SAXSdb — 2e56

▼

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

Lymphocyte antigen 96

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 17–160	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 MYR MYRISTIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.3；277 K；20% PEG8000, 120mM Na-acetate,70mM Na-cacodylate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 2.00 Å R-free 0.249

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 2E56	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2E59 Crystal structure of human MD-2 in complex with lipid IVa Deposited 2006-12-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 17–160（144 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 LP5 (R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE × 1 LP4 2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-4-O-phosphono-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；277 K；15% PEG3350, 40mM Na-citrate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 2.21 Å R-free 0.263
2Z65 Crystal structure of the human TLR4 TV3 hybrid-MD-2-Eritoran complex Deposited 2007-07-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 19–158（140 aa）	Not recorded	E55 3-O-DECYL-2-DEOXY-6-O-{2-DEOXY-3-O-[(3R)-3-METHOXYDECYL]-6-O-METHYL-2-[(11Z)-OCTADEC-11-ENOYLAMINO]-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSYL}-2-[(3-OXOTETRADECANOYL)AMINO]-1-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；296 K；0.2M Ammonium Sulfate, 0.1M Sodium Acetate, 20% PEG 4000, 5% Ethanol, pH 4.5, VAPOR DIFFUSION, temperature 296K	Resolution 2.70 Å R-free 0.289
2Z65 Crystal structure of the human TLR4 TV3 hybrid-MD-2-Eritoran complex Deposited 2007-07-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 19–158（140 aa）	Not recorded	E55 3-O-DECYL-2-DEOXY-6-O-{2-DEOXY-3-O-[(3R)-3-METHOXYDECYL]-6-O-METHYL-2-[(11Z)-OCTADEC-11-ENOYLAMINO]-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSYL}-2-[(3-OXOTETRADECANOYL)AMINO]-1-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；296 K；0.2M Ammonium Sulfate, 0.1M Sodium Acetate, 20% PEG 4000, 5% Ethanol, pH 4.5, VAPOR DIFFUSION, temperature 296K	Resolution 2.70 Å R-free 0.289
3FXI Crystal structure of the human TLR4-human MD-2-E.coli LPS Ra complex Deposited 2009-01-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 19–160（142 aa） Chain D 19–160（142 aa）	Not recorded	FTT 3-HYDROXY-TETRADECANOIC ACID × 8 DAO LAURIC ACID × 2 MYR MYRISTIC ACID × 2 PO4 PHOSPHATE ION × 8 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；278 K；50mM MgCl2, 0.1M Na-HEPES pH 7.5, 30% PEG MME 550, VAPOR DIFFUSION, HANGING DROP, temperature 278K	Resolution 3.10 Å R-free 0.281
3ULA Crystal structure of the TV3 mutant F63W-MD-2-Eritoran complex Deposited 2011-11-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 19–158（140 aa） Fragment：UNP RESIDUES 19-158	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 E55 3-O-DECYL-2-DEOXY-6-O-{2-DEOXY-3-O-[(3R)-3-METHOXYDECYL]-6-O-METHYL-2-[(11Z)-OCTADEC-11-ENOYLAMINO]-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSYL}-2-[(3-OXOTETRADECANOYL)AMINO]-1-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；296 K；0.1M sodium acetate (pH4.5), 22% w/v PEG 8000, 0.2M lithium sulfate, VAPOR DIFFUSION, temperature 296K	Resolution 3.60 Å R-free 0.341
3ULA Crystal structure of the TV3 mutant F63W-MD-2-Eritoran complex Deposited 2011-11-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 19–158（140 aa） Fragment：UNP RESIDUES 19-158	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 E55 3-O-DECYL-2-DEOXY-6-O-{2-DEOXY-3-O-[(3R)-3-METHOXYDECYL]-6-O-METHYL-2-[(11Z)-OCTADEC-11-ENOYLAMINO]-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSYL}-2-[(3-OXOTETRADECANOYL)AMINO]-1-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；296 K；0.1M sodium acetate (pH4.5), 22% w/v PEG 8000, 0.2M lithium sulfate, VAPOR DIFFUSION, temperature 296K	Resolution 3.60 Å R-free 0.341
4G8A Crystal structure of human TLR4 polymorphic variant D299G and T399I in complex with MD-2 and LPS Deposited 2012-07-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 17–160（144 aa） Chain D 17–160（144 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 LP4 2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-4-O-phosphono-beta-D-glucopyranose × 2 LP5 (R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE × 2 DAO LAURIC ACID × 2 MYR MYRISTIC ACID × 2 KDO 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；26-30% (w/v) PEG1000, 0.1M Tris-HCl (pH 8.0), VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.40 Å R-free 0.249

5 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LY96_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–144； UniProt 17–160

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2e56
Deposition date deposition_date	2006-12-19
Structure title title	Crystal structure of human MD-2
Keywords keywords	INNATE IMMUNITY, LIPID-BINDING, LIPID BINDING PROTEIN; LIPID BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	17.35 Å
Radius of gyration Rg (electron density) rg_electron	15.67 Å
Forward intensity I(0) i0	5432600.00
Molecular weight molecular_weight	17664.0 kDa
Excluded volume excluded_volume	22557 Å³
Envelope volume envelope_volume	26139 Å³
Hydration-shell volume shell_volume	14275 Å³
Envelope diameter envelope_diameter	52.7 Å
Shell Rg shell_rg	21.41 Å
Envelope Rg envelope_rg	15.92 Å
Shape Rg shape_rg	15.65 Å
Total Rg total_rg	16.86 Å
Total atoms total_atoms	1238
Residues n_residues	144
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	54.2 Å
Rg (real space) rg_real	17.24 Å
Rg uncertainty (real space) rg_real_error	0.29 Å
I(0) (real space) i0_real	5.4330e+06
I(0) uncertainty (real space) i0_real_error	6.1290e+04
Rg (reciprocal space) rg_reciprocal	17.26 Å
I(0) (reciprocal space) i0_reciprocal	5433000.0000
Solution quality estimate total_estimate	0.8996
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	53.5 Å
Skewness Skewness skewness	0.099
Kurtosis Kurtosis kurtosis	-0.400
Angular range angular_range	— – 0.4600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	467600.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.901; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.993

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Lymphocyte antigen 96
Molecular weight formula_weight	16586.1 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	1397

EAQKQYWVCNSSDASISYTYCDKMQYPISINVNPCIELKGSKGLLHIFYIPRRDLKQLYFNLYITVNTMNLPKRKEVICRGSDDDYSFCRALKGETVNTTISFSFKGIKFSKGKYKCVVEAISGSPEEMLFCLEFVILHQPNSN

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	Pichia pastoris

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	2

Entity 3 Entity 3 non-polymer

Description description	MYRISTIC ACID
Molecular weight formula_weight	228.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	143

▼

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2e56A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	770 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	53.113 Å
Unit-cell length b length_b	53.113 Å
Unit-cell length c length_c	111.447 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 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	48.390 Å
R factor r_factor	0.1965
R_work r_work	0.1941
R_free r_free	0.2492

fit	/app/data/saxs_computation/e5/2e56/2e56.fit
pddf	/app/data/pr_computation/e5/2e56/2e56.pr.out
profile	/app/data/saxs_computation/e5/2e56/2e56.dat

Crystal structure of human MD-2

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

Lymphocyte antigen 96

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