1qyy

Crystal Structure of N-Terminal Domain of Human Platelet Receptor Glycoprotein Ib-alpha at 2.8 Angstrom Resolution

Method: X-RAY DIFFRACTION D_max: 105.0 Å Quality: REASONABLE

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

Platelet glycoprotein Ib alpha chain

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 17–306	Fragment：N-Terminal Domain Mutation：C65A	;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 PT PLATINUM (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；PEG 6000, SODIUM NITRATE, SODIUM ACETATE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.282
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain G； UniProt 17–306	Fragment：N-Terminal Domain Mutation：C65A	PT PLATINUM (II) ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；PEG 6000, SODIUM NITRATE, SODIUM ACETATE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.282

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 1QYY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1GWB STRUCTURE OF GLYCOPROTEIN 1B Deposited 2002-03-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 16–296（281 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 16-296	Non-standard monomer：Yes (specific site not provided by mmCIF)	PT PLATINUM (II) ION × 2 ACY ACETIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.80 Å R-free 0.274
1GWB STRUCTURE OF GLYCOPROTEIN 1B Deposited 2002-03-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 16–296（281 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 16-296	Non-standard monomer：Yes (specific site not provided by mmCIF)	PT PLATINUM (II) ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.80 Å R-free 0.274
1M0Z Crystal Structure of the von Willebrand Factor Binding Domain of Glycoprotein Ib alpha Deposited 2002-06-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 17–306（290 aa） Fragment：von Willebrand Factor binding domain	Mutation：N21Q N159Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；301 K；ammonium sulfate, lithium sulfate, CAPS, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 301K	Resolution 1.85 Å R-free 0.216
1M0Z Crystal Structure of the von Willebrand Factor Binding Domain of Glycoprotein Ib alpha Deposited 2002-06-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 17–306（290 aa） Fragment：von Willebrand Factor binding domain	Mutation：N21Q N159Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；301 K；ammonium sulfate, lithium sulfate, CAPS, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 301K	Resolution 1.85 Å R-free 0.216
1M10 Crystal structure of the complex of Glycoprotein Ib alpha and the von Willebrand Factor A1 Domain Deposited 2002-06-16	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 B 17–306（290 aa） Fragment：von Willebrand Factor binding domain	Mutation：N21Q N159Q M239V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；PEG 3000, sodium chloride, MES, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.10 Å R-free 0.296
1OOK Crystal Structure of the Complex of Platelet Receptor GPIb-alpha and Human alpha-Thrombin Deposited 2003-03-03	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 G 17–306（290 aa） Fragment：N-terminal domain	Mutation：C65A Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 6000, Ammonium Phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 2.30 Å R-free 0.260
1P8V CRYSTAL STRUCTURE OF THE COMPLEX OF PLATELET RECEPTOR GPIB-ALPHA AND ALPHA-THROMBIN AT 2.6A Deposited 2003-05-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 17–294（278 aa） Fragment：Glycoprotein 1B alpha	Mutation：N21D Non-standard monomer：Yes (specific site not provided by mmCIF)	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 DFP DIISOPROPYL PHOSPHONATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；291 K；14% PEG 400, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 6.00	Resolution 2.60 Å R-free 0.238
1P9A Crystal Structure of N-Terminal Domain of Human Platelet Receptor Glycoprotein Ib-alpha at 1.7 Angstrom Resolution Deposited 2003-05-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain G 17–306（290 aa） Fragment：N-Terminal Domain	Mutation：C65A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；PEG 6000, Sodium Nitrate, Sodium Acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.70 Å R-free 0.224
1SQ0 Crystal Structure of the Complex of the Wild-type Von Willebrand Factor A1 domain and Glycoprotein Ib alpha at 2.6 Angstrom Resolution Deposited 2004-03-17	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 B 17–304（288 aa） Fragment：Glycoprotein Ib-(alpha)	Mutation：N21D, N159D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；PEG-3350; potassium thiocyanate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.60 Å R-free 0.239
1U0N The ternary von Willebrand Factor A1-glycoprotein Ibalpha-botrocetin complex Deposited 2004-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 17–281（265 aa） Fragment：Alpha chain	Mutation：N21Q,N159Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；Sodium citrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.95 Å R-free 0.276
