2vr3

Structural and Biochemical Characterization of Fibrinogen binding to ClfA from Staphylocccus aureus

Method: X-RAY DIFFRACTION D_max: 100.8 Å Quality: GOOD

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

CLUMPING FACTOR A

STAPHYLOCOCCUS AUREUS

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 229–545	Fragment：N2N3, RESIDUES 229-545 Mutation：YES	FIBRINOGEN GAMMA-CHAIN × 1 （P02679）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；16-20% PEG 8000, 100MM SUCCINIC ACID PH 6.0	Resolution 1.95 Å R-free 0.279
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 229–545	Fragment：N2N3, RESIDUES 229-545 Mutation：YES	FIBRINOGEN GAMMA-CHAIN × 1 （P02679）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；16-20% PEG 8000, 100MM SUCCINIC ACID PH 6.0	Resolution 1.95 Å R-free 0.279

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	CLFA_STAA8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–329； UniProt 229–545 Author chain B； PDBConstruct 13–329； UniProt 229–545

FIBRINOGEN GAMMA-CHAIN

OrganismNot specified

UniProt P02679

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 C； UniProt 425–437	Fragment：C-TERMINAL GAMMA-CHAIN PEPTIDE ANALOG, RESIDUES 425-437 Mutation：YES	CLUMPING FACTOR A × 1 （Q2G015）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；16-20% PEG 8000, 100MM SUCCINIC ACID PH 6.0	Resolution 1.95 Å R-free 0.279
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 425–437	Fragment：C-TERMINAL GAMMA-CHAIN PEPTIDE ANALOG, RESIDUES 425-437 Mutation：YES	CLUMPING FACTOR A × 1 （Q2G015）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；16-20% PEG 8000, 100MM SUCCINIC ACID PH 6.0	Resolution 1.95 Å R-free 0.279

