SAXSdb — 1g1s

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

P-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 Heteromer Protein × 4 其他Polymer 2 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 42–199 Chain B； UniProt 42–199	Fragment：LECTIN/EGF DOMAINS	PSGL-1 PEPTIDE × 2 （Q14242） ;N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-[beta-D-galactopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-galactopyranose ; × 2 SR STRONTIUM ION × 2 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 7 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；100 mM HEPES, 10 mM TRIS, 150 mN NaCl, 4 mM CaCl2, 50 mM SrCl2, 5% PEG 6000, 33% MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 291K	Resolution 1.90 Å R-free 0.235

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 1G1S	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1FSB STRUCTURE OF THE EGF DOMAIN OF P-SELECTIN, NMR, 19 STRUCTURES Deposited 1996-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 160–199（40 aa） Fragment：EGF DOMAIN, RESIDUES 119 - 158	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K	Resolution not provided
1G1Q Crystal structure of P-selectin lectin/EGF domains Deposited 2000-10-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 42–199（158 aa） Fragment：LECTIN/EGF DOMAINS Chain B 42–199（158 aa） Fragment：LECTIN/EGF DOMAINS Chain C 42–199（158 aa） Fragment：LECTIN/EGF DOMAINS Chain D 42–199（158 aa） Fragment：LECTIN/EGF DOMAINS	Not recorded	CA CALCIUM ION × 4 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Tris-HCl, NaCl, CaCl2, 2-methyl-2,4-pentanediol, PEG 6000, pH 8.5, VAPOR DIFFUSION, HANGING DROP at 291K	Resolution 2.40 Å R-free 0.252
1G1R Crystal structure of P-selectin lectin/EGF domains complexed with SLeX Deposited 2000-10-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 42–199（158 aa） Fragment：LECTIN/EGF DOMAINS Chain B 42–199（158 aa） Fragment：LECTIN/EGF DOMAINS Chain C 42–199（158 aa） Fragment：LECTIN/EGF DOMAINS Chain D 42–199（158 aa） Fragment：LECTIN/EGF DOMAINS	Not recorded	CA CALCIUM ION × 4 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Tris-HCl, NaCl, CaCl2, 2-methyl-2,4-pentanediol, PEG 6000, pH 8.5, VAPOR DIFFUSION, HANGING DROP at 291K	Resolution 3.40 Å R-free 0.322
1HES MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLEXED WITH P-selectin INTERNALIZATION PEPTIDE SHLGTYGVFTNAA Deposited 2000-11-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 813–830（18 aa） Fragment：INTERNALIZATION SIGNAL	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；289 K；HANGING DROP, 2.2M NACL, 0.4M NA/K PHOSPHATE, 10MM DTT 0.1M MES PH 7.1, 15% GLYCEROL, 16 DEGREES, MOLAR RATIO OF PEPTIDE TO PROTEIN 3:1	Resolution 3.00 Å R-free 0.266

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LEM3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–158； UniProt 42–199 Author chain B； PDBConstruct 1–158； UniProt 42–199

PSGL-1 PEPTIDE

Homo sapiens

UniProt Q14242

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 Heteromer Protein × 4 其他Polymer 2 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 42–60 Chain D； UniProt 42–60	Non-standard monomer：Yes (specific site not provided by mmCIF)	P-SELECTIN × 2 （P16109） ;N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-[beta-D-galactopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-galactopyranose ; × 2 SR STRONTIUM ION × 2 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 7 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；100 mM HEPES, 10 mM TRIS, 150 mN NaCl, 4 mM CaCl2, 50 mM SrCl2, 5% PEG 6000, 33% MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 291K	Resolution 1.90 Å R-free 0.235

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	SEPL_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–19； UniProt 42–60 Author chain D； PDBConstruct 1–19； UniProt 42–60

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	1g1s
Deposition date deposition_date	2000-10-13
Structure title title	P-SELECTIN LECTIN/EGF DOMAINS COMPLEXED WITH PSGL-1 PEPTIDE
Keywords keywords	selectin, lectin, egf, sulphated, slex, IMMUNE SYSTEM, MEMBRANE PROTEIN; IMMUNE SYSTEM, MEMBRANE PROTEIN
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	28.26 Å
Radius of gyration Rg (electron density) rg_electron	27.62 Å
Forward intensity I(0) i0	32511400.00
Molecular weight molecular_weight	43427.0 kDa
Excluded volume excluded_volume	53719 Å³
Envelope volume envelope_volume	69294 Å³
Hydration-shell volume shell_volume	21682 Å³
Envelope diameter envelope_diameter	89.7 Å
Shell Rg shell_rg	33.61 Å
Envelope Rg envelope_rg	27.24 Å
Shape Rg shape_rg	27.60 Å
Total Rg total_rg	28.31 Å
Total atoms total_atoms	3034
Residues n_residues	337
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	89.6 Å
Rg (real space) rg_real	28.34 Å
Rg uncertainty (real space) rg_real_error	0.59 Å
I(0) (real space) i0_real	3.2510e+07
I(0) uncertainty (real space) i0_real_error	4.3470e+05
Rg (reciprocal space) rg_reciprocal	28.32 Å
I(0) (reciprocal space) i0_reciprocal	32510000.0000
Solution quality estimate total_estimate	0.8812
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	22.4 Å
Skewness Skewness skewness	0.215
Kurtosis Kurtosis kurtosis	-0.820
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2683000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.901; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.818; Smooth: 0.930

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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	P-SELECTIN
Molecular weight formula_weight	19131.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3258

WTYHYSTKAYSWNISRKYCQNRYTDLVAIQNKNEIDYLNKVLPYYSSYYWIGIRKNNKTWTWVGTKKALTNEAENWADNEPNNKRNNEDCVEIYIKSPSAPGKWNDEHCLKKKHALCYTASCQDMSCSKQGECLETIGNYTCSCYPGFYGPECEYVRDDDDK

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 polymer

Description description	PSGL-1 PEPTIDE
Molecular weight formula_weight	3666.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

QATEYEYLDYDFLPETEPPRPMMDDDDK

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 3 Entity 3 branched

Description description	;N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-[beta-D-galactopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-galactopyranose ;
Molecular weight formula_weight	1186.1 kDa
Source method src_method	man
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	STRONTIUM ION
Molecular weight formula_weight	87.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	(4R)-2-METHYLPENTANE-2,4-DIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 6 Entity 6 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	224

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1g1sa1
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	d1g1sa2
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.3.11.1 — EGF-type module

Domain ID domain_id	d1g1sb1
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	d1g1sb2
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.3.11.1 — EGF-type module

CATH v4.4 (4 domains)

Domain ID domain_id	1g1sA01
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	1g1sA02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	10 — Laminin

Domain ID domain_id	1g1sB01
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	1g1sB02
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	63.445 Å
Unit-cell length b length_b	96.756 Å
Unit-cell length c length_c	187.289 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	16

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2040
R_work r_work	0.2040
R_free r_free	0.2350

fit	/app/data/saxs_computation/g1/1g1s/1g1s.fit
pddf	/app/data/pr_computation/g1/1g1s/1g1s.pr.out
profile	/app/data/saxs_computation/g1/1g1s/1g1s.dat

P-SELECTIN LECTIN/EGF DOMAINS COMPLEXED WITH PSGL-1 PEPTIDE

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

P-SELECTIN

State in the Current Structure

Other States of the Same Protein in the Database

PSGL-1 PEPTIDE

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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)