2BP3 Crystal structure of Filamin A domain 17 and GPIb alpha cytoplasmic domain complex Deposited 2005-04-18	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 T 572–593（22 aa） Fragment：CYTOPLASMIC DOMAIN, RESIDUES 572-593	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.2；1.75M AMMONIUM PHOSPHATE, PH 8.2, AFTER MICROSEEDING: 1.25M AMMONIUM SULFATE PH 8.2	Resolution 2.32 Å R-free 0.256
2BP3 Crystal structure of Filamin A domain 17 and GPIb alpha cytoplasmic domain complex Deposited 2005-04-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain S 572–593（22 aa） Fragment：CYTOPLASMIC DOMAIN, RESIDUES 572-593	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.2；1.75M AMMONIUM PHOSPHATE, PH 8.2, AFTER MICROSEEDING: 1.25M AMMONIUM SULFATE PH 8.2	Resolution 2.32 Å R-free 0.256
3P72 structure of platelet Glycoprotein 1b alpha with a bound peptide inhibitor Deposited 2010-10-12	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 A 17–281（265 aa） Fragment：UNP residues 17-281	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；298 K；1.9M ammonium sulfate, 80mM lithium sulfate, 100mM N-cyclohexyl-3-aminopropanesulfonic acid buffer. 1:1 mix buffer with 4mg/mL protein. lyophilised peptide added directly to crystallised protein drops., pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.90 Å R-free 0.286
3PMH Mechanism of Sulfotyrosine-Mediated Glycoprotein Ib Interaction with Two Distinct alpha-Thrombin Sites Deposited 2010-11-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 17–306（290 aa） Fragment：unp residues 17-306	Mutation：C65A Non-standard monomer：Yes (specific site not provided by mmCIF)	0G7 D-phenylalanyl-N-[(3S)-6-carbamimidamido-1-chloro-2-oxohexan-3-yl]-L-prolinamide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；277 K；16% PEG 6000, 0.2M ammonium phosphate, pH 7.0, VAPOR DIFFUSION, temperature 277K	Resolution 3.20 Å R-free 0.263
4C2A Crystal Structure of High-Affinity von Willebrand Factor A1 domain with R1306Q and I1309V Mutations in Complex with High Affinity GPIb alpha Deposited 2013-08-16	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 B 17–306（290 aa） Fragment：RESIDUES 17-306	Mutation：YES	CAC CACODYLATE ION × 1 ACT ACETATE ION × 1 CA CALCIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；CRYSTALS OF A1/VWD2-GPIBALPA/VWD2 COMPLEX APPEARED IN 12% PEG 8000, 0.1 M SODIUM CACODYLATE PH 6.5, 0.1 M CALCIUM ACETATE, AND 0.4 MG/ML RISTOCETIN (SIGMA-ALDRICH). THESE CRYSTALS WERE CRUSHED AND USED FOR SEEDING. CRYSTALS GREW IN 10 MG/ML COMPLEX, 14% PEG8000, 0.2 M CALCIUM ACETATE, 0.1 M SODIUM CACODYLATE, PH 6.5, AND 0.4 MG/ML RISTOCETIN. NEXT WE SOAKED THESE CRYSTALS IN 14% PEG8000, 0.2 M CALCIUM ACETATE, 0.1 SODIUM CACODYLATE, PH 6.5, AND 4 MG/ML RISTOCETIN.	Resolution 2.08 Å R-free 0.189
4C2B Crystal Structure of High-Affinity von Willebrand Factor A1 domain with Disulfide Mutation in Complex with High Affinity GPIb alpha Deposited 2013-08-16	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 B 17–306（290 aa）	Mutation：YES	SO4 SULFATE ION × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；CRYSTALS OF A1/SS-GPIB/VWD2 COMPLEX APPEARED IN DROPS WITH 20% PEG 4000, 0.16 M AMMONIUM SULFATE, 0.08M SODIUM ACETATE, PH 4.6, AND 20% GLYCEROL. THESE CRYSTALS WERE CRUSHED AND USED FOR SEEDING CRYSTAL GROWTH IN 8 MG/ML COMPLEX, 15% PEG 4000, 0.16 M AMMONIUM SULFATE, 0.08 M SODIUM ACETATE, PH 4.6, AND 20% GLYCEROL. SINCE THESE CRYSTALS WERE FORMED IN BUFFER CONTAINING 20% GLYCEROL, NO ADDITIONAL CRYOPROTECTION WAS USED.	Resolution 2.80 Å R-free 0.286
4C2B Crystal Structure of High-Affinity von Willebrand Factor A1 domain with Disulfide Mutation in Complex with High Affinity GPIb alpha Deposited 2013-08-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 17–306（290 aa）	Mutation：YES	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；CRYSTALS OF A1/SS-GPIB/VWD2 COMPLEX APPEARED IN DROPS WITH 20% PEG 4000, 0.16 M AMMONIUM SULFATE, 0.08M SODIUM ACETATE, PH 4.6, AND 20% GLYCEROL. THESE CRYSTALS WERE CRUSHED AND USED FOR SEEDING CRYSTAL GROWTH IN 8 MG/ML COMPLEX, 15% PEG 4000, 0.16 M AMMONIUM SULFATE, 0.08 M SODIUM ACETATE, PH 4.6, AND 20% GLYCEROL. SINCE THESE CRYSTALS WERE FORMED IN BUFFER CONTAINING 20% GLYCEROL, NO ADDITIONAL CRYOPROTECTION WAS USED.	Resolution 2.80 Å R-free 0.286
4C2B Crystal Structure of High-Affinity von Willebrand Factor A1 domain with Disulfide Mutation in Complex with High Affinity GPIb alpha Deposited 2013-08-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 17–306（290 aa）	Mutation：YES	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；CRYSTALS OF A1/SS-GPIB/VWD2 COMPLEX APPEARED IN DROPS WITH 20% PEG 4000, 0.16 M AMMONIUM SULFATE, 0.08M SODIUM ACETATE, PH 4.6, AND 20% GLYCEROL. THESE CRYSTALS WERE CRUSHED AND USED FOR SEEDING CRYSTAL GROWTH IN 8 MG/ML COMPLEX, 15% PEG 4000, 0.16 M AMMONIUM SULFATE, 0.08 M SODIUM ACETATE, PH 4.6, AND 20% GLYCEROL. SINCE THESE CRYSTALS WERE FORMED IN BUFFER CONTAINING 20% GLYCEROL, NO ADDITIONAL CRYOPROTECTION WAS USED.	Resolution 2.80 Å R-free 0.286
