SAXSdb — 5xo2

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

Paired immunoglobulin-like type 2 receptor alpha

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 × 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 Envelope glycoprotein B × 1 （P06437） N-acetyl-alpha-neuraminic acid-(2-6)-2-acetamido-2,4-dideoxy-alpha-D-xylo-hexopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1M MES monohydrate pH 6.5, 1.6M Magnesium sulfate heptahydrate	Resolution 2.20 Å R-free 0.262
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 Envelope glycoprotein B × 1 （P06437） N-acetyl-alpha-neuraminic acid-(2-6)-2-acetamido-2,4-dideoxy-alpha-D-xylo-hexopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1M MES monohydrate pH 6.5, 1.6M Magnesium sulfate heptahydrate	Resolution 2.20 Å R-free 0.262

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 5XO2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4NFB Structure of paired immunoglobulin-like type 2 receptor (PILR ) Deposited 2013-10-31	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 32–150（119 aa） Fragment：UNP residues 32-150	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.1M sodium citrate tribasic dehydrate pH 5.6, 20%(v/v) 2-propanol, 20%(w/v) polyethylene glycol 4,000, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.60 Å R-free 0.225
5XOF Crystal structure of human paired immunoglobulin-like type 2 receptor alpha with synthesized glycopeptide I Deposited 2017-05-28	Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 32–150（119 aa） Fragment：UNP residues 32-150	Not recorded	No recorded non-water small molecule	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
5XOF Crystal structure of human paired immunoglobulin-like type 2 receptor alpha with synthesized glycopeptide I Deposited 2017-05-28	Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 32–150（119 aa） Fragment：UNP residues 32-150	Not recorded	No recorded non-water small molecule	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
5XOF Crystal structure of human paired immunoglobulin-like type 2 receptor alpha with synthesized glycopeptide I Deposited 2017-05-28	Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 32–150（119 aa） Fragment：UNP residues 32-150	Not recorded	No recorded non-water small molecule	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
5XOF Crystal structure of human paired immunoglobulin-like type 2 receptor alpha with synthesized glycopeptide I Deposited 2017-05-28	Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 32–150（119 aa） Fragment：UNP residues 32-150	Not recorded	No recorded non-water small molecule	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
9PD2 Crystal structure of PILRA in complex with Fab portion of antagonist antibody Deposited 2025-06-30	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 32–150（119 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M CAPS pH 10.5, 20% PEG 8000, 0.2 M NaCl	Resolution 2.58 Å R-free 0.277

3 other PDB entries and 6 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

Peptide from Envelope glycoprotein B

OrganismNot specified

UniProt P06437

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 X； UniProt 50–56	Not recorded	Paired immunoglobulin-like type 2 receptor alpha × 1 （Q9UKJ1） N-acetyl-alpha-neuraminic acid-(2-6)-2-acetamido-2,4-dideoxy-alpha-D-xylo-hexopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1M MES monohydrate pH 6.5, 1.6M Magnesium sulfate heptahydrate	Resolution 2.20 Å R-free 0.262
2	Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric（2） Consistent with protein copy count	Chain Y； UniProt 50–56	Not recorded	Paired immunoglobulin-like type 2 receptor alpha × 1 （Q9UKJ1） N-acetyl-alpha-neuraminic acid-(2-6)-2-acetamido-2,4-dideoxy-alpha-D-xylo-hexopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1M MES monohydrate pH 6.5, 1.6M Magnesium sulfate heptahydrate	Resolution 2.20 Å R-free 0.262