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 2VR3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DUG STRUCTURE OF THE FIBRINOGEN G CHAIN INTEGRIN BINDING AND FACTOR XIIIA CROSSLINKING SITES OBTAINED THROUGH CARRIER PROTEIN DRIVEN CRYSTALLIZATION Deposited 2000-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 424–437（14 aa） Chain B 424–437（14 aa）	Not recorded	GSH Glutathione × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；PEG 3350, sodium acetate, sodium chloride, ammonium sulfate, Tris, reduced glutathione, pH 4.6, VAPOR DIFFUSION, HANGING DROP	Resolution 1.80 Å R-free 0.226
1FIB RECOMBINANT HUMAN GAMMA-FIBRINOGEN CARBOXYL TERMINAL FRAGMENT (RESIDUES 143-411) BOUND TO CALCIUM AT PH 6.0 Deposited 1996-04-02	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 169–437（269 aa） Fragment：CARBOXYL TERMINUS, RESIDUES 143 - 411	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å R-free 0.227
1FIC STRUCTURE OF HUMAN GAMMA FIBRINOGEN 30 KD CARBOXYL TERMINAL FRAGMENT Deposited 1996-08-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 169–437（269 aa） Fragment：30 KD CARBOXYL TERMINAL FRAGMENT Chain B 169–437（269 aa） Fragment：30 KD CARBOXYL TERMINAL FRAGMENT	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 2.50 Å R-free 0.244
1FID STRUCTURE OF HUMAN GAMMA FIBRINOGEN 30 KD CARBOXYL TERMINAL FRAGMENT Deposited 1996-08-24	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 169–437（269 aa） Fragment：30 KD CARBOXYL TERMINAL FRAGMENT	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.	Resolution 2.10 Å R-free 0.226
1FZA CRYSTAL STRUCTURE OF FIBRINOGEN FRAGMENT D Deposited 1997-08-05	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 C 111–432（322 aa） Fragment：FRAGMENT D Chain F 111–432（322 aa） Fragment：FRAGMENT D	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions SYMMETRY OPERATIONS FOR NON-STANDARD SETTING: X, Y, Z -X, Y+1/2, -Z	Resolution 2.90 Å R-free 0.363
1FZB CRYSTAL STRUCTURE OF CROSSLINKED FRAGMENT D Deposited 1997-08-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain C 111–432（322 aa） Fragment：DOUBLE FRAGMENT D Chain F 111–432（322 aa） Fragment：DOUBLE FRAGMENT D	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；13-14% PEG 3350, 50 MM TRIS PH 7.0, 10 MM CALCIUM CHLORIDE 1MM SODIUM AZIDE 5MM GLY-PRO-ARG-PRO-AMIDE	Resolution 2.90 Å R-free 0.318
1FZC CRYSTAL STRUCTURE OF FRAGMENT DOUBLE-D FROM HUMAN FIBRIN WITH TWO DIFFERENT BOUND LIGANDS Deposited 1998-05-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: decameric	Chain C 111–432（322 aa） Fragment：DOUBLE-D Chain F 111–432（322 aa） Fragment：DOUBLE-D	Not recorded	MAN alpha-D-mannopyranose × 1 CA CALCIUM ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；12% PEG 3350, 50 MM TRIS PH 7.0, 5 MM CALCIUM CHLORIDE, 1MM SODIUM AZIDE, 5MM GLY-PRO-ARG-PRO-AMIDE, 5MM GLY-HIS-ARG-PRO-AMIDE	Resolution 2.30 Å R-free 0.290
1FZE CRYSTAL STRUCTURE OF FRAGMENT DOUBLE-D FROM HUMAN FIBRIN Deposited 1998-12-23	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 C 115–432（318 aa） Fragment：FRAGMENT D Chain F 115–432（318 aa） Fragment：FRAGMENT D	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 3.00 Å R-free 0.318
1FZE CRYSTAL STRUCTURE OF FRAGMENT DOUBLE-D FROM HUMAN FIBRIN Deposited 1998-12-23	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 C 115–432（318 aa） Fragment：FRAGMENT D	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 3.00 Å R-free 0.318
1FZE CRYSTAL STRUCTURE OF FRAGMENT DOUBLE-D FROM HUMAN FIBRIN Deposited 1998-12-23	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 F 115–432（318 aa） Fragment：FRAGMENT D	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 3.00 Å R-free 0.318
1FZF CRYSTAL STRUCTURE OF FRAGMENT DOUBLE-D FROM HUMAN FIBRIN WITH THE PEPTIDE LIGAND GLY-HIS-ARG-PRO-AMIDE Deposited 1998-12-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain C 114–432（319 aa） Fragment：FRAGMENT DOUBLE-D Chain F 114–432（319 aa） Fragment：FRAGMENT DOUBLE-D	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；pH 7.8	Resolution 2.70 Å R-free 0.302
1FZG CRYSTAL STRUCTURE OF FRAGMENT D FROM HUMAN FIBRINOGEN WITH THE PEPTIDE LIGAND GLY-HIS-ARG-PRO-AMIDE Deposited 1999-01-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: decameric	Chain C 115–432（318 aa） Fragment：FRAGMENT DOUBLE-D Chain F 115–432（318 aa） Fragment：FRAGMENT DOUBLE-D	Not recorded	CA CALCIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；pH 7.8	Resolution 2.50 Å R-free 0.302
1LT9 Crystal Structure of Recombinant Human Fibrinogen Fragment D Deposited 2002-05-20	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 C 122–432（311 aa） Fragment：Fragment D (residues 96-406)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；9% PEG 3350, 70mM Calcium Chloride, 2mM Sodium Azide, 50mM Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.80 Å R-free 0.271
1LT9 Crystal Structure of Recombinant Human Fibrinogen Fragment D Deposited 2002-05-20	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 F 122–432（311 aa） Fragment：Fragment D (residues 96-406)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；9% PEG 3350, 70mM Calcium Chloride, 2mM Sodium Azide, 50mM Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.80 Å R-free 0.271
1LTJ Crystal Structure of Recombinant Human Fibrinogen Fragment D with the Peptide Ligands Gly-Pro-Arg-Pro-Amide and Gly-His-Arg-Pro-Amide Deposited 2002-05-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 122–432（311 aa） Fragment：Fragment D (residues 96-406)	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；7% PEG 3350, 12.5mM Calcium Chloride, 2mM Sodium Azide, 50mM Tris pH 8.5, 2mM GHRP-amide, 2mM GPRP-amide, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.80 Å R-free 0.270
1LTJ Crystal Structure of Recombinant Human Fibrinogen Fragment D with the Peptide Ligands Gly-Pro-Arg-Pro-Amide and Gly-His-Arg-Pro-Amide Deposited 2002-05-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain F 122–432（311 aa） Fragment：Fragment D (residues 96-406)	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；7% PEG 3350, 12.5mM Calcium Chloride, 2mM Sodium Azide, 50mM Tris pH 8.5, 2mM GHRP-amide, 2mM GPRP-amide, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.80 Å R-free 0.270
