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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：P04004 New Search
9PDB entries
12Biological assembly
16chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
1OC0 plasminogen activator inhibitor-1 complex with somatomedin B domain of vitronectin Deposited 2003-02-03 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain B 20–70（51 aa） Fragment：SOMATOMEDIN B, RESIDUES 20-70
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；10MM NAOAC, 50MM NACL, 2-9% PEG12000,25% PEG400, 50MM HEPES, PH 7.4
Resolution 2.28 Å R-free 0.252
1S4G Somatomedin-B Domain of human plasma vitronectin. Deposited 2004-01-16 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 20–70（51 aa） Fragment：Somatomedin B
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4.4；298 K；Ionic strength (raw mmCIF value) low
NMR sample composition Isolated from human plasma vitronectin by CNBr cleavage
Resolution not provided
1SSU Structural and biochemical evidence for disulfide bond heterogeneity in active forms of the somatomedin B domain of human vitronectin Deposited 2004-03-24 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 20–70（51 aa） Fragment：somatomedin B domain of human vitronectin
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.5；293 K；Ionic strength (raw mmCIF value) 180 mM；Pressure 1
NMR measurement conditions pH 7.5；293 K；Ionic strength (raw mmCIF value) 180 mM；Pressure 1
NMR sample composition N15-labeled protein 20 mM sodium phosphate pH 7.5 | 90% H2O/10% D2O
NMR sample composition unlabeled protein 20 mM sodium phosphate pH 7.5 | 90% H2O/10% D2O
Resolution not provided
2JQ8 Solution structure of the Somatomedin B domain from vitronectin produced in Pichia pastoris Deposited 2007-05-30 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 20–66（47 aa） Fragment：sequence database residues 20-66
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient
NMR sample composition 0.4 mM [U-99% 13C; U-99% 15N] SMB, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.7 mM SMB, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
3BT1 Structure of urokinase receptor, urokinase and vitronectin complex Deposited 2007-12-27 Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain B 21–60（40 aa） Fragment：sometomedin-B domain
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 7.5；295 K；12% PEG 3350, 50mM HEPES pH 7.5, MICRODIALYSIS, temperature 295K
Resolution 2.80 Å R-free 0.308
3BT2 Structure of urokinase receptor, urokinase and vitronectin complex Deposited 2007-12-27 Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count
Chain B 21–60（40 aa） Fragment：sometomedin-B domain
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 7.5；295 K；8% PEG 4000, 2.5% ethanol, 0.05% sodium azide, 50mM cacodylate pH 6.5, pH 7.5, MICRODIALYSIS, temperature 295K
Resolution 2.50 Å R-free 0.272
3BT2 Structure of urokinase receptor, urokinase and vitronectin complex Deposited 2007-12-27 Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 21–60（40 aa） Fragment：sometomedin-B domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 7.5；295 K；8% PEG 4000, 2.5% ethanol, 0.05% sodium azide, 50mM cacodylate pH 6.5, pH 7.5, MICRODIALYSIS, temperature 295K
Resolution 2.50 Å R-free 0.272
4K24 Structure of anti-uPAR Fab ATN-658 in complex with uPAR Deposited 2013-04-08 Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count
Chain B 21–60（40 aa） Fragment：UNP residues 21-60
