SAXSdb — 1ncn

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

T lymphocyte activation antigen CD86

Homo sapiens

UniProt P42081

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 26–134	Fragment：Ig V-type domain	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG4000, NaAC, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.70 Å R-free 0.278
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 26–134	Fragment：Ig V-type domain	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG4000, NaAC, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.70 Å R-free 0.278

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 1NCN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1I85 CRYSTAL STRUCTURE OF THE CTLA-4/B7-2 COMPLEX Deposited 2001-03-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 26–134（109 aa） Fragment：IG V-TYPE (RECEPTOR BINDING) DOMAIN Chain B 26–134（109 aa） Fragment：IG V-TYPE (RECEPTOR BINDING) DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；PEG20K, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.20 Å R-free 0.300
5YXK High resolution crystal structure of Human B7-2 IgV domain in P21 space group Deposited 2017-12-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 26–134（109 aa） Fragment：Ig-like V-type Chain B 26–134（109 aa） Fragment：Ig-like V-type	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.1M Tris HCl pH 8.5, 2.4M Ammonium phosphate dibasic	Resolution 1.90 Å R-free 0.248
5YXK High resolution crystal structure of Human B7-2 IgV domain in P21 space group Deposited 2017-12-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 26–134（109 aa） Fragment：Ig-like V-type Chain D 26–134（109 aa） Fragment：Ig-like V-type	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.1M Tris HCl pH 8.5, 2.4M Ammonium phosphate dibasic	Resolution 1.90 Å R-free 0.248
8FXX Cryo-EM structure of cowpox virus M2 in complex with human B7.2 (heptameric ring) Deposited 2023-01-25	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 × 14 PDB declaration: tetradecameric	Chain C 26–134（109 aa） Chain E 26–134（109 aa） Chain G 26–134（109 aa） Chain H 26–134（109 aa） Chain J 26–134（109 aa） Chain L 26–134（109 aa） Chain N 26–134（109 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；150 mM Nacl, 25 mM HEPES, pH7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.26 Å
8FXY Cryo-EM structure of cowpox virus M2 in complex with human B7.2 (hexameric ring) Deposited 2023-01-25	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 × 12 PDB declaration: dodecameric	Chain C 26–243（218 aa） Chain E 26–243（218 aa） Chain G 26–243（218 aa） Chain H 26–243（218 aa） Chain J 26–243（218 aa） Chain L 26–243（218 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；150 mM Nacl, 25 mM HEPES, pH7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.34 Å
8HXB Cryo-EM structure of MPXV M2 hexamer in complex with human B7.2 Deposited 2023-01-04	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain G 26–238（213 aa） Chain H 26–238（213 aa） Chain I 26–238（213 aa） Chain J 26–238（213 aa） Chain K 26–238（213 aa） Chain L 26–238（213 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
8HXC Cryo-EM structure of MPXV M2 heptamer in complex with human B7.2 Deposited 2023-01-04	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain H 26–238（213 aa） Chain I 26–238（213 aa） Chain J 26–238（213 aa） Chain K 26–238（213 aa） Chain L 26–238（213 aa） Chain M 26–238（213 aa） Chain N 26–238（213 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.12 Å

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

View Construct and Data Evidence

UniProt name	CD86_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–110； UniProt 26–134 Author chain B； PDBConstruct 2–110； UniProt 26–134

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	1ncn
Deposition date deposition_date	2002-12-05
Structure title title	the receptor-binding domain of human B7-2
Keywords keywords	Ig V, beta strands, 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	20.79 Å
Radius of gyration Rg (electron density) rg_electron	20.28 Å
Forward intensity I(0) i0	11963100.00
Molecular weight molecular_weight	25665.0 kDa
Excluded volume excluded_volume	32072 Å³
Envelope volume envelope_volume	37958 Å³
Hydration-shell volume shell_volume	16705 Å³
Envelope diameter envelope_diameter	75.5 Å
Shell Rg shell_rg	25.42 Å
Envelope Rg envelope_rg	20.61 Å
Shape Rg shape_rg	20.23 Å
Total Rg total_rg	21.21 Å
Total atoms total_atoms	1804
Residues n_residues	220
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	73.9 Å
Rg (real space) rg_real	20.94 Å
Rg uncertainty (real space) rg_real_error	0.63 Å
I(0) (real space) i0_real	1.1960e+07
I(0) uncertainty (real space) i0_real_error	1.6640e+05
Rg (reciprocal space) rg_reciprocal	20.91 Å
I(0) (reciprocal space) i0_reciprocal	11960000.0000
Solution quality estimate total_estimate	0.7488
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.3 Å
Skewness Skewness skewness	0.555
Kurtosis Kurtosis kurtosis	-0.098
Angular range angular_range	— – 0.3800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5062000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.650; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.784; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1ncna1
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	d1ncna2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1ncnb1
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	d1ncnb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	1ncnA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1ncnB00
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 (2)

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Unit-cell length a length_a	56.690 Å
Unit-cell length b length_b	63.010 Å
Unit-cell length c length_c	58.610 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 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	19.830 Å
R factor r_factor	0.2520
R_work r_work	0.2140
R_free r_free	0.2780

Description description	T lymphocyte activation antigen CD86
Molecular weight formula_weight	12849.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1804

the receptor-binding domain of human B7-2

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

T lymphocyte activation antigen CD86

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

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	Escherichia coli

fit	/app/data/saxs_computation/nc/1ncn/1ncn.fit
pddf	/app/data/pr_computation/nc/1ncn/1ncn.pr.out
profile	/app/data/saxs_computation/nc/1ncn/1ncn.dat