SAXSdb — 8so3

▼

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

Lymphocyte activation gene 3 protein

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain D； UniProt 1–525 Chain X； UniProt 1–525	Not recorded	favezelimab Fab heavy chain × 2 favezelimab Fab light chain × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.61 Å

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 8SO3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7TZG Structure of human LAG3 in complex with antibody single-chain variable fragment Deposited 2022-02-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 23–430（408 aa） Fragment：ectodomain Chain D 23–430（408 aa） Fragment：ectodomain	Mutation：M171I Mutation：M171I	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；1% Tacsimate at pH 5.0, 0.05 M sodium citrate tribasic dihydrate, pH 5.6 and 7% PEG3350	Resolution 3.71 Å R-free 0.275
7TZH Structure of human LAG3 domains 3-4 in complex with antibody single chain-variable fragment Deposited 2022-02-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 261–450（190 aa） Fragment：ectodomain	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293.15 K；0.1 M HEPES pH 7.1, 13% PEG20000	Resolution 2.43 Å R-free 0.255
7TZH Structure of human LAG3 domains 3-4 in complex with antibody single chain-variable fragment Deposited 2022-02-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 261–450（190 aa） Fragment：ectodomain	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293.15 K；0.1 M HEPES pH 7.1, 13% PEG20000	Resolution 2.43 Å R-free 0.255
7UM3 Crystal structure of a Fab in complex with a peptide derived from the LAG-3 D1 domain loop insertion Deposited 2022-04-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 82–97（16 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M Bis-Tris, pH 5.5, 25% PEG3350	Resolution 2.40 Å R-free 0.265
7UM3 Crystal structure of a Fab in complex with a peptide derived from the LAG-3 D1 domain loop insertion Deposited 2022-04-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 82–97（16 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M Bis-Tris, pH 5.5, 25% PEG3350	Resolution 2.40 Å R-free 0.265
8SR0 CryoEM structure of a therapeutic antibody (favezelimab) bound to human LAG3 local refined Deposited 2023-05-05	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 1–525（525 aa） Chain X 1–525（525 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.53 Å
9BF9 Human LAG-3-HLA-DR1 complex Deposited 2024-04-17	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 Heteromer；Protein × 8 PDB declaration: tetrameric	Chain D 23–429（407 aa）	Not recorded	SO4 SULFATE ION × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；22% PEG 8000, 0.16M Li2SO4, 0.1M HEPES pH 7.6	Resolution 3.40 Å R-free 0.253

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

View Construct and Data Evidence

UniProt name	LAG3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain D； PDBConstruct 1–525； UniProt 1–525 Author chain X； PDBConstruct 1–525； UniProt 1–525

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	8so3
Deposition date deposition_date	2023-04-28
Structure title title	CryoEM structure of a therapeutic antibody (favezelimab) bound to human LAG3
Keywords keywords	Lymphocyte activation gene 3 protein, favezelimab-LAG3 complex, cryoEM, Single particle reconstruction., IMMUNOSUPPRESSANT; IMMUNOSUPPRESSANT
Experimental Method method	ELECTRON MICROSCOPY

▼

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

Radius of gyration Rg (Guinier) rg_guinier	39.70 Å
Radius of gyration Rg (electron density) rg_electron	39.00 Å
Forward intensity I(0) i0	251571000.00
Molecular weight molecular_weight	124240.0 kDa
Excluded volume excluded_volume	153670 Å³
Envelope volume envelope_volume	242300 Å³
Hydration-shell volume shell_volume	51907 Å³
Envelope diameter envelope_diameter	125.4 Å
Shell Rg shell_rg	45.34 Å
Envelope Rg envelope_rg	37.15 Å
Shape Rg shape_rg	39.01 Å
Total Rg total_rg	39.40 Å
Total atoms total_atoms	16770
Residues n_residues	1205
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	123.1 Å
Rg (real space) rg_real	39.42 Å
Rg uncertainty (real space) rg_real_error	1.06 Å
I(0) (real space) i0_real	2.5160e+08
I(0) uncertainty (real space) i0_real_error	4.0170e+06
Rg (reciprocal space) rg_reciprocal	39.60 Å
I(0) (reciprocal space) i0_reciprocal	251600000.0000
Solution quality estimate total_estimate	0.8650
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	58.5 Å
Skewness Skewness skewness	0.019
Kurtosis Kurtosis kurtosis	-0.444
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	24210000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.809; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.822

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Lymphocyte activation gene 3 protein
Molecular weight formula_weight	57508.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,X
Atom count atom_count	16770

MWEAQFLGLLFLQPLWVAPVKPLQPGAEVPVVWAQEGAPAQLPCSPTIPLQDLSLLRRAGVTWQHQPDSGPPAAAPGHPLAPGPHPAAPSSWGPRPRRYTVLSVGPGGLRSGRLPLQPRVQLDERGRQRGDFSLWLRPARRADAGEYRAAVHLRDRALSCRLRLRLGQASMTASPPGSLRASDWVILNCSFSRPDRPASVHWFRNRGQGRVPVRESPHHHLAESFLFLPQVSPMDSGPWGCILTYRDGFNVSIMYNLTVLGLEPPTPLTVYAGAGSRVGLPCRLPAGVGTRSFLTAKWTPPGGGPDLLVTGDNGDFTLRLEDVSQAQAGTYTCHIHLQEQQLNATVTLAIITVTPKSFGSPGSLGKLLCEVTPVSGQERFVWSSLDTPSQRSFSGPWLEAQEAQLLSQPWQCQLYQGERLLGAAVYFTELSSPGAQRSGRAPGALPAGHLLLFLILGVLSLLLLVTGAFGFHLWRRQWRPRRFSALEQGIHPPQAQSKIEELEQEPEPEPEPEPEPEPEPEPEQL

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 polymer

Description description	favezelimab Fab heavy chain
Molecular weight formula_weight	27245.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,Y

MGWTWIFLFFLSGTAGVLSEVLLLQSGPELVKPGTSVKIPCKASGYTFTDYNVDWVKQRHGKGLEWIGDINPNNGGTIYSQKFKGKATLTVDKSSSTAFMELRSLTSEDTAVYFCARNYRWFGAMDHWGQGTSVTVSSTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTAGWSHPQFEK

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	favezelimab Fab light chain
Molecular weight formula_weight	25915.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,Z

METDTILLWVLLLWVPGSTGDIVLTQSPASLAVSPGQRATISCKASQSLDYEGDSDMNWYQQKPGQPPRLLISGASNLESGIPARFSGSGSGTDFTVNIHPVEEEDAATYYCQQSTEDPRTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKYQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

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	syn
Copy count entity_count	4

▶

8. Citations (1)

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.61 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	171144

fit	/app/data/saxs_computation/so/8so3/8so3.fit
pddf	/app/data/pr_computation/so/8so3/8so3.pr.out
profile	/app/data/saxs_computation/so/8so3/8so3.dat

CryoEM structure of a therapeutic antibody (favezelimab) bound to human LAG3

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

Lymphocyte activation gene 3 protein

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)