1N8E Fragment Double-D from Human Fibrin Deposited 2002-11-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 114–437（324 aa） Fragment：double-D gamma chain Chain F 114–437（324 aa） Fragment：double-D gamma chain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；PEG-3350, 50 mM Tris, 7.5 mM CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 4.50 Å R-free 0.416
1RE3 Crystal Structure of Fragment D of BbetaD398A Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide Deposited 2003-11-06	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 C 122–432（311 aa） Fragment：Fragment D of fibrinogen gamma chain	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；9% PEG 3350, 12.5 mM calcium chloride, 2 mM sodium azide, 50 mM Tris pH 8.5, , VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.45 Å R-free 0.263
1RE3 Crystal Structure of Fragment D of BbetaD398A Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide Deposited 2003-11-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain F 122–432（311 aa） Fragment：Fragment D of fibrinogen gamma chain	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；9% PEG 3350, 12.5 mM calcium chloride, 2 mM sodium azide, 50 mM Tris pH 8.5, , VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.45 Å R-free 0.263
1RE4 Crystal Structure of Fragment D of BbetaD398A Fibrinogen Deposited 2003-11-06	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 C 122–432（311 aa） Fragment：Fragment D of fibrinogen gamma chain	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；14-15% PEG 3350, 70 mM calcium chloride, 2 mM sodium azide, 50 mM Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.70 Å R-free 0.271
1RE4 Crystal Structure of Fragment D of BbetaD398A Fibrinogen Deposited 2003-11-06	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 F 122–432（311 aa） Fragment：Fragment D of fibrinogen gamma chain	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；14-15% PEG 3350, 70 mM calcium chloride, 2 mM sodium azide, 50 mM Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.70 Å R-free 0.271
1RF0 Crystal Structure of Fragment D of gammaE132A Fibrinogen Deposited 2003-11-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 122–432（311 aa） Fragment：Fibrinogen gamma chain	Mutation：E132A	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；14-15% PEG 3350, 70 mM calcium chloride, 2 mM sodium azide, 50 mM Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.81 Å R-free 0.286
1RF0 Crystal Structure of Fragment D of gammaE132A Fibrinogen Deposited 2003-11-07	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 F 122–432（311 aa） Fragment：Fibrinogen gamma chain	Mutation：E132A	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；14-15% PEG 3350, 70 mM calcium chloride, 2 mM sodium azide, 50 mM Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.81 Å R-free 0.286
1RF1 Crystal Structure of Fragment D of gammaE132A Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-amide Deposited 2003-11-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 122–432（311 aa） Fragment：Fibrinogen gamma chain	Mutation：E132A	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；9-10% PEG 3350, 12.5 mM calcium chloride, 2 mM sodium azide, 50 mM Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.53 Å R-free 0.281
1RF1 Crystal Structure of Fragment D of gammaE132A Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-amide Deposited 2003-11-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain F 122–432（311 aa） Fragment：Fibrinogen gamma chain	Mutation：E132A	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；9-10% PEG 3350, 12.5 mM calcium chloride, 2 mM sodium azide, 50 mM Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.53 Å R-free 0.281
2A45 Crystal structure of the complex between thrombin and the central "E" region of fibrin Deposited 2005-06-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain I 27–71（45 aa） Chain L 27–71（45 aa）	Not recorded	0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 2 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions MICRODIALYSIS；pH 7.9；298 K；PEG 3500, AMMONIUM PHOSPHATE, TRIS, pH 7.90, MICRODIALYSIS, temperature 298K	Resolution 3.65 Å R-free 0.290
2FFD Fibrinogen Fragment D with "A" knob peptide mimic GPRVVE Deposited 2005-12-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 122–432（311 aa） Fragment：residues 122-432	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；10% PEG3350, 12.5 mM CaCl2, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.89 Å R-free 0.268
2FFD Fibrinogen Fragment D with "A" knob peptide mimic GPRVVE Deposited 2005-12-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain F 122–432（311 aa） Fragment：residues 122-432	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；10% PEG3350, 12.5 mM CaCl2, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.89 Å R-free 0.268
2FIB RECOMBINANT HUMAN GAMMA-FIBRINOGEN CARBOXYL TERMINAL FRAGMENT (RESIDUES 143-411) COMPLEXED TO THE PEPTIDE GLY-PRO-ARG-PRO AT PH 6.0 Deposited 1997-06-03	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 A 169–437（269 aa） Fragment：GAMMA CHAIN, CARBOXYL TERMINAL FRAGMENT RESIDUES 143 - 411	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；PROTEIN WAS CRYSTALLIZED FROM 12% PEG8000, 70MM CACL2, 0.1 M MES, PH 6.0, 0.02%NAN3, ROOM TEMPERATURE, SITTING DROPS. THE CRYSTAL WAS SOAKED OVERNIGHT IN THE ORIGINAL SOLUTION PLUS 0.01M GLY-PRO-ARG-PRO (SIGMA), THEN BACK-SOAKED FOR 10 MINUTES., vapor diffusion - sitting drop	Resolution 2.01 Å R-free 0.282
2H43 Crystal Structure of Human Fragment D Complexed with Ala-His-Arg-Pro-amide Deposited 2006-05-23	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 C 115–433（319 aa）	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；fragment D, 5 mg/mil, 4mM AHRPam, 50mM Tris, pH 7.5, 7.5% PEG, 7.5mM CaCl2, 1mM sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.70 Å R-free 0.307
