SAXSdb — 9fnm

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

Isoform 2 of Haptoglobin alpha chain

OrganismNot specified

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 19–101 Chain B； UniProt 162–406	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 4.5；277 K；6% 2-propanol 0.1 M sodium acetate trihydrate 26% PEG MME 550	Resolution 2.52 Å R-free 0.227

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 9FNM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4WJG Structure of T. brucei haptoglobin-hemoglobin receptor binding to human haptoglobin-hemoglobin Deposited 2014-09-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: Decameric	Chain C 92–406（315 aa） Chain H 92–406（315 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 4 OXY OXYGEN MOLECULE × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；15% Polyethylene glycol (PEG) 1500, 0.1M Bis-Tris	Resolution 3.10 Å R-free 0.271
4WJG Structure of T. brucei haptoglobin-hemoglobin receptor binding to human haptoglobin-hemoglobin Deposited 2014-09-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 10 PDB declaration: Decameric	Chain M 92–406（315 aa） Chain R 92–406（315 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 4 OXY OXYGEN MOLECULE × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；15% Polyethylene glycol (PEG) 1500, 0.1M Bis-Tris	Resolution 3.10 Å R-free 0.271
4WJG Structure of T. brucei haptoglobin-hemoglobin receptor binding to human haptoglobin-hemoglobin Deposited 2014-09-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Heteromer；Protein × 10 PDB declaration: Decameric	Chain 2 92–406（315 aa） Chain W 92–406（315 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 4 OXY OXYGEN MOLECULE × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；15% Polyethylene glycol (PEG) 1500, 0.1M Bis-Tris	Resolution 3.10 Å R-free 0.271
4X0L Human haptoglobin-haemoglobin complex Deposited 2014-11-21	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 148–406（259 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 2 OXY OXYGEN MOLECULE × 2 GOL GLYCEROL × 2 SO4 SULFATE ION × 1 CAC CACODYLATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M NaCl, 0.1 M sodium cacodylate pH 6.5 and 2 M ammonium sulphate	Resolution 2.05 Å R-free 0.224
5HU6 Structure of the T. brucei haptoglobin-haemoglobin receptor bound to human haptolgobin-haemoglobin Deposited 2016-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 148–406（259 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 2 OXY OXYGEN MOLECULE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；12.5% v/v MPD, 0.03 M NaBr, 0.03M NaI, 0.03M NaF, 0.1 M MES/imidazole pH 6.5, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350	Resolution 2.90 Å R-free 0.226
6TB2 Structure of human haptoglobin-hemoglobin bound to S. aureus IsdH Deposited 2019-10-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 148–406（259 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M sodium citrate tribasic dihydrate, 20 % w/v PEG 3350	Resolution 2.90 Å R-free 0.270
8XMP Structure of CD163 in complex with Hb-Hp Deposited 2023-12-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain 2 1–347（347 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 CA CALCIUM ION × 23 HEM PROTOPORPHYRIN IX CONTAINING FE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.11 Å
8XMQ Structure of dimeric CD163 in complex with Hb-Hp Deposited 2023-12-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain 2 1–347（347 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 CA CALCIUM ION × 12 HEM PROTOPORPHYRIN IX CONTAINING FE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.21 Å
8XMW Local refinement of Hb-Hp bind to CD163 Deposited 2023-12-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain 2 1–347（347 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 6 HEM PROTOPORPHYRIN IX CONTAINING FE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.94 Å
9FHB Cryo-EM structure of human CD163 SRCR2-4 in complex with haptoglobin-hemoglobin Deposited 2024-05-27	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 × 4 PDB declaration: tetrameric	Chain C 1–406（406 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.87 Å
9FMU Cryo-EM structure of human CD163 SRCR1-9 in complex with haptoglobin-hemoglobin Deposited 2024-06-07	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 × 5 PDB declaration: pentameric	Chain C 1–347（347 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 CA CALCIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.46 Å
9FNO Cryo-EM structure of human CD163 SRCR1-9 in complex with haptoglobin-hemoglobin Deposited 2024-06-10	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain C 19–101（83 aa） Chain D 162–406（245 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 CA CALCIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.20 Å
9HEJ Dimeric CD163 bound to human haptoglobin-haemoglobin complex Deposited 2024-11-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain F 1–347（347 aa） Chain G 1–347（347 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 9 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 OXY OXYGEN MOLECULE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.82 Å
9HEK Trimeric CD163 bound to human haptoglobin-haemoglobin complex Deposited 2024-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain F 1–347（347 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 19 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 OXY OXYGEN MOLECULE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.15 Å
9NB6 Cryo-EM structure of the CD163/Hp(1-1)Hb complex Deposited 2025-02-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain F 1–347（347 aa） Chain G 1–347（347 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 CA CALCIUM ION × 23 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 OXY OXYGEN MOLECULE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9NB8 Cryo-EM structure of the CD163/HpSPHb complex Deposited 2025-02-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain F 147–406（260 aa）	Not recorded	CA CALCIUM ION × 21 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 OXY OXYGEN MOLECULE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å