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 5XO2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2GUM Crystal structure of the extracellular domain of glycoprotein B from Herpes Simplex Virus type I Deposited 2006-05-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 103–730（628 aa） Fragment：residues 103-730 Chain B 103–730（628 aa） Fragment：residues 103-730 Chain C 103–730（628 aa） Fragment：residues 103-730	Not recorded	NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；8% PEG 6000, 0.1 M Na Hepes, 15% 2-methyl-2,4-pentanediol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.275
3NW8 Glycoprotein B from Herpes simplex virus type 1, Y179S mutant, high-pH Deposited 2010-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain B 30–730（701 aa） Fragment：Ectodomain (UNP residues 30 to 730)	Mutation：Y179S	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 MRY MESO-ERYTHRITOL × 6 NA SODIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；10% PEG 4000, 0.2M NaCl, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.76 Å R-free 0.242
3NW8 Glycoprotein B from Herpes simplex virus type 1, Y179S mutant, high-pH Deposited 2010-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 30–730（701 aa） Fragment：Ectodomain (UNP residues 30 to 730)	Mutation：Y179S	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 MRY MESO-ERYTHRITOL × 12 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；10% PEG 4000, 0.2M NaCl, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.76 Å R-free 0.242
3NW8 Glycoprotein B from Herpes simplex virus type 1, Y179S mutant, high-pH Deposited 2010-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain C 30–730（701 aa） Fragment：Ectodomain (UNP residues 30 to 730)	Mutation：Y179S	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 MRY MESO-ERYTHRITOL × 9 NA SODIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；10% PEG 4000, 0.2M NaCl, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.76 Å R-free 0.242
3NW8 Glycoprotein B from Herpes simplex virus type 1, Y179S mutant, high-pH Deposited 2010-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain D 30–730（701 aa） Fragment：Ectodomain (UNP residues 30 to 730)	Mutation：Y179S	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 MRY MESO-ERYTHRITOL × 3 NA SODIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；10% PEG 4000, 0.2M NaCl, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.76 Å R-free 0.242
3NWA Glycoprotein B from Herpes simplex virus type 1, W174R mutant, low-pH Deposited 2010-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain B 30–730（701 aa） Fragment：Ectodomain (UNP residues 30 to 730)	Mutation：W174R	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 MRY MESO-ERYTHRITOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；7% PEG 4000, 0.5M NaCl, 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.26 Å R-free 0.227
3NWA Glycoprotein B from Herpes simplex virus type 1, W174R mutant, low-pH Deposited 2010-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 30–730（701 aa） Fragment：Ectodomain (UNP residues 30 to 730)	Mutation：W174R	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 MRY MESO-ERYTHRITOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；7% PEG 4000, 0.5M NaCl, 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.26 Å R-free 0.227
3NWA Glycoprotein B from Herpes simplex virus type 1, W174R mutant, low-pH Deposited 2010-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain C 30–730（701 aa） Fragment：Ectodomain (UNP residues 30 to 730)	Mutation：W174R	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 MRY MESO-ERYTHRITOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；7% PEG 4000, 0.5M NaCl, 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.26 Å R-free 0.227
3NWA Glycoprotein B from Herpes simplex virus type 1, W174R mutant, low-pH Deposited 2010-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain D 30–730（701 aa） Fragment：Ectodomain (UNP residues 30 to 730)	Mutation：W174R	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 MRY MESO-ERYTHRITOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；7% PEG 4000, 0.5M NaCl, 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.26 Å R-free 0.227
3NWD Glycoprotein B from Herpes simplex virus type 1, Y179S mutant, low-pH Deposited 2010-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain B 30–730（701 aa） Fragment：Ectodomain (UNP residues 30 to 730)	Mutation：Y179S	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；10% PEG 4000, 0.5M NaCl, 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.88 Å R-free 0.283
3NWD Glycoprotein B from Herpes simplex virus type 1, Y179S mutant, low-pH Deposited 2010-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 30–730（701 aa） Fragment：Ectodomain (UNP residues 30 to 730)	Mutation：Y179S	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；10% PEG 4000, 0.5M NaCl, 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.88 Å R-free 0.283
3NWD Glycoprotein B from Herpes simplex virus type 1, Y179S mutant, low-pH Deposited 2010-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain C 30–730（701 aa） Fragment：Ectodomain (UNP residues 30 to 730)	Mutation：Y179S	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 MRY MESO-ERYTHRITOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；10% PEG 4000, 0.5M NaCl, 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.88 Å R-free 0.283
3NWD Glycoprotein B from Herpes simplex virus type 1, Y179S mutant, low-pH Deposited 2010-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain D 30–730（701 aa） Fragment：Ectodomain (UNP residues 30 to 730)	Mutation：Y179S	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；10% PEG 4000, 0.5M NaCl, 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.88 Å R-free 0.283
3NWF Glycoprotein B from Herpes simplex virus type 1, low-pH Deposited 2010-07-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 30–730（701 aa） Fragment：Ectodomain (UNP residues 30 to 730)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 MRY MESO-ERYTHRITOL × 3 NA SODIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；15% PEG 4000, 0.3M NaCl, and 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.249
