SAXSdb — 3d5o

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

Serum amyloid P-component

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 20–223 Chain B； UniProt 20–223 Chain C； UniProt 20–223 Chain D； UniProt 20–223 Chain E； UniProt 20–223	Not recorded	Low affinity immunoglobulin gamma Fc region receptor II-a × 1 （P12318） SO4 SULFATE ION × 16 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；2.0 M NH4SO4, 5% iso-propanol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.279

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 3D5O	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1GYK Serum Amyloid P Component co-crystallised with MOBDG at neutral pH Deposited 2002-04-25	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 20–223（204 aa） Chain B 20–223（204 aa） Chain C 20–223（204 aa） Chain D 20–223（204 aa） Chain E 20–223（204 aa）	Not recorded	CA CALCIUM ION × 9 CDG METHYL 4,6-O-[(1R)-1-CARBOXYETHYLIDENE]-BETA-D-GALACTOPYRANOSIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.00	Resolution 2.20 Å R-free 0.224
1LGN DECAMERIC DAMP COMPLEX OF HUMAN SERUM AMYLOID P COMPONENT Deposited 1996-12-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 20–223（204 aa） Chain B 20–223（204 aa） Chain C 20–223（204 aa） Chain D 20–223（204 aa） Chain E 20–223（204 aa）	Not recorded	CA CALCIUM ION × 10 D5M 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；3 + 3 UL HANGING DROPS AT 277K PROTEIN SOLUTION: 20 MG/ML PROTEIN, 10 MM TRIS-HCL, PH 8.0, 140 MM NACL, 20 MM DAMP, 0.02 % NA-AZIDE. RESERVOIR SOLUTION: 100 MM BIS-TRIS PROPANE- HCL PH 8.0, 20 MM CALCIUM CHLORIDE, 12-14 % (W/V) POLYETHYLENEGLYCOL 4000., vapor diffusion - hanging drop	Resolution 2.80 Å R-free 0.252
1SAC THE STRUCTURE OF PENTAMERIC HUMAN SERUM AMYLOID P COMPONENT Deposited 1994-01-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 20–223（204 aa） Chain B 20–223（204 aa） Chain C 20–223（204 aa） Chain D 20–223（204 aa） Chain E 20–223（204 aa）	Not recorded	CA CALCIUM ION × 10 ACY ACETIC ACID × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
2A3W Decameric structure of human serum amyloid P-component bound to Bis-1,2-{[(Z)-2-carboxy-2-methyl-1,3-dioxane]-5-yloxycarbamoyl}-ethane Deposited 2005-06-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain A 20–223（204 aa） Chain B 20–223（204 aa） Chain C 20–223（204 aa） Chain D 20–223（204 aa） Chain E 20–223（204 aa） Chain F 20–223（204 aa） Chain G 20–223（204 aa） Chain H 20–223（204 aa） Chain I 20–223（204 aa） Chain J 20–223（204 aa）	Not recorded	CA CALCIUM ION × 20 CPJ BIS-1,2-{[(Z)-2-CARBOXY-2-METHYL-1,3-DIOXANE]-5-YLOXYCARBAMOYL}-ETHANE × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；294 K；PEG 4000, PEG 400, sodium acetate, calcium acetate, sorbitol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.20 Å R-free 0.229
2A3W Decameric structure of human serum amyloid P-component bound to Bis-1,2-{[(Z)-2-carboxy-2-methyl-1,3-dioxane]-5-yloxycarbamoyl}-ethane Deposited 2005-06-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain K 20–223（204 aa） Chain L 20–223（204 aa） Chain M 20–223（204 aa） Chain N 20–223（204 aa） Chain O 20–223（204 aa） Chain P 20–223（204 aa） Chain Q 20–223（204 aa） Chain R 20–223（204 aa） Chain S 20–223（204 aa） Chain T 20–223（204 aa）	Not recorded	CA CALCIUM ION × 20 CPJ BIS-1,2-{[(Z)-2-CARBOXY-2-METHYL-1,3-DIOXANE]-5-YLOXYCARBAMOYL}-ETHANE × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；294 K；PEG 4000, PEG 400, sodium acetate, calcium acetate, sorbitol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.20 Å R-free 0.229
2A3X Decameric crystal structure of human serum amyloid P-component bound to Bis-1,2-{[(Z)-2carboxy- 2-methyl-1,3-dioxane]- 5-yloxycarbonyl}-piperazine Deposited 2005-06-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain A 20–223（204 aa） Chain B 20–223（204 aa） Chain C 20–223（204 aa） Chain D 20–223（204 aa） Chain E 20–223（204 aa） Chain F 20–223（204 aa） Chain G 20–223（204 aa） Chain H 20–223（204 aa） Chain I 20–223（204 aa） Chain J 20–223（204 aa）	Not recorded	CA CALCIUM ION × 20 CPK BIS-1,2-{[(Z)-2CARBOXY-2-METHYL-1,3-DIOXANE]-5-YLOXYCARBONYL}-PIPERAZINE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；294 K；sodium acetate, calcium acetate, PEG 8000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.00 Å R-free 0.282
