SAXSdb — 4hd9

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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 23–225	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

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 4HD9	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 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
1GSM A reassessment of the MAdCAM-1 structure and its role in integrin recognition. Deposited 2002-01-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–224（206 aa） Fragment：EXTRACELLULAR REGION WITH TWO IG-LIKE DOMAINS	Not recorded	No recorded non-water small molecule	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
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 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 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 23–225（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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 23–225（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
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	MADCA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–203； UniProt 23–225

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	4hd9
Deposition date deposition_date	2012-10-02
Structure title title	Crystal structure of native human MAdCAM-1 D1D2 domain
Keywords keywords	immunoglobulin superfamily, rolling and firm adhesion, integrin alpha4beta7, 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	23.41 Å
Radius of gyration Rg (electron density) rg_electron	22.98 Å
Forward intensity I(0) i0	8395040.00
Molecular weight molecular_weight	21186.0 kDa
Excluded volume excluded_volume	26453 Å³
Envelope volume envelope_volume	33822 Å³
Hydration-shell volume shell_volume	14089 Å³
Envelope diameter envelope_diameter	88.5 Å
Shell Rg shell_rg	26.83 Å
Envelope Rg envelope_rg	23.46 Å
Shape Rg shape_rg	22.99 Å
Total Rg total_rg	23.56 Å
Total atoms total_atoms	2960
Residues n_residues	197
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	88.6 Å
Rg (real space) rg_real	23.79 Å
Rg uncertainty (real space) rg_real_error	0.93 Å
I(0) (real space) i0_real	8.3950e+06
I(0) uncertainty (real space) i0_real_error	1.2540e+05
Rg (reciprocal space) rg_reciprocal	23.70 Å
I(0) (reciprocal space) i0_reciprocal	8395000.0000
Solution quality estimate total_estimate	0.5361
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	0.617
Kurtosis Kurtosis kurtosis	-0.274
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2828000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.379; Stabil: 1.000; Sysdev: 0.223; Positv: 1.000; Valcen: 0.165; Smooth: 0.995

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Mucosal addressin cell adhesion molecule 1
Molecular weight formula_weight	22348.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3562

VKPLQVEPPEPVVAVALGASRQLTCRLACADRGASVQWRGLDTSLGAVQSDTGRSVLTVRNASLSAAGTRVCVGSCGGRTFQHTVQLLVYAFPNQLTVSPAALVPGDPEVACTAHKVTPVDPNALSFSLLVGGQELEGAQALGPEVQEEEEEPQGDEDVLFRVTERWRLPPLGTPVPPALYCQATMRLPGLELSHRQAIPVLHHHHHHH

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	Cricetulus griseus

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	247

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4hd9a1
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.1.1.0 — automated matches

Domain ID domain_id	d4hd9a2
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	4hd9A01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4hd9A02
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	64.476 Å
Unit-cell length b length_b	99.988 Å
Unit-cell length c length_c	69.668 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	1.700 Å
Low-resolution limit resolution_low	22.560 Å
R factor r_factor	0.1753
R_work r_work	0.1711
R_free r_free	0.2144

fit	/app/data/saxs_computation/hd/4hd9/4hd9.fit
pddf	/app/data/pr_computation/hd/4hd9/4hd9.pr.out
profile	/app/data/saxs_computation/hd/4hd9/4hd9.dat

Crystal structure of native human MAdCAM-1 D1D2 domain

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