3NWF Glycoprotein B from Herpes simplex virus type 1, low-pH Deposited 2010-07-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain B 30–730（701 aa） Fragment：Ectodomain (UNP residues 30 to 730)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 MRY MESO-ERYTHRITOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；15% PEG 4000, 0.3M NaCl, and 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.249
3NWF Glycoprotein B from Herpes simplex virus type 1, low-pH Deposited 2010-07-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain C 30–730（701 aa） Fragment：Ectodomain (UNP residues 30 to 730)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；15% PEG 4000, 0.3M NaCl, and 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.249
3NWF Glycoprotein B from Herpes simplex virus type 1, low-pH Deposited 2010-07-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain D 30–730（701 aa） Fragment：Ectodomain (UNP residues 30 to 730)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；15% PEG 4000, 0.3M NaCl, and 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.249
3WV0 O-glycan attached to herpes simplex virus type 1 glycoprotein gB is recognized by the Ig V-set domain of human paired immunoglobulin-like type 2 receptor alpha Deposited 2014-05-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain X 50–56（7 aa） Fragment：O-glycan with attached peptide, UNP residues 50-56	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；0.2 M ammonium sulfate 30% PEG 8000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.299
3WV0 O-glycan attached to herpes simplex virus type 1 glycoprotein gB is recognized by the Ig V-set domain of human paired immunoglobulin-like type 2 receptor alpha Deposited 2014-05-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain Y 50–56（7 aa） Fragment：O-glycan with attached peptide, UNP residues 50-56	Not recorded	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；0.2 M ammonium sulfate 30% PEG 8000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.299
4BOM Structure of herpesvirus fusion glycoprotein B-bilayer complex revealing the protein-membrane and lateral protein-protein interaction Deposited 2013-05-21	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 103–724（622 aa） Fragment：GLYCOPROTEIN B ECTODOMAIN, RESIDUES 103-724 Chain B 103–724（622 aa） Fragment：GLYCOPROTEIN B ECTODOMAIN, RESIDUES 103-724 Chain C 103–724（622 aa） Fragment：GLYCOPROTEIN B ECTODOMAIN, RESIDUES 103-724	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer PBS WITH SODIUM CITRATE；pH 5.5；PBS WITH SODIUM CITRATE cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；LIQUID NITROGEN PROPANE MIXTURE	Resolution 27.00 Å
4HSI Glycoprotein B from Herpes simplex virus type 1, A504P/R505G/Q507G/N511G mutant, low-pH Deposited 2012-10-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 61–730（670 aa） Fragment：ectodomain	Mutation：A504P, R505G, Q507G, N511G	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 MRY MESO-ERYTHRITOL × 3 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；15% PEG 4000, 0.2 M NaCl, 0.1 M Na-citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.10 Å R-free 0.255
4HSI Glycoprotein B from Herpes simplex virus type 1, A504P/R505G/Q507G/N511G mutant, low-pH Deposited 2012-10-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain B 61–730（670 aa） Fragment：ectodomain	Mutation：A504P, R505G, Q507G, N511G	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；15% PEG 4000, 0.2 M NaCl, 0.1 M Na-citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.10 Å R-free 0.255
4HSI Glycoprotein B from Herpes simplex virus type 1, A504P/R505G/Q507G/N511G mutant, low-pH Deposited 2012-10-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain C 61–730（670 aa） Fragment：ectodomain	Mutation：A504P, R505G, Q507G, N511G	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 MRY MESO-ERYTHRITOL × 3 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；15% PEG 4000, 0.2 M NaCl, 0.1 M Na-citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.10 Å R-free 0.255
4HSI Glycoprotein B from Herpes simplex virus type 1, A504P/R505G/Q507G/N511G mutant, low-pH Deposited 2012-10-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain D 61–730（670 aa） Fragment：ectodomain	Mutation：A504P, R505G, Q507G, N511G	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；15% PEG 4000, 0.2 M NaCl, 0.1 M Na-citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.10 Å R-free 0.255
4L1R Glycoprotein B from Herpes Simplex Virus type 1, A549T Rate-of-Entry mutant, low-pH Deposited 2013-06-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 30–730（701 aa） Fragment：Ectodomain (UNP residues 30 to 730)	Mutation：A549T	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；296 K；15% PEG 4000, 0.3 M NaCl, 0.1 M Sodium Citrate, pH 5.5, vapor diffusion, hanging drop, temperature 296K	Resolution 3.03 Å R-free 0.243
4L1R Glycoprotein B from Herpes Simplex Virus type 1, A549T Rate-of-Entry mutant, low-pH Deposited 2013-06-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain B 30–730（701 aa） Fragment：Ectodomain (UNP residues 30 to 730)	Mutation：A549T	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；296 K；15% PEG 4000, 0.3 M NaCl, 0.1 M Sodium Citrate, pH 5.5, vapor diffusion, hanging drop, temperature 296K	Resolution 3.03 Å R-free 0.243
7UHZ Post-fusion ectodomain of HSV-1 gB in complex with BMPC-23 Fab Deposited 2022-03-28	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 103–730（628 aa） Chain B 103–730（628 aa） Chain C 103–730（628 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7UI0 Post-fusion ectodomain of HSV-1 gB in complex with HSV010-13 Fab Deposited 2022-03-28	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 103–730（628 aa） Chain B 103–730（628 aa） Chain C 103–730（628 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8KFA Cryo-EM structure of HSV-1 gB with D48 Fab complex Deposited 2023-08-15	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 111–725（615 aa） Chain B 111–725（615 aa） Chain C 111–725（615 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.04 Å