2A3Y Pentameric crystal structure of human serum amyloid P-component bound to Bis-1,2-{[(Z)-2carboxy-2-methyl-1,3-dioxane]-5-yloxycarbamoyl}-ethane. Deposited 2005-06-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 20–223（204 aa） Chain B 20–223（204 aa） Chain C 20–223（204 aa） Chain D 20–223（204 aa） Chain E 20–223（204 aa）	Not recorded	CA CALCIUM ION × 10 CPJ BIS-1,2-{[(Z)-2-CARBOXY-2-METHYL-1,3-DIOXANE]-5-YLOXYCARBAMOYL}-ETHANE × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；294 K；sodium actetate, calcium acetate, PEG 8000, PEG 400, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.00 Å R-free 0.250
2W08 The structure of serum amyloid P component bound to 0-phospho- threonine Deposited 2008-08-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 20–223（204 aa） Chain B 20–223（204 aa） Chain C 20–223（204 aa） Chain D 20–223（204 aa） Chain E 20–223（204 aa）	Not recorded	CA CALCIUM ION × 10 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 TPO PHOSPHOTHREONINE × 5	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；0.06M TRIS-HCL PH8, 16% PEG 550MME, 0.01M CACL2, 0.08M NACL, 0.1% NAN3, 14.2MG/ML PROTEIN, 50MM LIGAND	Resolution 1.70 Å R-free 0.176
3KQR The structure of serum amyloid p component bound to phosphoethanolamine Deposited 2009-11-17	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 20–223（204 aa） Chain B 20–223（204 aa） Chain C 20–223（204 aa） Chain D 20–223（204 aa） Chain E 20–223（204 aa）	Not recorded	OPE PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER × 5 CA CALCIUM ION × 10 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.06M TRIS-HCL pH8, 16% PEG 550MME, 0.01M CaCl2, 0.14M NaCl, 0.1% NaN3,14.2mg/ml Protein, 0.05M Ligand, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.50 Å R-free 0.161
4AVS Structure of N-Acetyl-L-Proline bound to Serum Amyloid P Component Deposited 2012-05-29	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 20–223（204 aa） Chain B 20–223（204 aa） Chain C 20–223（204 aa） Chain D 20–223（204 aa） Chain E 20–223（204 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 CA CALCIUM ION × 10 N7P 1-ACETYL-L-PROLINE × 5	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；0.06 M TRIS-HCL, PH 8, 16% PEG 550 MME, 0.01 M CACL2, 0.08 M NACL AND 0.1% NAN3	Resolution 1.40 Å R-free 0.170
4AVT Structure of CPHPC bound to Serum Amyloid P Component Deposited 2012-05-29	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 20–223（204 aa） Chain C 20–223（204 aa） Chain E 20–223（204 aa） Chain G 20–223（204 aa） Chain I 20–223（204 aa）	Not recorded	CA CALCIUM ION × 10 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 GHE (2R)-1-[6-[(2R)-2-carboxypyrrolidin-1-yl]-6-oxidanylidene-hexanoyl]pyrrolidine-2-carboxylic acid × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.6；60MM TRIS-HCL, 80MM NACL, 15% PEG550 MME, pH 7.6	Resolution 3.20 Å R-free 0.197
4AVT Structure of CPHPC bound to Serum Amyloid P Component Deposited 2012-05-29	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain B 20–223（204 aa） Chain D 20–223（204 aa） Chain F 20–223（204 aa） Chain H 20–223（204 aa） Chain J 20–223（204 aa）	Not recorded	CA CALCIUM ION × 10 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 GHE (2R)-1-[6-[(2R)-2-carboxypyrrolidin-1-yl]-6-oxidanylidene-hexanoyl]pyrrolidine-2-carboxylic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.6；60MM TRIS-HCL, 80MM NACL, 15% PEG550 MME, pH 7.6	Resolution 3.20 Å R-free 0.197
4AVV Structure of CPHPC bound to Serum Amyloid P Component Deposited 2012-05-29	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 20–223（204 aa） Chain B 20–223（204 aa） Chain C 20–223（204 aa） Chain D 20–223（204 aa） Chain E 20–223（204 aa）	Not recorded	ACT ACETATE ION × 8 GHE (2R)-1-[6-[(2R)-2-carboxypyrrolidin-1-yl]-6-oxidanylidene-hexanoyl]pyrrolidine-2-carboxylic acid × 5 CD CADMIUM ION × 35 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 SIA N-acetyl-alpha-neuraminic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；PH 4.6	Resolution 1.60 Å R-free 0.175
4AYU Structure of N-Acetyl-D-Proline bound to serum amyloid P component Deposited 2012-06-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 20–223（204 aa） Chain B 20–223（204 aa） Chain C 20–223（204 aa） Chain D 20–223（204 aa） Chain E 20–223（204 aa）	Not recorded	CA CALCIUM ION × 10 N8P N-ACETYL-D-PROLINE × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；60 MM TRIS-HCL PH 8.0, 10 MM CACL2, 84 MM NACL, 20% GLYCEROL V/V, 17% PEG550 MME V/V	Resolution 1.50 Å R-free 0.168

