SAXSdb — 1ayo

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

ALPHA-2-MACROGLOBULIN

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	Other combination Homooligomer Protein × 2 其他Polymer 1 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1338–1468 Chain B； UniProt 1338–1468	Fragment：RECEPTOR-BINDING DOMAIN	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.9；38% PEGMMES 2000, 25 MM CACL2, 100 MM HEPES, PH 6.9	Resolution 1.90 Å R-free 0.239

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 1AYO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BV8 RECEPTOR DOMAIN FROM ALPHA-2-MACROGLOBULIN Deposited 1998-09-22	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 1337–1474（138 aa） Fragment：RECEPTOR BINDING DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.1；298 K；Ionic strength (raw mmCIF value) 0.4；Pressure 1	Resolution not provided
2P9R Human alpha2-macroglogulin is composed of multiple domains, as predicted by homology with complement component C3 Deposited 2007-03-26	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 126–227（102 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；295 K；11% PEG 3350, 200mM di-ammonium hydrogen citrate, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.30 Å R-free 0.281
2P9R Human alpha2-macroglogulin is composed of multiple domains, as predicted by homology with complement component C3 Deposited 2007-03-26	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 126–227（102 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；295 K；11% PEG 3350, 200mM di-ammonium hydrogen citrate, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.30 Å R-free 0.281
6TAV Crystal structure of endopeptidase-induced alpha2-macroglobulin Deposited 2019-10-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–1474（1474 aa） Chain B 1–1474（1474 aa） Chain C 1–1474（1474 aa） Chain D 1–1474（1474 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Equivolumetric drops consisting of 0.2M tribasic ammonium citrate, pH6.4, 15% (w/v) polyethylene glycol 3350, plus 0.05M sodium fluoride as an additive, and protein solution at 4.9 absorption units at lambda=280nm yielded a single large well-shaped monocrystal after several months. This crystal could not be reproduced despite extensive trials.	Resolution 4.20 Å R-free 0.282
7O7L (h-alpha2M)4 native I Deposited 2021-04-13	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 Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–1474（1474 aa） Chain B 1–1474（1474 aa） Chain C 1–1474（1474 aa） Chain D 1–1474（1474 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.50 Å
7O7M (h-alpha2M)4 native II Deposited 2021-04-13	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 Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–1474（1474 aa） Chain B 1–1474（1474 aa） Chain C 1–1474（1474 aa） Chain D 1–1474（1474 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.60 Å
7O7N (h-alpha2M)4 semiactivated I state Deposited 2021-04-13	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 Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–1474（1474 aa） Chain B 1–1474（1474 aa） Chain C 1–1474（1474 aa） Chain D 1–1474（1474 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.30 Å
7O7O (h-alpha2M)4 semiactivated II state Deposited 2021-04-13	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 Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–1474（1474 aa） Chain B 1–1474（1474 aa） Chain C 1–1474（1474 aa） Chain D 1–1474（1474 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.80 Å
7O7P (h-alpha2M)4 activated state Deposited 2021-04-13	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 Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–1474（1474 aa） Chain B 1–1474（1474 aa） Chain C 1–1474（1474 aa） Chain D 1–1474（1474 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.60 Å
7O7Q (h-alpha2M)4 trypsin-activated state Deposited 2021-04-13	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 Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–1474（1474 aa） Chain B 1–1474（1474 aa） Chain C 1–1474（1474 aa） Chain D 1–1474（1474 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7O7R (h-alpha2M)4 plasmin-activated I state Deposited 2021-04-13	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 Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–1474（1474 aa） Chain B 1–1474（1474 aa） Chain C 1–1474（1474 aa） Chain D 1–1474（1474 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
7O7S (h-alpha2M)4 plasmin-activated II state Deposited 2021-04-13	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 Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–1474（1474 aa） Chain B 1–1474（1474 aa） Chain C 1–1474（1474 aa） Chain D 1–1474（1474 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å
7VON Native alpha-2-macroglobulin monomer Deposited 2021-10-14	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 27–1468（1442 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.20 Å
7VOO Induced alpha-2-macroglobulin monomer Deposited 2021-10-14	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 Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–1335（1309 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å

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

View Construct and Data Evidence

UniProt name	A2MG_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–130； UniProt 1338–1468 Author chain B； PDBConstruct 1–130； UniProt 1338–1468

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	1ayo
Deposition date deposition_date	1997-11-07
Structure title title	RECEPTOR BINDING DOMAIN OF BOVINE ALPHA-2-MACROGLOBULIN
Keywords keywords	MACROGLOBULIN, RECEPTOR BINDING DOMAIN; MACROGLOBULIN
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	22.22 Å
Radius of gyration Rg (electron density) rg_electron	21.20 Å
Forward intensity I(0) i0	14397000.00
Molecular weight molecular_weight	29409.0 kDa
Excluded volume excluded_volume	37231 Å³
Envelope volume envelope_volume	45267 Å³
Hydration-shell volume shell_volume	18623 Å³
Envelope diameter envelope_diameter	73.3 Å
Shell Rg shell_rg	26.71 Å
Envelope Rg envelope_rg	21.24 Å
Shape Rg shape_rg	21.23 Å
Total Rg total_rg	21.93 Å
Total atoms total_atoms	2066
Residues n_residues	260
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	71.7 Å
Rg (real space) rg_real	22.21 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	1.4400e+07
I(0) uncertainty (real space) i0_real_error	1.7980e+05
Rg (reciprocal space) rg_reciprocal	22.22 Å
I(0) (reciprocal space) i0_reciprocal	14400000.0000
Solution quality estimate total_estimate	0.9023
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	23.5 Å
Skewness Skewness skewness	0.283
Kurtosis Kurtosis kurtosis	-0.473
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2925000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; Smooth: 0.971

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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	ALPHA-2-MACROGLOBULIN
Molecular weight formula_weight	14505.5 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2370

EFPFALEVQTLPQTCDGPKAHTSFQISLSVSYIGSRPASNMAIVDVKMVSGFIPLKPTVKMLERSNVSRTEVSNNHVLIYLDKVTNETLTLTFTVLQDIPVRDLKPAIVKVYDYYETDEFAVAEYSAPCS

Entity 2 Entity 2 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
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	304

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1ayoa_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.29 — Macroglobulin
Family Family family	b.1.29.1 — Alpha-macroglobulin receptor domain

Domain ID domain_id	d1ayob_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.29 — Macroglobulin
Family Family family	b.1.29.1 — Alpha-macroglobulin receptor domain

CATH v4.4 (2 domains)

Domain ID domain_id	1ayoA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	690 — Alpha-macroglobulin, receptor-binding domain

Domain ID domain_id	1ayoB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	690 — Alpha-macroglobulin, receptor-binding domain

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8. Citations (1)

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Unit-cell length a length_a	107.570 Å
Unit-cell length b length_b	107.570 Å
Unit-cell length c length_c	72.229 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 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	33.000 Å
R factor r_factor	0.1947
R_work r_work	—
R_free r_free	0.2394

fit	/app/data/saxs_computation/ay/1ayo/1ayo.fit
pddf	/app/data/pr_computation/ay/1ayo/1ayo.pr.out
profile	/app/data/saxs_computation/ay/1ayo/1ayo.dat

RECEPTOR BINDING DOMAIN OF BOVINE ALPHA-2-MACROGLOBULIN

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

ALPHA-2-MACROGLOBULIN

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