4C2B Crystal Structure of High-Affinity von Willebrand Factor A1 domain with Disulfide Mutation in Complex with High Affinity GPIb alpha Deposited 2013-08-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 17–306（290 aa）	Mutation：YES	SO4 SULFATE ION × 4 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；CRYSTALS OF A1/SS-GPIB/VWD2 COMPLEX APPEARED IN DROPS WITH 20% PEG 4000, 0.16 M AMMONIUM SULFATE, 0.08M SODIUM ACETATE, PH 4.6, AND 20% GLYCEROL. THESE CRYSTALS WERE CRUSHED AND USED FOR SEEDING CRYSTAL GROWTH IN 8 MG/ML COMPLEX, 15% PEG 4000, 0.16 M AMMONIUM SULFATE, 0.08 M SODIUM ACETATE, PH 4.6, AND 20% GLYCEROL. SINCE THESE CRYSTALS WERE FORMED IN BUFFER CONTAINING 20% GLYCEROL, NO ADDITIONAL CRYOPROTECTION WAS USED.	Resolution 2.80 Å R-free 0.286
4CH2 Low-salt crystal structure of a thrombin-GpIbalpha peptide complex Deposited 2013-11-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain P 287–300（14 aa） Fragment：C-TERMINAL FRAGMENT OF GPIBALPHA, 271-284	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 2 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；50 MM SODIUM FORMATE, 16% PEG-3350, pH 7.4	Resolution 1.60 Å R-free 0.187
4CH2 Low-salt crystal structure of a thrombin-GpIbalpha peptide complex Deposited 2013-11-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain Q 287–300（14 aa） Fragment：C-TERMINAL FRAGMENT OF GPIBALPHA, 271-284	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 2 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；50 MM SODIUM FORMATE, 16% PEG-3350, pH 7.4	Resolution 1.60 Å R-free 0.187
4CH8 High-salt crystal structure of a thrombin-GpIbalpha peptide complex Deposited 2013-11-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain P 287–300（14 aa） Fragment：C-TERMINAL FRAGMENT OF GPIBALPHA, RESIDUES 271-284	Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 1 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；100 MM SODIUM FORMATE, 18% PEG-3350, pH 7.4	Resolution 1.75 Å R-free 0.242
4CH8 High-salt crystal structure of a thrombin-GpIbalpha peptide complex Deposited 2013-11-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain Q 287–300（14 aa） Fragment：C-TERMINAL FRAGMENT OF GPIBALPHA, RESIDUES 271-284	Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 1 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；100 MM SODIUM FORMATE, 18% PEG-3350, pH 7.4	Resolution 1.75 Å R-free 0.242
4CH8 High-salt crystal structure of a thrombin-GpIbalpha peptide complex Deposited 2013-11-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain R 287–300（14 aa） Fragment：C-TERMINAL FRAGMENT OF GPIBALPHA, RESIDUES 271-284	Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 1 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；100 MM SODIUM FORMATE, 18% PEG-3350, pH 7.4	Resolution 1.75 Å R-free 0.242
4CH8 High-salt crystal structure of a thrombin-GpIbalpha peptide complex Deposited 2013-11-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain S 287–300（14 aa） Fragment：C-TERMINAL FRAGMENT OF GPIBALPHA, RESIDUES 271-284	Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 1 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；100 MM SODIUM FORMATE, 18% PEG-3350, pH 7.4	Resolution 1.75 Å R-free 0.242
4MGX Crystal structure of human filamin C domains 4-5 and GPIB alpha cytoplasmic domain complex Deposited 2013-08-29	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 B 577–585（9 aa） Fragment：cytoplasmic domain (UNP residues 577-585)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；297 K；0.1 M HEPES, pH 7.5, 20% w/v PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 3.16 Å R-free 0.277
6XFQ Structure of a novel antithrombotic agent Agkisacucetin in complex with the platelet glycoprotein Ib receptor Deposited 2020-06-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 17–321（305 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；15% PEG4000, 0.1M HEPES, pH 7.5	Resolution 3.30 Å R-free 0.311
8WE2 14-3-3 zeta complexed with S609 phosphorylated peptide derived from GPIb alpha cytoplasmic domain Deposited 2023-09-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain Q 646–652（7 aa） Chain R 646–652（7 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium Acetate, 20% PEG 3350	Resolution 2.11 Å R-free 0.238
8WF6 14-3-3 zeta complexed with S559 phosphorylated peptide derived from GPIb alpha cytoplasmic domain Deposited 2023-09-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain Q 596–607（12 aa） Chain R 596–607（12 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；2% Tacsimate pH7.0, 0.1M Hepes pH7.5, 20% PEG 3350	Resolution 2.47 Å R-free 0.238
8WF6 14-3-3 zeta complexed with S559 phosphorylated peptide derived from GPIb alpha cytoplasmic domain Deposited 2023-09-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 596–607（12 aa） Chain F 596–607（12 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	SIN SUCCINIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；2% Tacsimate pH7.0, 0.1M Hepes pH7.5, 20% PEG 3350	Resolution 2.47 Å R-free 0.238
8WFS Cryo-EM structure of GPIb-IX Complex Deposited 2023-09-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric	Chain a 523–652（130 aa）	Mutation：S559E, S609E	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.36 Å

