5xof

Crystal structure of human paired immunoglobulin-like type 2 receptor alpha with synthesized glycopeptide I

Method: X-RAY DIFFRACTION Dmax: 87.0 Å Quality: EXCELLENT

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

Paired immunoglobulin-like type 2 receptor alpha

Homo sapiens

UniProt Q9UKJ1

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 × 2 其他Polymer 1 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 32–150 Fragment:UNP residues 32-150 Peptide from Nitric oxide synthase, endothelial × 1 (P29474) N-acetyl-alpha-neuraminic acid-(2-6)-2-acetamido-2-deoxy-alpha-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.1M Tris-HCl pH8.5, 25% (w/v) PEG 6000 Resolution 1.96 Å R-free 0.269
2 Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 32–150 Fragment:UNP residues 32-150 Peptide from Nitric oxide synthase, endothelial × 1 (P29474) N-acetyl-alpha-neuraminic acid-(2-6)-2-acetamido-2-deoxy-alpha-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.1M Tris-HCl pH8.5, 25% (w/v) PEG 6000 Resolution 1.96 Å R-free 0.269
3 Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 32–150 Fragment:UNP residues 32-150 Peptide from Nitric oxide synthase, endothelial × 1 (P29474) N-acetyl-alpha-neuraminic acid-(2-6)-2-acetamido-2-deoxy-alpha-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.1M Tris-HCl pH8.5, 25% (w/v) PEG 6000 Resolution 1.96 Å R-free 0.269
4 Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 32–150 Fragment:UNP residues 32-150 Peptide from Nitric oxide synthase, endothelial × 1 (P29474) N-acetyl-alpha-neuraminic acid-(2-6)-2-acetamido-2-deoxy-alpha-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.1M Tris-HCl pH8.5, 25% (w/v) PEG 6000 Resolution 1.96 Å R-free 0.269

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.

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

View Construct and Data Evidence
UniProt name PILRA_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–120; UniProt 32–150 Author chain B; PDBConstruct 2–120; UniProt 32–150 Author chain C; PDBConstruct 2–120; UniProt 32–150 Author chain D; PDBConstruct 2–120; UniProt 32–150

Peptide from Nitric oxide synthase, endothelial

OrganismNot specified

UniProt P29474

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 × 2 其他Polymer 1 PDB declaration: dimeric(2) Consistent with protein copy count Chain O; UniProt 30–36 Not recorded Paired immunoglobulin-like type 2 receptor alpha × 1 (Q9UKJ1) N-acetyl-alpha-neuraminic acid-(2-6)-2-acetamido-2-deoxy-alpha-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.1M Tris-HCl pH8.5, 25% (w/v) PEG 6000 Resolution 1.96 Å R-free 0.269
2 Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric(2) Consistent with protein copy count Chain P; UniProt 30–36 Not recorded Paired immunoglobulin-like type 2 receptor alpha × 1 (Q9UKJ1) N-acetyl-alpha-neuraminic acid-(2-6)-2-acetamido-2-deoxy-alpha-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.1M Tris-HCl pH8.5, 25% (w/v) PEG 6000 Resolution 1.96 Å R-free 0.269
3 Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric(2) Consistent with protein copy count Chain Q; UniProt 30–36 Not recorded Paired immunoglobulin-like type 2 receptor alpha × 1 (Q9UKJ1) N-acetyl-alpha-neuraminic acid-(2-6)-2-acetamido-2-deoxy-alpha-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.1M Tris-HCl pH8.5, 25% (w/v) PEG 6000 Resolution 1.96 Å R-free 0.269
4 Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric(2) Consistent with protein copy count Chain R; UniProt 30–36 Not recorded Paired immunoglobulin-like type 2 receptor alpha × 1 (Q9UKJ1) N-acetyl-alpha-neuraminic acid-(2-6)-2-acetamido-2-deoxy-alpha-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.1M Tris-HCl pH8.5, 25% (w/v) PEG 6000 Resolution 1.96 Å R-free 0.269

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.

94 other PDB entries and 180 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NOS3_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain O; PDBConstruct 1–7; UniProt 30–36 Author chain P; PDBConstruct 1–7; UniProt 30–36 Author chain Q; PDBConstruct 1–7; UniProt 30–36 Author chain R; PDBConstruct 1–7; UniProt 30–36

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

SAXS profile for 5xof

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5xof
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5xof
Deposition date deposition_date2017-05-28
Structure title titleCrystal structure of human paired immunoglobulin-like type 2 receptor alpha with synthesized glycopeptide I
Keywords keywordsmembrane protein, immune receptor, viral entry inhibitor, glycopeptide, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier27.85
Radius of gyration Rg (electron density) rg_electron26.82
Forward intensity I(0) i060709900.00
Molecular weight molecular_weight60126.0 kDa
Excluded volume excluded_volume74993 ų
Envelope volume envelope_volume93046 ų
Hydration-shell volume shell_volume29308 ų
Envelope diameter envelope_diameter92.3
Shell Rg shell_rg33.66
Envelope Rg envelope_rg26.54
Shape Rg shape_rg26.81
Total Rg total_rg27.60
Total atoms total_atoms4252
Residues n_residues507
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax87.0
Rg (real space) rg_real27.75
Rg uncertainty (real space) rg_real_error0.51
I(0) (real space) i0_real6.0710e+07
I(0) uncertainty (real space) i0_real_error9.2480e+05
Rg (reciprocal space) rg_reciprocal27.78
I(0) (reciprocal space) i0_reciprocal60710000.0000
Solution quality estimate total_estimate0.9084
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.6
Skewness Skewness skewness0.191
Kurtosis Kurtosis kurtosis-0.488
Angular range angular_range— – 0.2850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha16050000.0000
Real-space data points n_real_points58
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.946; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.968

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id5xofA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5xofB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5xofC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5xofD00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)