SAXSdb — 1gsm

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

MUCOSAL ADDRESSIN CELL ADHESION MOLECULE-1

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 19–224	Fragment：EXTRACELLULAR REGION WITH TWO IG-LIKE DOMAINS	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；PROTEIN SOLUTION:10 MG/ML. CRYSTALLIZATION SOLUTION: 16% PEG 4000, 0.5M LI2SO4, PH 7.75.	Resolution 1.90 Å R-free 0.250

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 1GSM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BQS THE CRYSTAL STRUCTURE OF MUCOSAL ADDRESSIN CELL ADHESION MOLECULE-1 (MADCAM-1) Deposited 1998-08-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–231（209 aa） Fragment：EXTRACELLULAR REGION WITH TWO IG-LIKE DOMAINS	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；PROTEIN SOLUTION:17 MG/ML. CRYSTALLIZATION SOLUTION: 10% PEG 400, 0.5M LI2SO4, PH 7.5-8.0., VAPOR DIFFUSION, HANGING DROP	Resolution 2.20 Å R-free 0.280
4HBQ Crystal structure of a loop deleted mutant of Human MAdCAM-1 D1D2 Deposited 2012-09-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–224（202 aa）	Not recorded	SO4 SULFATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.1 M Tris pH 8.5, 0.2 M (NH4)2SO4, 12% polyethylene glycol (PEG) 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.40 Å R-free 0.178
4HBQ Crystal structure of a loop deleted mutant of Human MAdCAM-1 D1D2 Deposited 2012-09-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 23–224（202 aa）	Not recorded	SO4 SULFATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.1 M Tris pH 8.5, 0.2 M (NH4)2SO4, 12% polyethylene glycol (PEG) 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.40 Å R-free 0.178
4HBQ Crystal structure of a loop deleted mutant of Human MAdCAM-1 D1D2 Deposited 2012-09-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–224（202 aa） Chain B 23–224（202 aa）	Not recorded	SO4 SULFATE ION × 2 GOL GLYCEROL × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.1 M Tris pH 8.5, 0.2 M (NH4)2SO4, 12% polyethylene glycol (PEG) 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.40 Å R-free 0.178
4HC1 Crystal structure of a loop deleted mutant of human MAdCAM-1 D1D2 complexed with Fab 10G3 Deposited 2012-09-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 23–224（202 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；293 K；0.1 M Tris pH 7.0, 10% (w/v) PEG monomethyl ether (PEGMME) 2000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.87 Å R-free 0.253
4HC1 Crystal structure of a loop deleted mutant of human MAdCAM-1 D1D2 complexed with Fab 10G3 Deposited 2012-09-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 23–224（202 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；293 K；0.1 M Tris pH 7.0, 10% (w/v) PEG monomethyl ether (PEGMME) 2000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.87 Å R-free 0.253
4HCR Crystal structure of human MAdCAM-1 D1D2 complexed with Fab PF-547659 Deposited 2012-10-01	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 23–225（203 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1 M Citrate pH 6.0, 18% (w/v) PEG 3350, 12% (w/v) myo-inositol, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.208
4HCR Crystal structure of human MAdCAM-1 D1D2 complexed with Fab PF-547659 Deposited 2012-10-01	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 23–225（203 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1 M Citrate pH 6.0, 18% (w/v) PEG 3350, 12% (w/v) myo-inositol, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.208
4HD9 Crystal structure of native human MAdCAM-1 D1D2 domain Deposited 2012-10-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–225（203 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；293 K；10% PEG4K, 0.5M Li2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.70 Å R-free 0.214
9P95 CryoEM structure of integrin alpha4beta7 bound to MAdCAM-1 Deposited 2025-06-24	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 1–317（317 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 3 MN MANGANESE (II) ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；0.05% CHAPS added immediately before vitrification cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.05 Å

6 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q13477
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–206； UniProt 19–224

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	1gsm
Deposition date deposition_date	2002-01-08
Structure title title	A reassessment of the MAdCAM-1 structure and its role in integrin recognition.
Keywords keywords	;CELL ADHESION PROTEIN, MADCAM-1, IMMUNOGLOBULIN FOLD, I-SET FOLD, CELL ADHESION GLYCOPROTEIN, INTEGRIN RECOGINITION, MEMBRANE PROTEIN ;; CELL ADHESION 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	23.64 Å
Radius of gyration Rg (electron density) rg_electron	23.22 Å
Forward intensity I(0) i0	8934590.00
Molecular weight molecular_weight	21796.0 kDa
Excluded volume excluded_volume	27177 Å³
Envelope volume envelope_volume	35043 Å³
Hydration-shell volume shell_volume	14455 Å³
Envelope diameter envelope_diameter	89.8 Å
Shell Rg shell_rg	27.00 Å
Envelope Rg envelope_rg	23.68 Å
Shape Rg shape_rg	23.19 Å
Total Rg total_rg	23.89 Å
Total atoms total_atoms	1531
Residues n_residues	206
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	87.4 Å
Rg (real space) rg_real	24.02 Å
Rg uncertainty (real space) rg_real_error	0.89 Å
I(0) (real space) i0_real	8.9350e+06
I(0) uncertainty (real space) i0_real_error	1.4570e+05
Rg (reciprocal space) rg_reciprocal	23.93 Å
I(0) (reciprocal space) i0_reciprocal	8934000.0000
Solution quality estimate total_estimate	0.7364
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.1 Å
Skewness Skewness skewness	0.619
Kurtosis Kurtosis kurtosis	-0.224
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2806000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.461; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.202; Smooth: 0.986

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1gsma1
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	d1gsma2
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 (2 domains)

Domain ID domain_id	1gsmA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1gsmA02
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)

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Unit-cell length a length_a	64.000 Å
Unit-cell length b length_b	99.200 Å
Unit-cell length c length_c	70.500 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	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	29.490 Å
R factor r_factor	0.2180
R_work r_work	0.2170
R_free r_free	0.2500

Description description	MUCOSAL ADDRESSIN CELL ADHESION MOLECULE-1
Molecular weight formula_weight	22294.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1715

A reassessment of the MAdCAM-1 structure and its role in integrin recognition.

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

MUCOSAL ADDRESSIN CELL ADHESION MOLECULE-1

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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	MUS MUSCULUS

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	184

fit	/app/data/saxs_computation/gs/1gsm/1gsm.fit
pddf	/app/data/pr_computation/gs/1gsm/1gsm.pr.out
profile	/app/data/saxs_computation/gs/1gsm/1gsm.dat