposition_date2002-06-17
Structure title titleNMR solution structure of human Saposin C
Keywords keywordsdisulfide bridges, alpha-helices, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier13.22 Å
Radius of gyration Rg (electron density) rg_electron12.98 Å
Forward intensity I(0) i0484977000.00
Molecular weight molecular_weight188160.0 kDa
Excluded volume excluded_volume236310 ų
Envelope volume envelope_volume23947 ų
Hydration-shell volume shell_volume13132 ų
Envelope diameter envelope_diameter55.9 Å
Shell Rg shell_rg21.27 Å
Envelope Rg envelope_rg16.77 Å
Shape Rg shape_rg12.98 Å
Total Rg total_rg13.15 Å
Total atoms total_atoms26200
Residues n_residues1680
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax37.1 Å
Rg (real space) rg_real12.85 Å
Rg uncertainty (real space) rg_real_error0.05 Å
I(0) (real space) i0_real4.7030e+08
I(0) uncertainty (real space) i0_real_error3.9640e+06
Rg (reciprocal space) rg_reciprocal13.20 Å
I(0) (reciprocal space) i0_reciprocal485000000.0000
Solution quality estimate total_estimate0.7069
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary15.5 Å
Skewness Skewness skewness0.076
Kurtosis Kurtosis kurtosis-0.395
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha6.3510
Highest regularization parameter α highest_alpha103600.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.934; Stabil: 0.963; Sysdev: 0.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.518
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1m12a1
Class classa — All alpha proteins
Fold Fold folda.64 — Saposin-like
Superfamily Superfamily superfamilya.64.1 — Saposin
Family Family familya.64.1.1 — NKL-like
Domain ID domain_idd1m12a2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id1m12A00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology225 — NK-Lysin
Homologous superfamily homologous superfamily10 — Saposin-like
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8. Citations (1)

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9. Files and Curves (10)