20 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GPBA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–290； UniProt 17–306 Author chain G； PDBConstruct 1–290； UniProt 17–306

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	1qyy
Deposition date deposition_date	2003-09-12
Structure title title	Crystal Structure of N-Terminal Domain of Human Platelet Receptor Glycoprotein Ib-alpha at 2.8 Angstrom Resolution
Keywords keywords	Platelet Receptors, Glycocalicin, Leucine Rich Repeats, 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	30.46 Å
Radius of gyration Rg (electron density) rg_electron	30.49 Å
Forward intensity I(0) i0	56526800.00
Molecular weight molecular_weight	60484.0 kDa
Excluded volume excluded_volume	76225 Å³
Envelope volume envelope_volume	96198 Å³
Hydration-shell volume shell_volume	28466 Å³
Envelope diameter envelope_diameter	111.1 Å
Shell Rg shell_rg	34.72 Å
Envelope Rg envelope_rg	30.68 Å
Shape Rg shape_rg	30.46 Å
Total Rg total_rg	31.00 Å
Total atoms total_atoms	4221
Residues n_residues	532
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	105.0 Å
Rg (real space) rg_real	30.77 Å
Rg uncertainty (real space) rg_real_error	0.86 Å
I(0) (real space) i0_real	5.6530e+07
I(0) uncertainty (real space) i0_real_error	8.7570e+05
Rg (reciprocal space) rg_reciprocal	30.64 Å
I(0) (reciprocal space) i0_reciprocal	56520000.0000
Solution quality estimate total_estimate	0.6093
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	26.2 Å
Skewness Skewness skewness	0.562
Kurtosis Kurtosis kurtosis	-0.321
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13160000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.702; Stabil: 1.000; Sysdev: 0.077; Positv: 1.000; Valcen: 0.675; Smooth: 0.906