12 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SAMP_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–204； UniProt 20–223 Author chain B； PDBConstruct 1–204； UniProt 20–223 Author chain C； PDBConstruct 1–204； UniProt 20–223 Author chain D； PDBConstruct 1–204； UniProt 20–223 Author chain E； PDBConstruct 1–204； UniProt 20–223

Low affinity immunoglobulin gamma Fc region receptor II-a

Homo sapiens

UniProt P12318

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain F； UniProt 37–207	Not recorded	Serum amyloid P-component × 5 （P02743） SO4 SULFATE ION × 16 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；2.0 M NH4SO4, 5% iso-propanol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.279

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 3D5O	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1FCG ECTODOMAIN OF HUMAN FC GAMMA RECEPTOR, FCGRIIA Deposited 1999-04-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 34–207（174 aa） Fragment：EXTRACELLULAR DOMAINS	Mutation：S88F, R134H	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；HANGING DROP VAPOUR DIFFUSION WITH EQUAL VOLUMES OF FC(GAMMA)RIIA AT 6 MG/ML AND MOTHER LIQUOR (0.2 M AMMONIUM ACETATE, 30% W/V PEG 4000, 0.1 M SODIUM CITRATE PH 5.6) MIXED IN 3 MICRO L DROPLETS AND ALLOWED TO EQUILIBRATE AT 22 C FOR 3-9 DAYS.	Resolution 2.00 Å R-free 0.242
1H9V Human Fc-gamma-Receptor IIa (FcgRIIa), monoclinic Deposited 2001-03-21	Different construct 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 37–208（172 aa） Fragment：IMMUNOGLOBULIN G BINDING DOMAIN RESIDUE 5-177	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；0.2M NAOAC PH 4.6, 26% PEG 8000	Resolution 3.00 Å
3RY4 1.5 Angstrom resolution structure of glycosylated fcgammariia (low-responder polymorphism) Deposited 2011-05-11	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 37–206（170 aa） Fragment：EXTRACELLULAR DOMAIN, residues 37-206	Mutation：S88P	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；30% (W/V) PEG 4000, 0.2M AMMONIUM ACETATE, 0.1M SODIUM CITRATE, PH 5.60, VAPOR DIFFUSION, TEMPERATURE 291.0K	Resolution 1.50 Å R-free 0.230
3RY5 Three-dimensional structure of glycosylated fcgammariia (high-responder polymorphism) Deposited 2011-05-11	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 37–206（170 aa） Fragment：EXTRACELLULAR DOMAIN, residues 114-327	Mutation：H134R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；30% (W/V) PEG 4000, 0.2M AMMONIUM SULFATE, PH 7.50, VAPOR DIFFUSION, TEMPERATURE 291.0K	Resolution 2.30 Å R-free 0.275
3RY6 Complex of fcgammariia (CD32) and the FC of human IGG1 Deposited 2011-05-11	Different construct 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 40–206（167 aa） Fragment：UNP residues 40-206	Not recorded	GOL GLYCEROL × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.4；20% (W/V) PEG 3350, 5MM TRIS, 0.15M NACL, 2MM MOPS, 0.2M TRI-POTASSIUM ACETATE, PH 7.40, VAPOR DIFFUSION, TEMPERATURE 291.0K	Resolution 3.80 Å R-free 0.426
8CHA Fc gamma RIIa 27W/131H variant ectodomain Deposited 2023-02-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–209（209 aa）	Mutation：Q27W	FLC CITRATE ANION × 1 PO4 PHOSPHATE ION × 3 16P 3,6,9,12,15,18-HEXAOXAICOSANE × 1 PGE TRIETHYLENE GLYCOL × 1 DXE 1,2-DIMETHOXYETHANE × 1 FWN 2-[2-(2-ethoxyethoxy)ethoxy]ethanol × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；293.15 K；0.1M sodium phosphate citrate, pH4.2, 41% (v/v) PEG 300	Resolution 1.81 Å R-free 0.225
9MCX CRYSTAL STRUCTURE OF HUMAN IGG1 FC FRAGMENT-FC-GAMMA RECEPTOR IIA COMPLEX H131 VARIANT Deposited 2024-12-05	Different construct 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 37–209（173 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；25% PEG 2000 MME, 0.1 M HEPES pH 7.5	Resolution 2.38 Å R-free 0.234
9N5P CRYSTAL STRUCTURE OF HUMAN IGG2 FC FRAGMENT-FC-GAMMA RECEPTOR IIA COMPLEX H131 VARIANT Deposited 2025-02-04	Different construct 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 37–209（173 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.1 M HEPES pH 7.5, 25% PEG 2000 MME	Resolution 2.01 Å R-free 0.232

