SAXSdb — 4hbq

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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 23–224	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 23–224	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
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 23–224 Chain B； UniProt 23–224	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

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 4HBQ	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
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
4HC1 Crystal structure of a loop deleted mutant of human MAdCAM-1 D1D2 complexed with Fab 10G3 Deposited 2012-09-28	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 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 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 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 23–225（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 8 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 1–198； UniProt 23–224 Author chain B； PDBConstruct 1–198； UniProt 23–224

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	4hbq
Deposition date deposition_date	2012-09-28
Structure title title	Crystal structure of a loop deleted mutant of Human MAdCAM-1 D1D2
Keywords keywords	immunoglobulin superfamily, 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	31.06 Å
Radius of gyration Rg (electron density) rg_electron	31.10 Å
Forward intensity I(0) i0	32124900.00
Molecular weight molecular_weight	43850.0 kDa
Excluded volume excluded_volume	54785 Å³
Envelope volume envelope_volume	74690 Å³
Hydration-shell volume shell_volume	21560 Å³
Envelope diameter envelope_diameter	109.3 Å
Shell Rg shell_rg	34.72 Å
Envelope Rg envelope_rg	31.71 Å
Shape Rg shape_rg	31.13 Å
Total Rg total_rg	31.33 Å
Total atoms total_atoms	6164
Residues n_residues	412
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	101.9 Å
Rg (real space) rg_real	31.24 Å
Rg uncertainty (real space) rg_real_error	1.07 Å
I(0) (real space) i0_real	3.2120e+07
I(0) uncertainty (real space) i0_real_error	5.8970e+05
Rg (reciprocal space) rg_reciprocal	31.17 Å
I(0) (reciprocal space) i0_reciprocal	32120000.0000
Solution quality estimate total_estimate	0.8379
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.0 Å
Skewness Skewness skewness	0.298
Kurtosis Kurtosis kurtosis	-0.751
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4357000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.812; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.590; Smooth: 0.864

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Mucosal addressin cell adhesion molecule 1
Molecular weight formula_weight	21699.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7883

VKPLQVEPPEPVVAVALGASRQLTCRLACADRGASVQWRGLDTSLGAVQSDTGRSVLTVRNASLSAAGTRVCVGSCGGRTFQHTVQLLVYAFPNQLTVSPAALVPGDPEVACTAHKVTPVDPNALSFSLLVGGQELEGAQALGPEVQQEPIGGDVLFRVTERWRLPPLGTPVPPALYCQATMRLPGLELSHRQAIPVLGGENLYFQ

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	Homo sapiens

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

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

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	man
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	508

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d4hbqa1
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	d4hbqa2
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	d4hbqa3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4hbqb1
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	d4hbqb2
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	d4hbqb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	4hbqA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4hbqA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4hbqB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4hbqB02
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	58.320 Å
Unit-cell length b length_b	69.700 Å
Unit-cell length c length_c	101.200 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	44.728 Å
R factor r_factor	0.1441
R_work r_work	0.1434
R_free r_free	0.1785

fit	/app/data/saxs_computation/hb/4hbq/4hbq.fit
pddf	/app/data/pr_computation/hb/4hbq/4hbq.pr.out
profile	/app/data/saxs_computation/hb/4hbq/4hbq.dat

Crystal structure of a loop deleted mutant of Human MAdCAM-1 D1D2

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