2H43 Crystal Structure of Human Fragment D Complexed with Ala-His-Arg-Pro-amide Deposited 2006-05-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain F 115–433（319 aa）	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；fragment D, 5 mg/mil, 4mM AHRPam, 50mM Tris, pH 7.5, 7.5% PEG, 7.5mM CaCl2, 1mM sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.70 Å R-free 0.307
2HLO Crystal Structure of Fragment D-dimer from Human Fibrin Complexed with Gly-hydroxyPro-Arg-Pro-amide Deposited 2006-07-08	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 C 114–437（324 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；10mg/ml fibrinogen, 2mM Gly-hydroxyPro-Arg-Pro-amide, 7.5mM CaCl2, 10% PEG, 50mM Tris, 2mM sodium azide, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.60 Å R-free 0.268
2HLO Crystal Structure of Fragment D-dimer from Human Fibrin Complexed with Gly-hydroxyPro-Arg-Pro-amide Deposited 2006-07-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain F 114–437（324 aa）	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；10mg/ml fibrinogen, 2mM Gly-hydroxyPro-Arg-Pro-amide, 7.5mM CaCl2, 10% PEG, 50mM Tris, 2mM sodium azide, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.60 Å R-free 0.268
2HWL Crystal structure of thrombin in complex with fibrinogen gamma' peptide Deposited 2006-08-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain P 439–452（14 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；25% PEG 4000, 100 mM HEPES sodium salt buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.249
2OYH Crystal Structure of Fragment D of gammaD298,301A Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide Deposited 2007-02-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 122–432（311 aa） Fragment：Residues 122-432	Mutation：D298A, D301A	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；5 microL of 10 mg/mL protein in HBS with 3 mM GHRP were mixed with an identical volume of well solution containing 50 mM Tris, pH 8.5, 2 mM NaN3, 12.5 mM CaCl2, and 11% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.40 Å R-free 0.259
2OYH Crystal Structure of Fragment D of gammaD298,301A Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide Deposited 2007-02-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain F 122–432（311 aa） Fragment：Residues 122-432	Mutation：D298A, D301A	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；5 microL of 10 mg/mL protein in HBS with 3 mM GHRP were mixed with an identical volume of well solution containing 50 mM Tris, pH 8.5, 2 mM NaN3, 12.5 mM CaCl2, and 11% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.40 Å R-free 0.259
2OYI Crystal Structure of Fragment D of gammaD298,301A Fibrinogen with the Peptide Ligand Gly-Pro-Arg-Pro-Amide Deposited 2007-02-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 122–432（311 aa） Fragment：Residues 96-406	Mutation：D298A, D301A	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；5 microL of 10 mg/mL protein in HBS with 3 mM GPRP were mixed with an identical volume of well solution containing 50 mM Tris, pH 8.5, 2 mM NaN3, 12.5 mM CaCl2, and 11% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.70 Å R-free 0.256
2OYI Crystal Structure of Fragment D of gammaD298,301A Fibrinogen with the Peptide Ligand Gly-Pro-Arg-Pro-Amide Deposited 2007-02-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain F 122–432（311 aa） Fragment：Residues 96-406	Mutation：D298A, D301A	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；5 microL of 10 mg/mL protein in HBS with 3 mM GPRP were mixed with an identical volume of well solution containing 50 mM Tris, pH 8.5, 2 mM NaN3, 12.5 mM CaCl2, and 11% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.70 Å R-free 0.256
2XNX BC1 fragment of streptococcal M1 protein in complex with human fibrinogen Deposited 2010-08-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain C 114–432（319 aa） Fragment：FRAGMENT D, RESIDUES 114-432 Chain F 114–432（319 aa） Fragment：FRAGMENT D, RESIDUES 114-432 Chain I 114–432（319 aa） Fragment：FRAGMENT D, RESIDUES 114-432 Chain L 114–432（319 aa） Fragment：FRAGMENT D, RESIDUES 114-432	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 16% PEG 3350, 0.2 M SODIUM TARTRATE WITH SEEDS GROWN IN 0.6 M K2/NA2 PO4, 0.12 M (NH4)2SO4, 0.1 M HEPES, PH 7.5	Resolution 3.30 Å R-free 0.325
2XNY A fragment of streptococcal M1 protein in complex with human fibrinogen Deposited 2010-08-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 114–432（319 aa） Fragment：FRAGMENT D, RESIDUES 114-432	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 1.3 M AMMONIUM TARTRATE, 0.1 M MES, PH 6.25.	Resolution 7.50 Å R-free 0.408
2XNY A fragment of streptococcal M1 protein in complex with human fibrinogen Deposited 2010-08-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 114–432（319 aa） Fragment：FRAGMENT D, RESIDUES 114-432	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 1.3 M AMMONIUM TARTRATE, 0.1 M MES, PH 6.25.	Resolution 7.50 Å R-free 0.408
3BVH Crystal Structure of Recombinant gammaD364A Fibrinogen Fragment D with the Peptide Ligand Gly-Pro-Arg-Pro-Amide Deposited 2008-01-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 128–420（293 aa） Fragment：residues 128-420	Mutation：D390A	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；9 % PEG 3350, 50 mM Tris-HCl pH 8.5, 2 mM sodium azide, 12.5 mM sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.60 Å R-free 0.260
3BVH Crystal Structure of Recombinant gammaD364A Fibrinogen Fragment D with the Peptide Ligand Gly-Pro-Arg-Pro-Amide Deposited 2008-01-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain F 128–420（293 aa） Fragment：residues 128-420	Mutation：D390A	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；9 % PEG 3350, 50 mM Tris-HCl pH 8.5, 2 mM sodium azide, 12.5 mM sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.60 Å R-free 0.260