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FCG2A_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain F； PDBConstruct 1–171； UniProt 37–207

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3d5o
Deposition date deposition_date	2008-05-16
Structure title title	Structural recognition and functional activation of FcrR by innate pentraxins
Keywords keywords	;complex structure, SAP, Fc RIIa, Fc receptor activation, pentraxins, Amyloid, Glycoprotein, Lectin, Metal-binding, Secreted, Cell membrane, IgG-binding protein, Immunoglobulin domain, Membrane, Phosphoprotein, Receptor, Transmembrane, IMMUNE SYSTEM ;; IMMUNE SYSTEM
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	36.30 Å
Radius of gyration Rg (electron density) rg_electron	35.35 Å
Forward intensity I(0) i0	273443000.00
Molecular weight molecular_weight	136220.0 kDa
Excluded volume excluded_volume	171180 Å³
Envelope volume envelope_volume	217800 Å³
Hydration-shell volume shell_volume	51111 Å³
Envelope diameter envelope_diameter	116.1 Å
Shell Rg shell_rg	42.36 Å
Envelope Rg envelope_rg	34.62 Å
Shape Rg shape_rg	35.35 Å
Total Rg total_rg	35.85 Å
Total atoms total_atoms	9624
Residues n_residues	1191
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	112.6 Å
Rg (real space) rg_real	36.10 Å
Rg uncertainty (real space) rg_real_error	0.77 Å
I(0) (real space) i0_real	2.7340e+08
I(0) uncertainty (real space) i0_real_error	4.5660e+06
Rg (reciprocal space) rg_reciprocal	36.23 Å
I(0) (reciprocal space) i0_reciprocal	273500000.0000
Solution quality estimate total_estimate	0.9009
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	51.2 Å
Skewness Skewness skewness	0.064
Kurtosis Kurtosis kurtosis	-0.587
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	102300000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.926

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Serum amyloid P-component
Molecular weight formula_weight	23282.5 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	9655

HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV

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 polymer

Description description	Low affinity immunoglobulin gamma Fc region receptor II-a
Molecular weight formula_weight	20074.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

APPKAVLKLEPPWINVLQEDSVTLTCQGARSPESDSIQWFHNGNLIPTHTQPSYRFKANNNDSGEYTCQTGQTSLSDPVHLTVLSEWLVLQTPHLEFQEGETIMLRCHSWKDKPLVKVTFFQNGKSQKFSRLDPTFSIPQANHSHSGDYHCTGNIGYTLFSSKPVTITVQVHHHHHH

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 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	31

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7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d3d5oa_
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.5 — Pentraxin (pentaxin)

Domain ID domain_id	d3d5ob_
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.5 — Pentraxin (pentaxin)

Domain ID domain_id	d3d5oc_
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.5 — Pentraxin (pentaxin)

Domain ID domain_id	d3d5od_
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.5 — Pentraxin (pentaxin)

Domain ID domain_id	d3d5oe_
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.5 — Pentraxin (pentaxin)

Domain ID domain_id	d3d5of1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.4 — I set domains

Domain ID domain_id	d3d5of2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.4 — I set domains

CATH v4.4 (7 domains)

Domain ID domain_id	3d5oA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	3d5oB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	3d5oC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	3d5oD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	3d5oE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	3d5oF01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3d5oF02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

▶

Unit-cell length a length_a	64.197 Å
Unit-cell length b length_b	143.477 Å
Unit-cell length c length_c	161.588 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	20

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2210
R_work r_work	0.2070
R_free r_free	0.2790

fit	/app/data/saxs_computation/d5/3d5o/3d5o.fit
pddf	/app/data/pr_computation/d5/3d5o/3d5o.pr.out
profile	/app/data/saxs_computation/d5/3d5o/3d5o.dat

Structural recognition and functional activation of FcrR by innate pentraxins

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

Serum amyloid P-component

State in the Current Structure

Other States of the Same Protein in the Database

Low affinity immunoglobulin gamma Fc region receptor II-a

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

CATH v4.4 (7 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)