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Platelet glycoprotein Ib alpha chain
Molecular weight formula_weight	32306.8 kDa
Mutation mutation	C65A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,G
Atom count atom_count	4277

HPICEVSKVASHLEVNCDKRNLTALPPDLPKDTTILHLSENLLYTFSLATLMPYTRLTQLNLDRAELTKLQVDGTLPVLGTLDLSHNQLQSLPLLGQTLPALTVLDVSFNRLTSLPLGALRGLGELQELYLKGNELKTLPPGLLTPTPKLEKLSLANNNLTELPAGLLNGLENLDTLLLQENSLYTIPKGFFGSHLLPFAFLHGNPWLCNCEILYFRRWLQDNAENVYVWKQGVDVKAMTSNVASVQCDNSDKFPVYKYPGKGCPTLGDEGDTDLYDYYPEEDTEGDKVR

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	Drosophila melanogaster

Entity 2 Entity 2 branched

Description description	;alpha-D-mannopyranose-(1-3)-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	748.7 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	PLATINUM (II) ION
Molecular weight formula_weight	195.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	56

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1qyya_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Superfamily Superfamily superfamily	c.10.2 — L domain-like
Family Family family	c.10.2.7 — Ngr ectodomain-like

Domain ID domain_id	d1qyyg_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Superfamily Superfamily superfamily	c.10.2 — L domain-like
Family Family family	c.10.2.7 — Ngr ectodomain-like

CATH v4.4 (2 domains)

Domain ID domain_id	1qyyA00
Class class	3 — Alpha Beta
Architecture architecture	80 — Alpha-Beta Horseshoe
Topology topology	10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily	10 — Ribonuclease Inhibitor

Domain ID domain_id	1qyyG00
Class class	3 — Alpha Beta
Architecture architecture	80 — Alpha-Beta Horseshoe
Topology topology	10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily	10 — Ribonuclease Inhibitor

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8. Citations (1)

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Unit-cell length a length_a	51.610 Å
Unit-cell length b length_b	113.820 Å
Unit-cell length c length_c	56.210 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.21 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2230
R_work r_work	0.2190
R_free r_free	0.2820

fit	/app/data/saxs_computation/qy/1qyy/1qyy.fit
pddf	/app/data/pr_computation/qy/1qyy/1qyy.pr.out
profile	/app/data/saxs_computation/qy/1qyy/1qyy.dat