3E1I Crystal Structure of BbetaD432A Variant Fibrinogen Fragment D with the Peptide Ligand Gly-His-Arg-Pro-amide Deposited 2008-08-04	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 C 114–432（319 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；50 mM Tris, 12.5 mM calcium chloride, 12% PEG 3350, 2 mM sodium azide, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.30 Å R-free 0.242
3E1I Crystal Structure of BbetaD432A Variant Fibrinogen Fragment D with the Peptide Ligand Gly-His-Arg-Pro-amide Deposited 2008-08-04	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 F 114–432（319 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；50 mM Tris, 12.5 mM calcium chloride, 12% PEG 3350, 2 mM sodium azide, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.30 Å R-free 0.242
3FIB RECOMBINANT HUMAN GAMMA-FIBRINOGEN CARBOXYL TERMINAL FRAGMENT (RESIDUES 143-411) BOUND TO CALCIUM AT PH 6.0: A FURTHER REFINEMENT OF PDB ENTRY 1FIB, AND DIFFERS FROM 1FIB BY THE MODELLING OF A CIS PEPTIDE BOND BETWEEN RESIDUES K338 AND C339 Deposited 1997-07-14	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 170–418（249 aa） Fragment：RESIDUES 143 - 411	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；18% PEG 8000, 0.1 M MES PH 6.0, 70MM CACL2, SITTING DROP VAPOR DIFFUSION	Resolution 2.10 Å R-free 0.206
3GHG Crystal Structure of Human Fibrinogen Deposited 2009-03-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: decameric	Chain C 27–437（411 aa） Fragment：mature chain Chain F 27–437（411 aa） Fragment：mature chain	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；2% PEG 3350, 0.2 M TMAO, 75 mM NaCl, 50 mM Tris, 1 mM CaCl2, 1 mM HPRPam, 1 mM GHRPam, 1 mM sodium azide, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.90 Å R-free 0.309
3GHG Crystal Structure of Human Fibrinogen Deposited 2009-03-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 10 PDB declaration: decameric	Chain I 27–437（411 aa） Fragment：mature chain Chain L 27–437（411 aa） Fragment：mature chain	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；2% PEG 3350, 0.2 M TMAO, 75 mM NaCl, 50 mM Tris, 1 mM CaCl2, 1 mM HPRPam, 1 mM GHRPam, 1 mM sodium azide, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.90 Å R-free 0.309
3H32 Crystal structure of D-dimer from human fibrin complexed with Gly-His-Arg-Pro-Tyr-amide Deposited 2009-04-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain C 121–437（317 aa） Fragment：UNP residues 27-437 Chain F 121–437（317 aa） Fragment：UNP residues 27-437	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；Equal volumes of (a) 5 mg/mL D-dimer, 0.5 mM GHRPYam, 0.3 mM GPRPam, 0.05 M Tris-HCl pH 8.0 and (b) 1% PEG 3350, 1 mM Iodoacetamide, 1 mM CaCl2, 2mM Sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 3.60 Å R-free 0.320
3HUS Crystal structure of recombinant gamma N308K fibrinogen fragment D with the peptide ligand Gly-Pro-Arg-Pro-amide Deposited 2009-06-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 122–432（311 aa） Fragment：Fragment D: UNP residues 122-432	Mutation：N308K	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；9% PEG 3350, 50 mM Tris-HCl pH 8.5, 2 mM Sodium azide, 12.5 mM Calcium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 3.04 Å R-free 0.288
3HUS Crystal structure of recombinant gamma N308K fibrinogen fragment D with the peptide ligand Gly-Pro-Arg-Pro-amide Deposited 2009-06-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain F 122–432（311 aa） Fragment：Fragment D: UNP residues 122-432	Mutation：N308K	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；9% PEG 3350, 50 mM Tris-HCl pH 8.5, 2 mM Sodium azide, 12.5 mM Calcium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 3.04 Å R-free 0.288
4B60 Structure of rFnBPA(189-505) in complex with fibrinogen gamma chain C- terminal peptide Deposited 2012-08-08	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 421–437（17 aa） Fragment：C-TERMINUS, RESIDUES 421-433	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions PEG 2K MME 25%, 0.2 M CA AC, ISOPROPANOL 10%	Resolution 1.83 Å R-free 0.246
4B60 Structure of rFnBPA(189-505) in complex with fibrinogen gamma chain C- terminal peptide Deposited 2012-08-08	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 421–437（17 aa） Fragment：C-TERMINUS, RESIDUES 421-433	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions PEG 2K MME 25%, 0.2 M CA AC, ISOPROPANOL 10%	Resolution 1.83 Å R-free 0.246
9KHB Crystal structure of wild-type human fibrinogen gamma chain C-terminal domain (gamma-nodule) Deposited 2024-11-10	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 169–437（269 aa）	Not recorded	GOL GLYCEROL × 3 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；Reservoir solution (22% PEG 8000, 150 mM 2-Morpholinoethanesulfonic acid, pH 6.0, 70 mM calcium choride) Protein solution (20 mM 2-[4-(2-Hydroxyethyl)-1-piperazinyl]ethanesulfonic acid, pH7.4, 120 mM sodium choride, 70 mM calcium choride)	Resolution 1.03 Å R-free 0.139
9KHC Crystal structure of wild-type human fibrinogen gamma chain C-terminal domain (gamma-nodule) complexed with GPRP peptide Deposited 2024-11-10	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 A 169–437（269 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；The reservoir solution contains 0.1 M MES pH 6.0, 20% PEG8000, and 70 mM CaCl2. After clystals were grown, the reservoir solution containing 20 mM GPRP was added to the drop.	Resolution 1.32 Å R-free 0.203
9KHC Crystal structure of wild-type human fibrinogen gamma chain C-terminal domain (gamma-nodule) complexed with GPRP peptide Deposited 2024-11-10	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 C 169–437（269 aa）	Not recorded	CA CALCIUM ION × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；The reservoir solution contains 0.1 M MES pH 6.0, 20% PEG8000, and 70 mM CaCl2. After clystals were grown, the reservoir solution containing 20 mM GPRP was added to the drop.	Resolution 1.32 Å R-free 0.203