12 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GB_HHV1K
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain X； PDBConstruct 1–7； UniProt 50–56 Author chain Y； PDBConstruct 1–7； UniProt 50–56

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	5xo2
Deposition date deposition_date	2017-05-25
Structure title title	Crystal structure of human paired immunoglobulin-like type 2 receptor alpha with synthesized glycopeptide II
Keywords keywords	membrane protein, immune receptor, viral entry inhibitor, glycopeptide, IMMUNE SYSTEM; IMMUNE SYSTEM
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	21.69 Å
Radius of gyration Rg (electron density) rg_electron	20.99 Å
Forward intensity I(0) i0	15900900.00
Molecular weight molecular_weight	30022.0 kDa
Excluded volume excluded_volume	37490 Å³
Envelope volume envelope_volume	43787 Å³
Hydration-shell volume shell_volume	18321 Å³
Envelope diameter envelope_diameter	79.1 Å
Shell Rg shell_rg	26.59 Å
Envelope Rg envelope_rg	21.01 Å
Shape Rg shape_rg	20.97 Å
Total Rg total_rg	21.82 Å
Total atoms total_atoms	2124
Residues n_residues	254
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	76.2 Å
Rg (real space) rg_real	21.75 Å
Rg uncertainty (real space) rg_real_error	0.74 Å
I(0) (real space) i0_real	1.5900e+07
I(0) uncertainty (real space) i0_real_error	2.3730e+05
Rg (reciprocal space) rg_reciprocal	21.74 Å
I(0) (reciprocal space) i0_reciprocal	15900000.0000
Solution quality estimate total_estimate	0.5893
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	20.5 Å
Skewness Skewness skewness	0.408
Kurtosis Kurtosis kurtosis	-0.239
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6755000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.743; Stabil: 0.999; Sysdev: 0.207; Positv: 1.000; Valcen: 0.811; 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	Paired immunoglobulin-like type 2 receptor alpha
Molecular weight formula_weight	13967.7 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	2173

MLYGVTQPKHLSASMGGSVEIPFSFYYPWELATAPDVRISWRRGHFHGQSFYSTRPPSIHKDYVNRLFLNWTEGQKSGFLRISNLQKQDQSVYFCRVELDTRSSGRQQWQSIEGTKLSIT

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	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Peptide from Envelope glycoprotein B
Molecular weight formula_weight	609.7 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X,Y

GPATPAP

Entity 3 Entity 3 branched

Description description	N-acetyl-alpha-neuraminic acid-(2-6)-2-acetamido-2,4-dideoxy-alpha-D-xylo-hexopyranose
Molecular weight formula_weight	496.5 kDa
Source method src_method	man
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	49

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5xo2A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5xo2B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	81.280 Å
Unit-cell length b length_b	63.329 Å
Unit-cell length c length_c	55.072 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.08 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.201 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2286
R_work r_work	0.2163
R_free r_free	0.2616

fit	/app/data/saxs_computation/xo/5xo2/5xo2.fit
pddf	/app/data/pr_computation/xo/5xo2/5xo2.pr.out
profile	/app/data/saxs_computation/xo/5xo2/5xo2.dat

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

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

Paired immunoglobulin-like type 2 receptor alpha

State in the Current Structure

Other States of the Same Protein in the Database

Peptide from Envelope glycoprotein B

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 branched

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)