SAXSdb — 5vc1

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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 39–195	Fragment：UNP residues 39-195 Mutation：N22Q, N139Q	;beta-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 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

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 5VC1	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 mutation/modification 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
3CFW L-selectin lectin and EGF domains Deposited 2008-03-04	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 39–194（156 aa） Fragment：EGF domain (UNP residues 39-194)	Not recorded	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

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 1–157； UniProt 39–195

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	5vc1
Deposition date deposition_date	2017-03-30
Structure title title	Crystal structure of L-selectin lectin/EGF domains
Keywords keywords	L-selectin; glycoprotein, cell adhesion; CELL ADHESION
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	17.96 Å
Radius of gyration Rg (electron density) rg_electron	16.92 Å
Forward intensity I(0) i0	7444520.00
Molecular weight molecular_weight	19215.0 kDa
Excluded volume excluded_volume	23715 Å³
Envelope volume envelope_volume	27954 Å³
Hydration-shell volume shell_volume	14492 Å³
Envelope diameter envelope_diameter	65.8 Å
Shell Rg shell_rg	22.52 Å
Envelope Rg envelope_rg	17.63 Å
Shape Rg shape_rg	16.88 Å
Total Rg total_rg	18.00 Å
Total atoms total_atoms	1345
Residues n_residues	153
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	63.1 Å
Rg (real space) rg_real	17.97 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	7.4450e+06
I(0) uncertainty (real space) i0_real_error	9.2780e+04
Rg (reciprocal space) rg_reciprocal	17.97 Å
I(0) (reciprocal space) i0_reciprocal	7445000.0000
Solution quality estimate total_estimate	0.6278
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	22.2 Å
Skewness Skewness skewness	0.381
Kurtosis Kurtosis kurtosis	-0.157
Angular range angular_range	— – 0.4450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1129000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.716; Stabil: 1.000; Sysdev: 0.346; Positv: 1.000; Valcen: 0.971; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	L-selectin
Molecular weight formula_weight	18412.7 kDa
Mutation mutation	N22Q, N139Q
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	1431

WTYHYSEKPMNWQRARRFCRDQYTDLVAIQNKAEIEYLEKTLPFSRSYYWIGIRKIGGIWTWVGTNKSLTEEAENWGDGEPNNKKNKEDCVEIYIKRNKDAGKWNDDACHKLKAALCYTASCQPWSCSGHGECVEIINQYTCNCDVGYYGPQCQFVI

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	Homo sapiens

Entity 2 Entity 2 branched

Description description	;beta-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	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

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

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	77

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5vc1a1
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.169.1.0 — automated matches

Domain ID domain_id	d5vc1a2
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	5vc1A01
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	5vc1A02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	10 — Laminin

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8. Citations (1)

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Unit-cell length a length_a	118.598 Å
Unit-cell length b length_b	118.598 Å
Unit-cell length c length_c	118.598 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	1.940 Å
Low-resolution limit resolution_low	31.697 Å
R factor r_factor	0.2034
R_work r_work	0.2018
R_free r_free	0.2311

fit	/app/data/saxs_computation/vc/5vc1/5vc1.fit
pddf	/app/data/pr_computation/vc/5vc1/5vc1.pr.out
profile	/app/data/saxs_computation/vc/5vc1/5vc1.dat

Crystal structure of L-selectin lectin/EGF domains