36 other PDB entries and 56 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FIBG_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–13； UniProt 425–437 Author chain D； PDBConstruct 1–13； UniProt 425–437

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	2vr3
Deposition date deposition_date	2008-03-25
Structure title title	Structural and Biochemical Characterization of Fibrinogen binding to ClfA from Staphylocccus aureus
Keywords keywords	;PLATELET AGGREGATION, PEPTIDOGLYCAN-ANCHOR, CELL ADHESION, STAPHYLOCOCCUS AUREUS, FIBRINOGEN GAMMA-CHAIN, SECRETED, CELL WALL, VIRULENCE, CLUMPING FACTOR ;; 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	29.74 Å
Radius of gyration Rg (electron density) rg_electron	29.10 Å
Forward intensity I(0) i0	73467200.00
Molecular weight molecular_weight	66536.0 kDa
Excluded volume excluded_volume	82761 Å³
Envelope volume envelope_volume	104360 Å³
Hydration-shell volume shell_volume	30614 Å³
Envelope diameter envelope_diameter	104.2 Å
Shell Rg shell_rg	35.39 Å
Envelope Rg envelope_rg	28.96 Å
Shape Rg shape_rg	29.12 Å
Total Rg total_rg	29.63 Å
Total atoms total_atoms	4699
Residues n_residues	644
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	100.8 Å
Rg (real space) rg_real	29.77 Å
Rg uncertainty (real space) rg_real_error	0.80 Å
I(0) (real space) i0_real	7.3470e+07
I(0) uncertainty (real space) i0_real_error	1.0190e+06
Rg (reciprocal space) rg_reciprocal	29.76 Å
I(0) (reciprocal space) i0_reciprocal	73470000.0000
Solution quality estimate total_estimate	0.8120
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	36.1 Å
Skewness Skewness skewness	0.356
Kurtosis Kurtosis kurtosis	-0.347
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	17860000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.865; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	CLUMPING FACTOR A
Molecular weight formula_weight	35801.5 kDa
Mutation mutation	YES
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	5226

