SAXSdb — 1ci5

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

PROTEIN (LYMPHOCYTE FUNCTION-ASSOCIATED ANTIGEN 3(CD58))

Homo sapiens

UniProt P19256

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 29–123	Fragment：ADHESION DOMAIN Mutation：F1S/V9K/V21Q/V58K/T85S/L93G	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 7.5；298 K；Ionic strength (raw mmCIF value) 10 mM NAPO4；Pressure 1 NMR sample composition：10% D2O	Resolution not provided

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 1CI5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CCZ CRYSTAL STRUCTURE OF THE CD2-BINDING DOMAIN OF CD58 (LYMPHOCYTE FUNCTION-ASSOCIATED ANTIGEN 3) AT 1.8-A RESOLUTION Deposited 1999-03-02	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–122（94 aa） Fragment：CD2-BINDING DOMAIN	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；0.1M SODIUM ACETATE PH 4.6, 2.0 M SODIUM CHLORIDE	Resolution 1.80 Å R-free 0.243

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LFA3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–95； UniProt 29–123

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	1ci5
Deposition date deposition_date	1999-04-07
Structure title title	GLYCAN-FREE MUTANT ADHESION DOMAIN OF HUMAN CD58 (LFA-3)
Keywords keywords	ADHESION GLYCOPROTEIN, IMMUNOGLOBULIN SUPERFAMILY V-SET DOMAIN, CELL SURFACE RECEPTOR, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	13.24 Å
Radius of gyration Rg (electron density) rg_electron	12.82 Å
Forward intensity I(0) i0	663523000.00
Molecular weight molecular_weight	219760.0 kDa
Excluded volume excluded_volume	274850 Å³
Envelope volume envelope_volume	22192 Å³
Hydration-shell volume shell_volume	13120 Å³
Envelope diameter envelope_diameter	47.7 Å
Shell Rg shell_rg	20.16 Å
Envelope Rg envelope_rg	14.53 Å
Shape Rg shape_rg	12.78 Å
Total Rg total_rg	13.08 Å
Total atoms total_atoms	30460
Residues n_residues	1900
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	44.9 Å
Rg (real space) rg_real	13.18 Å
Rg uncertainty (real space) rg_real_error	0.31 Å
I(0) (real space) i0_real	6.6350e+08
I(0) uncertainty (real space) i0_real_error	7.7220e+06
Rg (reciprocal space) rg_reciprocal	13.18 Å
I(0) (reciprocal space) i0_reciprocal	663500000.0000
Solution quality estimate total_estimate	0.7911
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.5 Å
Skewness Skewness skewness	0.211
Kurtosis Kurtosis kurtosis	-0.263
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	274200.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.761; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; 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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1ci5a1
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)

CATH v4.4 (1 domains)

Domain ID domain_id	1ci5A00
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	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	1

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

Description description	PROTEIN (LYMPHOCYTE FUNCTION-ASSOCIATED ANTIGEN 3(CD58))
Molecular weight formula_weight	11003.2 kDa
Mutation mutation	F1S/V9K/V21Q/V58K/T85S/L93G
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	30460

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 BL21(DE3)

GLYCAN-FREE MUTANT ADHESION DOMAIN OF HUMAN CD58 (LFA-3)

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

PROTEIN (LYMPHOCYTE FUNCTION-ASSOCIATED ANTIGEN 3(CD58))

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/ci/1ci5/1ci5.fit
pddf	/app/data/pr_computation/ci/1ci5/1ci5.pr.out
profile	/app/data/saxs_computation/ci/1ci5/1ci5.dat