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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

Method: X-RAY DIFFRACTION Dmax: 62.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

FIBRINOGEN GAMMA CHAIN RESIDUES

Homo sapiens

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 170–418 Fragment：RESIDUES 143 - 411 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

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 3FIB 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 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 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 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 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 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 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 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 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 ligand/ion 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 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 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 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 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 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 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 oligomeric state 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 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 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 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 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
2VR3 Structural and Biochemical Characterization of Fibrinogen binding to ClfA from Staphylocccus aureus Deposited 2008-03-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 425–437（13 aa） Fragment：C-TERMINAL GAMMA-CHAIN PEPTIDE ANALOG, RESIDUES 425-437
Mutation：YES No recorded non-water small molecule 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
2VR3 Structural and Biochemical Characterization of Fibrinogen binding to ClfA from Staphylocccus aureus Deposited 2008-03-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 425–437（13 aa） Fragment：C-TERMINAL GAMMA-CHAIN PEPTIDE ANALOG, RESIDUES 425-437
Mutation：YES No recorded non-water small molecule 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
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 ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 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
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 oligomeric state Different ligand/ion 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 oligomeric state 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 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 oligomeric state 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 oligomeric state 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 57 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FIBG_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–249； UniProt 170–418

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

SAXS profile for 3fib

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3fib
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3fib
Deposition date deposition_date1997-07-14
Structure title titleRECOMBINANT 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
Keywords keywordsFIBRINOGEN, BLOOD COAGULATION, FIBRIN POLYMERIZATION, CIS PEPTIDE BONDS; BLOOD COAGULATION
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier18.52 Å
Radius of gyration Rg (electron density) rg_electron17.41 Å
Forward intensity I(0) i014469900.00
Molecular weight molecular_weight28227.0 kDa
Excluded volume excluded_volume35018 ų
Envelope volume envelope_volume38994 ų
Hydration-shell volume shell_volume18509 ų
Envelope diameter envelope_diameter61.6 Å
Shell Rg shell_rg23.92 Å
Envelope Rg envelope_rg17.73 Å
Shape Rg shape_rg17.37 Å
Total Rg total_rg18.44 Å
Total atoms total_atoms1996
Residues n_residues249
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax62.1 Å
Rg (real space) rg_real18.42 Å
Rg uncertainty (real space) rg_real_error0.35 Å
I(0) (real space) i0_real1.4470e+07
I(0) uncertainty (real space) i0_real_error1.8940e+05
Rg (reciprocal space) rg_reciprocal18.44 Å
I(0) (reciprocal space) i0_reciprocal14470000.0000
Solution quality estimate total_estimate0.7952
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.8 Å
Skewness Skewness skewness0.216
Kurtosis Kurtosis kurtosis-0.289
Angular range angular_range— – 0.4300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4053000.0000
Real-space data points n_real_points74
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.778; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; 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)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3fiba_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.171 — Fibrinogen C-terminal domain-like
Superfamily Superfamily superfamilyd.171.1 — Fibrinogen C-terminal domain-like
Family Family familyd.171.1.1 — Fibrinogen C-terminal domain-like

CATH v4.4 (2 domains)

Domain ID domain_id3fibA01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology215 — Gamma Fibrinogen; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Gamma Fibrinogen, chain A, domain 1
Domain ID domain_id3fibA02
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
Homologous superfamily homologous superfamily10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2
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8. Citations (2)

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9. Files and Curves (10)