SAXSdb — 8tui

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

Killer cell immunoglobulin-like receptor 2DL3

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	Other combination Heteromer Protein × 3 其他Polymer 1 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 22–245	Fragment：extracellular domain	Lirilumab Fab Heavy Chain × 1 Lirilumab Fab Light chain × 1 ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；295 K；200 mM Potassium Sodium Tartrate and 20%(w/v) PEG 3350	Resolution 2.75 Å R-free 0.254

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 8TUI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B6U CRYSTAL STRUCTURE OF THE HUMAN KILLER CELL INHIBITORY RECEPTOR (KIR2DL3) SPECIFIC FOR HLA-CW3 RELATED ALLELES Deposited 1999-01-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 22–245（224 aa） Fragment：EXTRACELLULAR REGION	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 3.00 Å R-free 0.320
6PAG Killer cell immunoglobulin-like receptor 2DL3 in complex with HLA-C*07:02 Deposited 2019-06-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 22–225（204 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.2 M Ammonium acetate, 0.1 M Tris-HCl pH.8.0 and 25% PEG 3350.	Resolution 2.50 Å R-free 0.254

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	KI2L3_HUMAN
Isoform	P43628-1
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–224； UniProt 22–245

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	8tui
Deposition date deposition_date	2023-08-16
Structure title title	Crystal structure of Fab-Lirilumab bound to KIR2DL3
Keywords keywords	antibody, KIR2DL3, complex, lirilumab, 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	29.45 Å
Radius of gyration Rg (electron density) rg_electron	29.21 Å
Forward intensity I(0) i0	57744800.00
Molecular weight molecular_weight	59239.0 kDa
Excluded volume excluded_volume	73882 Å³
Envelope volume envelope_volume	95256 Å³
Hydration-shell volume shell_volume	28964 Å³
Envelope diameter envelope_diameter	108.8 Å
Shell Rg shell_rg	34.41 Å
Envelope Rg envelope_rg	29.37 Å
Shape Rg shape_rg	29.16 Å
Total Rg total_rg	29.83 Å
Total atoms total_atoms	4171
Residues n_residues	534
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	106.0 Å
Rg (real space) rg_real	29.68 Å
Rg uncertainty (real space) rg_real_error	1.09 Å
I(0) (real space) i0_real	5.7740e+07
I(0) uncertainty (real space) i0_real_error	8.7030e+05
Rg (reciprocal space) rg_reciprocal	29.58 Å
I(0) (reciprocal space) i0_reciprocal	57740000.0000
Solution quality estimate total_estimate	0.8308
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	0
Primary peak position r_peak_primary	— Å
Skewness Skewness skewness	0.574
Kurtosis Kurtosis kurtosis	-0.143
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10890000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.681; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.794; Smooth: 0.959

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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	Lirilumab Fab Heavy Chain
Molecular weight formula_weight	27793.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H
Atom count atom_count	4176

QSQVQLVQSGAEVKKPGSSVKVSCKASGGTFSFYAISWVRQAPGQGLEWMGGFIPIFGAANYAQKFQGRVTITADESTSTAYMELSSLRSDDTAVYYCARIPSGSYYYDYDMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCASLVPRGSGWSHPQFEKGGGSGGGSGGGSWSHPQFEK

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Cricetulus griseus

Entity 2 Entity 2 polymer

Description description	Lirilumab Fab Light chain
Molecular weight formula_weight	23548.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

EIVLTQSPVTLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWMYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Cricetulus griseus

Entity 3 Entity 3 polymer

Description description	Killer cell immunoglobulin-like receptor 2DL3
Molecular weight formula_weight	28189.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

HEGVHRKPSLLAHPGPLVKSEETVILQCWSDVRFQHFLLHREGKFKDTLHLIGEHHDGVSKANFSIGPMMQDLAGTYRCYGSVTHSPYQLSAPSDPLDIVITGLYEKPSLSAQPGPTVLAGESVTLSCSSRSSYDMYHLSREGEAHERRFSAGPKVNGTFQADFPLGPATHGGTYRCFGSFRDSPYEWSNSSDPLLVSVTGNPSNSWPSPTEPSSETGNPRHLHAAAEQKLISEEDLNLDLVPRGSSSHHHHHHSSG

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 4 Entity 4 branched

Description description	;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	1260.2 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	5

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8. Citations (1)

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Unit-cell length a length_a	58.379 Å
Unit-cell length b length_b	84.270 Å
Unit-cell length c length_c	62.268 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	115.86 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	2.750 Å
Low-resolution limit resolution_low	46.660 Å
R factor r_factor	0.2126
R_work r_work	0.2109
R_free r_free	0.2540

fit	/app/data/saxs_computation/tu/8tui/8tui.fit
pddf	/app/data/pr_computation/tu/8tui/8tui.pr.out
profile	/app/data/saxs_computation/tu/8tui/8tui.dat

Crystal structure of Fab-Lirilumab bound to KIR2DL3

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

Killer cell immunoglobulin-like receptor 2DL3

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 (5)

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 branched

Entity 5 Entity 5 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)