MRGSHHHHHHGSGTDITNQLTNVTVGIDSGTTVYPHQAGYVKLNYGFSVPNSAVKGDTFKITVPKELNLNGVTSTAKVPPIMAGDQVLANGVIDSDGNVIYTFTDYVNTKCDVKATLTMPAYIDPENVKKTGNVTLATGIGSTTANKTVLVDYEKYGKFYNLSIKGTIDQIDKTNNTYRQTIYVNPSGDNVIAPVLTGNLKPNTDSNALIDQQNTSIKVYKVDNAADLSESYFVNPENFEDVTNSVNITFPNPNQYKVEFNTPDDQITTPYIVVVNGHIDPNSKGDLALRSTLYGYNSNIIWRSMSWDNEVAFNNGSGSGDGIDCPVVP

来源 Source

来源生物 organism	STAPHYLOCOCCUS AUREUS
NCBI Class编号 ncbi_taxonomy_id	1280
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	FIBRINOGEN GAMMA-CHAIN
Molecular weight formula_weight	1276.4 kDa
Mutation mutation	YES
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

QHHLGGAKQAGAV

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	527

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2vr3A01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1280 —

Domain ID domain_id	2vr3A02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1290 —

Domain ID domain_id	2vr3B01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1280 —

Domain ID domain_id	2vr3B02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1290 —

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8. Citations (1)

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Unit-cell length a length_a	35.427 Å
Unit-cell length b length_b	61.836 Å
Unit-cell length c length_c	81.777 Å
Unit-cell angle α angle_alpha	85.44 °
Unit-cell angle β angle_beta	81.84 °
Unit-cell angle γ angle_gamma	82.45 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2126
R_work r_work	0.2112
R_free r_free	0.2793

fit	/app/data/saxs_computation/vr/2vr3/2vr3.fit
pddf	/app/data/pr_computation/vr/2vr3/2vr3.pr.out
profile	/app/data/saxs_computation/vr/2vr3/2vr3.dat

Structural and Biochemical Characterization of Fibrinogen binding to ClfA from Staphylocccus aureus

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

CLUMPING FACTOR A

State in the Current Structure

Other States of the Same Protein in the Database

FIBRINOGEN GAMMA-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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)