14 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HPT_HUMAN
Isoform	P00738-2
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–83； UniProt 19–101 Author chain B； PDBConstruct 1–245； UniProt 162–406

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	9fnm
Deposition date deposition_date	2024-06-10
最后修订 last_revision	2025-02-12
Structure title title	Structure of human haptoglobin
Keywords keywords	acute phase, hemolysis, hemoglobin binding, reactive oxygen specis, PROTEIN BINDING; PROTEIN BINDING
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	23.70 Å
Radius of gyration Rg (electron density) rg_electron	23.34 Å
Forward intensity I(0) i0	20887900.00
Molecular weight molecular_weight	35010.0 kDa
Excluded volume excluded_volume	43924 Å³
Envelope volume envelope_volume	55671 Å³
Hydration-shell volume shell_volume	21577 Å³
Envelope diameter envelope_diameter	103.0 Å
Shell Rg shell_rg	28.11 Å
Envelope Rg envelope_rg	25.07 Å
Shape Rg shape_rg	23.35 Å
Total Rg total_rg	23.93 Å
Total atoms total_atoms	2465
Residues n_residues	312
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	98.7 Å
Rg (real space) rg_real	24.12 Å
Rg uncertainty (real space) rg_real_error	1.20 Å
I(0) (real space) i0_real	2.0890e+07
I(0) uncertainty (real space) i0_real_error	2.9330e+05
Rg (reciprocal space) rg_reciprocal	24.02 Å
I(0) (reciprocal space) i0_reciprocal	20890000.0000
Solution quality estimate total_estimate	0.4872
Solution quality rating solution_quality	SUSPICIOUS a SUSPICIOUS solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.7 Å
Skewness Skewness skewness	0.885
Kurtosis Kurtosis kurtosis	0.714
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4960000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.208; Stabil: 1.000; Sysdev: 0.154; Positv: 1.000; Valcen: 0.270; Smooth: 0.976

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Isoform 2 of Haptoglobin alpha chain
Molecular weight formula_weight	9204.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2558

VDSGNDVTDIADDGCPKPPEIAHGYVEHSVRYQCKNYYKLRTEGDGVYTLNNEKQWINKAVGDKLPECEAVCGKPKNPANPVQ

Entity 2 Entity 2 polymer

Description description	Haptoglobin beta chain
Molecular weight formula_weight	27298.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

ILGGHLDAKGSFPWQAKMVSHHNLTTGATLINEQWLLTTAKNLFLNHSENATAKDIAPTLTLYVGKKQLVEIEKVVLHPNYSQVDIGLIKLKQKVSVNERVMPICLPSKDYAEVGRVGYVSGWGRNANFKFTDHLKYVMLPVADQDQCIRHYEGSTVPEKKTPKSPVGVQPILNEHTFCAGMSKYQEDTCYGDAGSAFAVHDLEEDTWYATGILSFDKSCAVAEYGVYVKVTSIQDWVQKTIAEN

Entity 3 Entity 3 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	93

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8. Citations (1)

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Unit-cell length a length_a	89.887 Å
Unit-cell length b length_b	77.639 Å
Unit-cell length c length_c	65.085 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.51 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.520 Å
Low-resolution limit resolution_low	28.110 Å
R factor r_factor	0.1948
R_work r_work	0.1912
R_free r_free	0.2272

fit	/app/data/saxs_computation/fn/9fnm/9fnm.fit
pddf	/app/data/pr_computation/fn/9fnm/9fnm.pr.out
profile	/app/data/saxs_computation/fn/9fnm/9fnm.dat

Structure of human haptoglobin

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

Isoform 2 of Haptoglobin alpha chain

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)