1g1r

Crystal structure of P-selectin lectin/EGF domains complexed with SLeX

Method: X-RAY DIFFRACTION D_max: 108.8 Å Quality: GOOD

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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 Homooligomer Protein × 4 其他Polymer 3 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 42–199 Chain B； UniProt 42–199 Chain C； UniProt 42–199 Chain D； UniProt 42–199	Fragment：LECTIN/EGF DOMAINS	;N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]methyl 2-acetamido-2-deoxy-beta-D-glucopyranoside ; × 3 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

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 1G1R	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 oligomeric state 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
1G1S P-SELECTIN LECTIN/EGF DOMAINS COMPLEXED WITH PSGL-1 PEPTIDE 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 Heteromer；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	Not recorded	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
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 Author chain C； PDBConstruct 1–158； UniProt 42–199 Author chain D； PDBConstruct 1–158； UniProt 42–199

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1g1r
Deposition date deposition_date	2000-10-13
Structure title title	Crystal structure of P-selectin lectin/EGF domains complexed with SLeX
Keywords keywords	Lectin, EGF, Adhesion molecule, 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	33.71 Å
Radius of gyration Rg (electron density) rg_electron	33.24 Å
Forward intensity I(0) i0	102426000.00
Molecular weight molecular_weight	77714.0 kDa
Excluded volume excluded_volume	95843 Å³
Envelope volume envelope_volume	133290 Å³
Hydration-shell volume shell_volume	34485 Å³
Envelope diameter envelope_diameter	116.3 Å
Shell Rg shell_rg	38.84 Å
Envelope Rg envelope_rg	32.39 Å
Shape Rg shape_rg	33.23 Å
Total Rg total_rg	33.73 Å
Total atoms total_atoms	5451
Residues n_residues	639
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	108.8 Å
Rg (real space) rg_real	33.61 Å
Rg uncertainty (real space) rg_real_error	1.07 Å
I(0) (real space) i0_real	1.0240e+08
I(0) uncertainty (real space) i0_real_error	1.5330e+06
Rg (reciprocal space) rg_reciprocal	33.68 Å
I(0) (reciprocal space) i0_reciprocal	102400000.0000
Solution quality estimate total_estimate	0.8213
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	46.3 Å
Skewness Skewness skewness	0.083
Kurtosis Kurtosis kurtosis	-0.550
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5293000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.894; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	5451

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 branched

Description description	;N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]methyl 2-acetamido-2-deoxy-beta-D-glucopyranoside ;
Molecular weight formula_weight	834.8 kDa
Source method src_method	man
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 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	2

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7. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1g1ra1
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	d1g1ra2
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	d1g1ra3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1g1rb1
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	d1g1rb2
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	d1g1rb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1g1rc1
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	d1g1rc2
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	d1g1rc3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1g1rd1
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	d1g1rd2
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	d1g1rd3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (8 domains)

Domain ID domain_id	1g1rA01
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	1g1rA02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	10 — Laminin

Domain ID domain_id	1g1rB01
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	1g1rB02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	10 — Laminin

Domain ID domain_id	1g1rC01
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	1g1rC02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	10 — Laminin

Domain ID domain_id	1g1rD01
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	1g1rD02
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	81.140 Å
Unit-cell length b length_b	60.520 Å
Unit-cell length c length_c	91.440 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.28 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.400 Å
Low-resolution limit resolution_low	14.000 Å
R factor r_factor	0.2270
R_work r_work	0.2270
R_free r_free	0.3220

fit	/app/data/saxs_computation/g1/1g1r/1g1r.fit
pddf	/app/data/pr_computation/g1/1g1r/1g1r.pr.out
profile	/app/data/saxs_computation/g1/1g1r/1g1r.dat