SAXSdb — 3bov

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

Programmed cell death 1 ligand 2

Mus musculus

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 20–123	Fragment：Immunoglobulin-like V-type: residues 20-123	NA SODIUM ION × 1 FMT FORMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.4 M Magnesium Formate, 0.1 M Tris-HCl pH 8.5, Vapor diffusion, Sitting drop, temperature 277K, VAPOR DIFFUSION, SITTING DROP	Resolution 1.77 Å R-free 0.223

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 3BOV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3BP5 Crystal structure of the mouse PD-1 and PD-L2 complex Deposited 2007-12-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 20–220（201 aa） Fragment：Extrocellular domain	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions Sitting drop；pH 8.5；291 K；20% PEG 6000, 0.1 M Tris pH 8.5, Sitting drop, temperature 291K	Resolution 1.80 Å R-free 0.228
3BP6 Crystal structure of the mouse PD-1 Mutant and PD-L2 complex Deposited 2007-12-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 20–220（201 aa） Fragment：Extrocellular domain	Not recorded	GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions Sitting drop；pH 8.5；291 K；20% PEG 6000, 0.1 M Tris pH 8.5, Sitting drop, temperature 291K	Resolution 1.60 Å R-free 0.218
3RNK Crystal structure of the complex between mouse PD-1 mutant and PD-L2 IgV domain Deposited 2011-04-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 20–123（104 aa） Fragment：Rsidues 20-123	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；0.1M HEPES pH 7, 0.1M Magnesium chloride, 15% PEG 4000, Vapor diffusion, Sitting drop, temperature 291K	Resolution 1.74 Å R-free 0.247
3RNQ Crystal structure of the complex between the extracellular domains of mouse PD-1 mutant and PD-L2 Deposited 2011-04-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 20–220（201 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；0.1M Tris pH 8, 17.5% PEG 6000, Vapor diffusion, Sitting drop, temperature 298K	Resolution 1.60 Å R-free 0.207

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PD1L2_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–105； UniProt 20–123

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	3bov
Deposition date deposition_date	2007-12-17
Structure title title	Crystal structure of the receptor binding domain of mouse PD-L2
Keywords keywords	PD-L2; B7-DC, Programmed death-1 Ligand2, Glycoprotein, Immunoglobulin domain, Membrane, Receptor, Transmembrane, 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	15.23 Å
Radius of gyration Rg (electron density) rg_electron	14.13 Å
Forward intensity I(0) i0	2839950.00
Molecular weight molecular_weight	11744.0 kDa
Excluded volume excluded_volume	14728 Å³
Envelope volume envelope_volume	17245 Å³
Hydration-shell volume shell_volume	10853 Å³
Envelope diameter envelope_diameter	57.6 Å
Shell Rg shell_rg	19.41 Å
Envelope Rg envelope_rg	14.68 Å
Shape Rg shape_rg	14.12 Å
Total Rg total_rg	15.35 Å
Total atoms total_atoms	824
Residues n_residues	104
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	61.1 Å
Rg (real space) rg_real	15.25 Å
Rg uncertainty (real space) rg_real_error	0.58 Å
I(0) (real space) i0_real	2.8400e+06
I(0) uncertainty (real space) i0_real_error	3.5540e+04
Rg (reciprocal space) rg_reciprocal	15.25 Å
I(0) (reciprocal space) i0_reciprocal	2840000.0000
Solution quality estimate total_estimate	0.6833
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.8 Å
Skewness Skewness skewness	0.465
Kurtosis Kurtosis kurtosis	0.118
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	839600.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.423; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.611; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Programmed cell death 1 ligand 2
Molecular weight formula_weight	11822.4 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	944

MLFTVTAPKEVYTVDVGSSVSLECDFDRRECTELEGIRASLQKVENDTSLQSERATLLEEQLPLGKALFHIPSVQVRDSGQYRCLVICGAAWDYKYLTVKVKASY

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	81

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3bova_
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

CATH v4.4 (1 domains)

Domain ID domain_id	3bovA00
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	45.173 Å
Unit-cell length b length_b	116.637 Å
Unit-cell length c length_c	45.108 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 2
Space-group number int_tables_number	21
Crystal system crystal_system	—

Resolution resolution	1.770 Å
Low-resolution limit resolution_low	45.130 Å
R factor r_factor	0.1920
R_work r_work	0.1900
R_free r_free	0.2230

fit	/app/data/saxs_computation/bo/3bov/3bov.fit
pddf	/app/data/pr_computation/bo/3bov/3bov.pr.out
profile	/app/data/saxs_computation/bo/3bov/3bov.dat

Crystal structure of the receptor binding domain of mouse PD-L2

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

Programmed cell death 1 ligand 2

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