SAXSdb — 3cfw

▼

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

L-selectin

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 39–194	Fragment：EGF domain (UNP residues 39-194)	;alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.17 M Sodium acetate trihydrate, 0.085 M Tris-HCl, pH 8.5, 25.5 % w/v PEG 4000,15% v/v Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.248

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 3CFW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2LGF Solution structure of Ca2+/calmodulin complexed with a peptide representing the calmodulin-binding domain of L-selectin Deposited 2011-07-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 349–363（15 aa） Fragment：sequence database residues 349-363	Not recorded	CA CALCIUM ION × 4	SOLUTION NMR NMR measurement conditions pH 6.8；303 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR measurement conditions pH 6.8；303 K；Ionic strength (raw mmCIF value) 0.3；Pressure ambient NMR sample composition 0.5-0.8 mM [U-13C; U-15N] protein_1, 0.5-0.8 mM protein_2, 4 mM CALCIUM ION, 0.5 mM DSS, 100 mM potassium chloride, 0.03 % sodium azide, 20 mM Bis-Tris, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5-0.8 mM [U-2H; U-15N] protein_1, 0.5-0.8 mM protein_2, 4 mM CALCIUM ION, 0.5 mM DSS, 100 mM potassium chloride, 0.03 % sodium azide, 20 mM Bis-Tris, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5-0.8 mM [1H/13C-methyl Met; U-2H; U-15N] protein_1, 0.5-0.8 mM protein_2, 4 mM CALCIUM ION, 0.5 mM DSS, 100 mM potassium chloride, 0.03 % sodium azide, 20 mM Bis-Tris, 100% D2O \| 100% D2O NMR sample composition 0.5-0.8 mM [U-13C; U-15N] protein_1, 0.5-0.8 mM protein_2, 4 mM CALCIUM ION, 0.5 mM DSS, 300 mM potassium chloride, 0.03 % sodium azide, 20 mM Bis-Tris, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5-0.8 mM [U-13C; U-15N] protein_1, 0.5-0.8 mM protein_2, 4 mM CALCIUM ION, 0.5 mM DSS, 300 mM potassium chloride, 0.03 % sodium azide, 20 mM Bis-Tris, 16 w/v Pf1 phage, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
5VC1 Crystal structure of L-selectin lectin/EGF domains Deposited 2017-03-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 39–195（157 aa） Fragment：UNP residues 39-195	Mutation：N22Q, N139Q	PG4 TETRAETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 GOL GLYCEROL × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；100 mM sodium cacodylate pH 7.5, 200 mM calcium acetate, 40% (v/v) PEG 600	Resolution 1.94 Å R-free 0.231

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LYAM1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–156； UniProt 39–194

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3cfw
Deposition date deposition_date	2008-03-04
Structure title title	L-selectin lectin and EGF domains
Keywords keywords	L-selectin, lectin, EGF, Cell adhesion, EGF-like domain, Glycoprotein, Membrane, Sushi, Transmembrane; CELL ADHESION
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	18.22 Å
Radius of gyration Rg (electron density) rg_electron	17.34 Å
Forward intensity I(0) i0	7570900.00
Molecular weight molecular_weight	19374.0 kDa
Excluded volume excluded_volume	23879 Å³
Envelope volume envelope_volume	28351 Å³
Hydration-shell volume shell_volume	14461 Å³
Envelope diameter envelope_diameter	67.0 Å
Shell Rg shell_rg	22.73 Å
Envelope Rg envelope_rg	18.06 Å
Shape Rg shape_rg	17.30 Å
Total Rg total_rg	18.35 Å
Total atoms total_atoms	1358
Residues n_residues	156
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	70.3 Å
Rg (real space) rg_real	18.24 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	7.5710e+06
I(0) uncertainty (real space) i0_real_error	1.0520e+05
Rg (reciprocal space) rg_reciprocal	18.23 Å
I(0) (reciprocal space) i0_reciprocal	7571000.0000
Solution quality estimate total_estimate	0.8066
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.9 Å
Skewness Skewness skewness	0.399
Kurtosis Kurtosis kurtosis	-0.166
Angular range angular_range	— – 0.4350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1125000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.548; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.838; Smooth: 1.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	L-selectin
Molecular weight formula_weight	19209.5 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	1496

WTYHYSEKPMNWQRARRFCRDNYTDLVAIQNKAEIEYLEKTLPFSRSYYWIGIRKIGGIWTWVGTNKSLTEEAENWGDGEPNNKKNKEDCVEIYIKRNKDAGKWNDDACHKLKAALCYTASCQPWSCSGHGECVEIINNYTCNCDVGYYGPQCQFVQVDPRLID

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 branched

Description description	;alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	910.8 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 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	1

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	138

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3cfwa1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.1 — C-type lectin domain

Domain ID domain_id	d3cfwa2
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.11 — EGF/Laminin
Family Family family	g.3.11.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	3cfwA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

Domain ID domain_id	3cfwA02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	10 — Laminin

▶

8. Citations (1)

▶

Unit-cell length a length_a	118.477 Å
Unit-cell length b length_b	118.477 Å
Unit-cell length c length_c	118.477 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	24

Space group space_group	I 2 3
Space-group number int_tables_number	197
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	—
R_work r_work	0.2006
R_free r_free	0.2485

fit	/app/data/saxs_computation/cf/3cfw/3cfw.fit
pddf	/app/data/pr_computation/cf/3cfw/3cfw.pr.out
profile	/app/data/saxs_computation/cf/3cfw/3cfw.dat

L-selectin lectin and EGF domains

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

L-selectin

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