Not recorded MAN alpha-D-mannopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；0.1M HEPES pH 7.5, 55%(v/v) Tacsimate, 2%(v/v) 2-methyl-1,3-propanediol, vapor diffusion, sitting drop, temperature 295K
Resolution 4.50 Å R-free 0.275
6O5E Crystal structure of the Vitronectin hemopexin-like domain Deposited 2019-03-01 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 154–285（132 aa） Fragment：hemopexin-like domain (UNP residues 154-285, 324-354, 435-474)
Chain A 324–354（31 aa） Fragment：hemopexin-like domain (UNP residues 154-285, 324-354, 435-474)
Chain A 435–474（40 aa） Fragment：hemopexin-like domain (UNP residues 154-285, 324-354, 435-474)
Mutation：C180S, C215S Mutation：C180S, C215S Mutation：C180S, C215S NA SODIUM ION × 2 CL CHLORIDE ION × 1 SO4 SULFATE ION × 1 IMD IMIDAZOLE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；1 uL protein solution + 1 uL precipitate solution [0.09 M imidazole/MES, pH 6.5, 27 mM sodium nitrate, 27 mM sodium phosphate dibasic, 27 mM ammonium sulfate, 11.25% v/v MPD, 11.25% w/v PEG1000, 11.25% w/v PEG3350, 3% w/v D-(+)-trehalose]
Resolution 1.90 Å R-free 0.210
6O5E Crystal structure of the Vitronectin hemopexin-like domain Deposited 2019-03-01 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 154–285（132 aa） Fragment：hemopexin-like domain (UNP residues 154-285, 324-354, 435-474)
Chain B 324–354（31 aa） Fragment：hemopexin-like domain (UNP residues 154-285, 324-354, 435-474)
Chain B 435–474（40 aa） Fragment：hemopexin-like domain (UNP residues 154-285, 324-354, 435-474)
Mutation：C180S, C215S Mutation：C180S, C215S Mutation：C180S, C215S NA SODIUM ION × 2 CL CHLORIDE ION × 1 SO4 SULFATE ION × 2 NO3 NITRATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；1 uL protein solution + 1 uL precipitate solution [0.09 M imidazole/MES, pH 6.5, 27 mM sodium nitrate, 27 mM sodium phosphate dibasic, 27 mM ammonium sulfate, 11.25% v/v MPD, 11.25% w/v PEG1000, 11.25% w/v PEG3350, 3% w/v D-(+)-trehalose]
Resolution 1.90 Å R-free 0.210
7RJ9 Crystal structure of the Vitronectin hemopexin-like domain binding Calcium Deposited 2021-07-20 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 154–474（321 aa） Fragment：UNP RESIDUES 154-285, 324-354, 435-474
Mutation：C180S, C215S, delta 286-323, delta 355-434 CA CALCIUM ION × 1 CL CHLORIDE ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1 UL PROTEIN SOLUTION + 1 UL PRECIPITATE SOLUTION contaning 0.09 M IMIDAZOLE/MES, PH 6.5, 27 mM SODIUM NITRATE, 27 mM SODIUM PHOSPHATE, 27 mM AMMONIUM SULFATE, 11.25% V/V MPD, 11.25% W/V PEG1000, 11.25% W/V PEG3350, 3% W/V D- (+)-TREHALOSE. Crystals were soaked with the well solution containing 100 mM CaCl2 and missing SODIUM PHOSPHATE, AMMONIUM SULFATE, and IMIDAZOLE/MES
Resolution 1.70 Å R-free 0.210
7RJ9 Crystal structure of the Vitronectin hemopexin-like domain binding Calcium Deposited 2021-07-20 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 154–474（321 aa） Fragment：UNP RESIDUES 154-285, 324-354, 435-474
Mutation：C180S, C215S, delta 286-323, delta 355-434 CA CALCIUM ION × 1 CL CHLORIDE ION × 1 NA SODIUM ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1 UL PROTEIN SOLUTION + 1 UL PRECIPITATE SOLUTION contaning 0.09 M IMIDAZOLE/MES, PH 6.5, 27 mM SODIUM NITRATE, 27 mM SODIUM PHOSPHATE, 27 mM AMMONIUM SULFATE, 11.25% V/V MPD, 11.25% W/V PEG1000, 11.25% W/V PEG3350, 3% W/V D- (+)-TREHALOSE. Crystals were soaked with the well solution containing 100 mM CaCl2 and missing SODIUM PHOSPHATE, AMMONIUM SULFATE, and IMIDAZOLE/MES
Resolution 1.70 Å R-free 0.210

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.