SAXSdb — 1ccz

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

PROTEIN (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 29–122	Fragment：CD2-BINDING DOMAIN	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

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 1CCZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CI5 GLYCAN-FREE MUTANT ADHESION DOMAIN OF HUMAN CD58 (LFA-3) Deposited 1999-04-07	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 29–123（95 aa） Fragment：ADHESION DOMAIN	Mutation：F1S/V9K/V21Q/V58K/T85S/L93G	No recorded non-water small molecule	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

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 1–94； UniProt 29–122

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	1ccz
Deposition date deposition_date	1999-03-02
Structure title title	CRYSTAL STRUCTURE OF THE CD2-BINDING DOMAIN OF CD58 (LYMPHOCYTE FUNCTION-ASSOCIATED ANTIGEN 3) AT 1.8-A RESOLUTION
Keywords keywords	CD58, LFA-3, GLYCOPROTEIN; GLYCOPROTEIN
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	23.26 Å
Radius of gyration Rg (electron density) rg_electron	22.91 Å
Forward intensity I(0) i0	7581470.00
Molecular weight molecular_weight	20524.0 kDa
Excluded volume excluded_volume	25691 Å³
Envelope volume envelope_volume	31481 Å³
Hydration-shell volume shell_volume	13055 Å³
Envelope diameter envelope_diameter	82.8 Å
Shell Rg shell_rg	26.72 Å
Envelope Rg envelope_rg	23.38 Å
Shape Rg shape_rg	22.89 Å
Total Rg total_rg	23.54 Å
Total atoms total_atoms	1440
Residues n_residues	171
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	83.5 Å
Rg (real space) rg_real	23.66 Å
Rg uncertainty (real space) rg_real_error	0.91 Å
I(0) (real space) i0_real	7.5810e+06
I(0) uncertainty (real space) i0_real_error	1.1620e+05
Rg (reciprocal space) rg_reciprocal	23.57 Å
I(0) (reciprocal space) i0_reciprocal	7581000.0000
Solution quality estimate total_estimate	0.4943
Solution quality rating solution_quality	SUSPICIOUS a SUSPICIOUS solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.0 Å
Skewness Skewness skewness	0.592
Kurtosis Kurtosis kurtosis	-0.472
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2302000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.354; Stabil: 1.000; Sysdev: 0.115; Positv: 1.000; Valcen: 0.162; Smooth: 0.854

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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	PROTEIN (CD58)
Molecular weight formula_weight	19937.6 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	1650

FSQQIYGVVYGNVTFHVPSNVPLKEVLWKKQKDKVAELENSEFRAFSSFKNRVYLDTVSGSLTIYNLTSSDEDEYEMESPNITDTMKFFLYVLEMVSKPMIYWECSNATLTCEVLEGTDVELKLYQGKEHLRSLRQKTMSYQWTNLRAPFKCKAVNRVSQESEMEVVNCPE

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	Cricetulus griseus

Entity 2 Entity 2 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	197

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1ccza1
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	d1ccza2
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.1.1.3 — C2 set domains

CATH v4.4 (2 domains)

Domain ID domain_id	1cczA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1cczA02
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	116.430 Å
Unit-cell length b length_b	116.430 Å
Unit-cell length c length_c	51.520 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	—
R_work r_work	0.2018
R_free r_free	0.2430

fit	/app/data/saxs_computation/cc/1ccz/1ccz.fit
pddf	/app/data/pr_computation/cc/1ccz/1ccz.pr.out
profile	/app/data/saxs_computation/cc/1ccz/1ccz.dat

CRYSTAL STRUCTURE OF THE CD2-BINDING DOMAIN OF CD58 (LYMPHOCYTE FUNCTION-ASSOCIATED ANTIGEN 3) AT 1.8-A RESOLUTION

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

PROTEIN (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

Refinement Refinement

Diffraction experiment Diffraction