3p72

structure of platelet Glycoprotein 1b alpha with a bound peptide inhibitor

Method: X-RAY DIFFRACTION D_max: 85.6 Å Quality: GOOD

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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	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 17–281	Fragment：UNP residues 17-281	OS1 peptide × 1 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

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 3P72	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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 construct Different mutation/modification Different oligomeric state 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
1QYY Crystal Structure of N-Terminal Domain of Human Platelet Receptor Glycoprotein Ib-alpha at 2.8 Angstrom Resolution Deposited 2003-09-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 17–306（290 aa） Fragment：N-Terminal Domain	Mutation：C65A	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
1QYY Crystal Structure of N-Terminal Domain of Human Platelet Receptor Glycoprotein Ib-alpha at 2.8 Angstrom Resolution Deposited 2003-09-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 17–306（290 aa） 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
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 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 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 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
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 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 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 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 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 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 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 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 32 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GP1BA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–265； UniProt 17–281

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	3p72
Deposition date deposition_date	2010-10-12
Structure title title	structure of platelet Glycoprotein 1b alpha with a bound peptide inhibitor
Keywords keywords	Leucine-rich repeat, Coagulation, Inhibitor, Blood Clotting-Inhibitor complex; Blood Clotting/Inhibitor
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	21.86 Å
Radius of gyration Rg (electron density) rg_electron	21.11 Å
Forward intensity I(0) i0	16041500.00
Molecular weight molecular_weight	31215.0 kDa
Excluded volume excluded_volume	39588 Å³
Envelope volume envelope_volume	46946 Å³
Hydration-shell volume shell_volume	19596 Å³
Envelope diameter envelope_diameter	87.6 Å
Shell Rg shell_rg	26.58 Å
Envelope Rg envelope_rg	21.78 Å
Shape Rg shape_rg	21.06 Å
Total Rg total_rg	22.03 Å
Total atoms total_atoms	2193
Residues n_residues	280
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	85.6 Å
Rg (real space) rg_real	22.02 Å
Rg uncertainty (real space) rg_real_error	0.85 Å
I(0) (real space) i0_real	1.6040e+07
I(0) uncertainty (real space) i0_real_error	2.2460e+05
Rg (reciprocal space) rg_reciprocal	21.99 Å
I(0) (reciprocal space) i0_reciprocal	16040000.0000
Solution quality estimate total_estimate	0.7584
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.3 Å
Skewness Skewness skewness	0.615
Kurtosis Kurtosis kurtosis	0.293
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2389000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.436; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.613; Smooth: 0.934

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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	Platelet glycoprotein Ib alpha chain
Molecular weight formula_weight	29953.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2426

HPICEVSKVASHLEVNCDKRQLTALPPDLPKDTTILHLSENLLYTFSLATLMPYTRLTQLNLDRCELTKLQVDGTLPVLGTLDLSHNQLQSLPLLGQTLPALTVLDVSFNRLTSLPLGALRGLGELQELYLKGNELKTLPPGLLTPTPKLEKLSLANNQLTELPAGLLNGLENLDTLLLQENSLYTIPKGFFGSHLLPFAFLHGNPWLCNCEILYFRRWLQDNAENVYVWKQGVDVKAMTSNVASVQCDNSDKFPVYKYPGKGCPLVPR

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	Homo sapiens

Entity 2 Entity 2 polymer

Description description	OS1 peptide
Molecular weight formula_weight	1292.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

CTERMALHNLC

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	218

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3p72a1
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	d3p72a2
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 (1 domains)

Domain ID domain_id	3p72A00
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	58.817 Å
Unit-cell length b length_b	58.817 Å
Unit-cell length c length_c	163.027 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	54.300 Å
R factor r_factor	0.2206
R_work r_work	0.2172
R_free r_free	0.2863

fit	/app/data/saxs_computation/p7/3p72/3p72.fit
pddf	/app/data/pr_computation/p7/3p72/3p72.pr.out
profile	/app/data/saxs_computation/p7/3p72/3p72.dat

structure of platelet Glycoprotein 1b alpha with a bound peptide inhibitor

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

Platelet glycoprotein Ib alpha chain

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 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)