SAXSdb — 3rnk

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

Programmed cell death protein 1

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 34–150	Fragment：Residues 34-150 Mutation：C83S, A132L	Programmed cell death 1 ligand 2 × 1 （Q9WUL5）	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

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 3RNK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1NPU CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF MURINE PD-1 Deposited 2003-01-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 34–150（117 aa） Fragment：Ig V-type domain	Mutation：C50S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG8000, NaAc, NaCacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.228
3BIK Crystal Structure of the PD-1/PD-L1 Complex Deposited 2007-11-30	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 25–157（133 aa） Fragment：EXTRACELLULAR DOMAIN	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；20% PEG 3350, 200MM NH4H2PO4, pH 6.00, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.65 Å R-free 0.268
3BIK Crystal Structure of the PD-1/PD-L1 Complex Deposited 2007-11-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 25–157（133 aa） Fragment：EXTRACELLULAR DOMAIN	Mutation：YES	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；20% PEG 3350, 200MM NH4H2PO4, pH 6.00, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.65 Å R-free 0.268
3BP5 Crystal structure of the mouse PD-1 and PD-L2 complex Deposited 2007-12-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 34–150（117 aa） Fragment：Extrocellular domain	Mutation：C50S	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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 34–150（117 aa） Fragment：Extrocellular domain	Mutation：C50S, A99L	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
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 mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 34–150（117 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
3SBW Crystal structure of the complex between the extracellular domains of mouse PD-1 mutant and human PD-L1 Deposited 2011-06-06	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 34–150（117 aa） Fragment：UNP residues 34-150	Mutation：C83S, A132L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；277 K；0.1M Sodium citrate pH 5, 20% PEG 8000, Vapor diffusion, Sitting drop, temperature 277K	Resolution 2.28 Å R-free 0.270
3SBW Crystal structure of the complex between the extracellular domains of mouse PD-1 mutant and human PD-L1 Deposited 2011-06-06	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 34–150（117 aa） Fragment：UNP residues 34-150	Mutation：C83S, A132L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；277 K；0.1M Sodium citrate pH 5, 20% PEG 8000, Vapor diffusion, Sitting drop, temperature 277K	Resolution 2.28 Å R-free 0.270

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PDCD1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–117； UniProt 34–150

Programmed cell death 1 ligand 2

Mus musculus

UniProt Q9WUL5

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 20–123	Fragment：Rsidues 20-123	Programmed cell death protein 1 × 1 （Q02242）	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

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 3RNK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3BOV Crystal structure of the receptor binding domain of mouse PD-L2 Deposited 2007-12-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 20–123（104 aa） Fragment：Immunoglobulin-like V-type: residues 20-123	Not recorded	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
3BP5 Crystal structure of the mouse PD-1 and PD-L2 complex Deposited 2007-12-18	Different construct 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 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
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 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	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–104； 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	3rnk
Deposition date deposition_date	2011-04-22
Structure title title	Crystal structure of the complex between mouse PD-1 mutant and PD-L2 IgV domain
Keywords keywords	PD-1; PD-L2; B7-DC; Programmed death-1 Ligand 2, complex, costimulatory, IgV, 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	18.87 Å
Radius of gyration Rg (electron density) rg_electron	18.00 Å
Forward intensity I(0) i0	10759800.00
Molecular weight molecular_weight	24160.0 kDa
Excluded volume excluded_volume	30158 Å³
Envelope volume envelope_volume	35553 Å³
Hydration-shell volume shell_volume	16911 Å³
Envelope diameter envelope_diameter	66.7 Å
Shell Rg shell_rg	23.70 Å
Envelope Rg envelope_rg	18.43 Å
Shape Rg shape_rg	18.00 Å
Total Rg total_rg	18.89 Å
Total atoms total_atoms	1700
Residues n_residues	216
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	64.1 Å
Rg (real space) rg_real	18.84 Å
Rg uncertainty (real space) rg_real_error	0.40 Å
I(0) (real space) i0_real	1.0760e+07
I(0) uncertainty (real space) i0_real_error	1.2840e+05
Rg (reciprocal space) rg_reciprocal	18.85 Å
I(0) (reciprocal space) i0_reciprocal	10760000.0000
Solution quality estimate total_estimate	0.7965
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	57.0 Å
Skewness Skewness skewness	0.345
Kurtosis Kurtosis kurtosis	-0.255
Angular range angular_range	— – 0.4200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4066000.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.793; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Programmed cell death protein 1
Molecular weight formula_weight	13218.8 kDa
Mutation mutation	C83S, A132L
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	1818

SLTFYPAWLTVSEGANATFTCSLSNWSEDLMLNWNRLSPSNQTEKQAAFSNGLSQPVQDARFQIIQLPNRHDFHMNILDTRRNDSGIYLCGAISLHPKLKIEESPGAELVVTERILE

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	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Programmed cell death 1 ligand 2
Molecular weight formula_weight	11691.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

LFTVTAPKEVYTVDVGSSVSLECDFDRRECTELEGIRASLQKVENDTSLQSERATLLEEQLPLGKALFHIPSVQVRDSGQYRCLVICGAAWDYKYLTVKVKASY

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	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	110

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3rnka_
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.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d3rnkb_
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 (2 domains)

Domain ID domain_id	3rnkA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3rnkB00
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	36.057 Å
Unit-cell length b length_b	60.246 Å
Unit-cell length c length_c	80.087 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.740 Å
Low-resolution limit resolution_low	48.170 Å
R factor r_factor	0.1974
R_work r_work	0.1947
R_free r_free	0.2469

fit	/app/data/saxs_computation/rn/3rnk/3rnk.fit
pddf	/app/data/pr_computation/rn/3rnk/3rnk.pr.out
profile	/app/data/saxs_computation/rn/3rnk/3rnk.dat

Crystal structure of the complex between mouse PD-1 mutant and PD-L2 IgV domain

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

Programmed cell death protein 1

State in the Current Structure

Other States of the Same Protein in the Database

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)