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- PDB-3f6u: Crystal structure of human Activated Protein C (APC) complexed wi... -

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Basic information

Entry
Database: PDB / ID: 3f6u
TitleCrystal structure of human Activated Protein C (APC) complexed with PPACK
Components(Vitamin K-dependent protein C ...) x 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / BLOOD COAGULATION / Serine protease / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


protein C (activated) / positive regulation of establishment of endothelial barrier / negative regulation of coagulation / negative regulation of blood coagulation / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Intrinsic Pathway of Fibrin Clot Formation / Cell surface interactions at the vascular wall ...protein C (activated) / positive regulation of establishment of endothelial barrier / negative regulation of coagulation / negative regulation of blood coagulation / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Intrinsic Pathway of Fibrin Clot Formation / Cell surface interactions at the vascular wall / Post-translational protein phosphorylation / negative regulation of inflammatory response / Golgi lumen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / endoplasmic reticulum lumen / serine-type endopeptidase activity / calcium ion binding / negative regulation of apoptotic process / Golgi apparatus / endoplasmic reticulum / proteolysis / extracellular space / extracellular region
Similarity search - Function
Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / Laminin / Laminin / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. ...Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / Laminin / Laminin / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Ribbon / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
D-Phe-Pro-Arg-CH2Cl / Chem-0G6 / Vitamin K-dependent protein C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSchmidt, A.E. / Padmanabhan, K. / Underwood, M.C. / Bode, W. / Mather, T. / Bajaj, S.P.
CitationJournal: Embo J. / Year: 1996
Title: The 2.8 A crystal structure of Gla-domainless activated protein C.
Authors: Mather, T. / Oganessyan, V. / Hof, P. / Huber, R. / Foundling, S. / Esmon, C. / Bode, W.
History
DepositionNov 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Aug 10, 2011Group: Other
Revision 1.3Oct 26, 2011Group: Other
Revision 1.4Apr 25, 2012Group: Data collection / Other
Revision 1.5Feb 27, 2013Group: Other
Revision 1.6Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details
Remark 0THIS ENTRY 3F6U REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA R1AUTSF DETERMINED ...THIS ENTRY 3F6U REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA R1AUTSF DETERMINED BY AUTHORS OF THE PDB ENTRY 1AUT: AUTHOR T.MATHER,V.OGANESSYAN,P.HOF,W.BODE,R.HUBER,S.FOUNDLING,C.ESMON
Remark 200AUTHOR USED THE SF DATA FROM ENTRY 1AUT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Vitamin K-dependent protein C heavy chain
L: Vitamin K-dependent protein C light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2855
Polymers37,7682
Non-polymers5173
Water2,648147
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-6.7 kcal/mol
Surface area17800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.060, 89.600, 101.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Vitamin K-dependent protein C ... , 2 types, 2 molecules HL

#1: Protein Vitamin K-dependent protein C heavy chain / Autoprothrombin IIA / Anticoagulant protein C / Blood coagulation factor XIV


Mass: 26965.836 Da / Num. of mol.: 1 / Fragment: UNP residues 212-451 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P04070, protein C (activated)
#2: Protein Vitamin K-dependent protein C light chain / Autoprothrombin IIA / Anticoagulant protein C / Blood coagulation factor XIV


Mass: 10802.432 Da / Num. of mol.: 1 / Fragment: UNP residues 91-188 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P04070, protein C (activated)

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Non-polymers , 4 types, 150 molecules

#3: Chemical ChemComp-0G6 / D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide / PPACK / PPACK


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 453.986 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H34ClN6O3 / Details: PPACK inhibitor / References: D-Phe-Pro-Arg-CH2Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHE INHIBITOR IS BOUND TO THE ACTIVE SITE OF THE ENZYME. THE UNBOUND FORM OF THE INHIBITOR IS D-PHE- ...THE INHIBITOR IS BOUND TO THE ACTIVE SITE OF THE ENZYME. THE UNBOUND FORM OF THE INHIBITOR IS D-PHE-PRO-ARG-CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN IT FORMS TWO COVALENT BONDS: 1) A COVALENT BOND TO SER 195 FORMING A HEMIKETAL AR7 AND 2) A COVALENT BOND TO NE2 OF HIS 57

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.43 Å3/Da / Density % sol: 64.1 % / Description: AUTHORS USED THE SF DATA FROM ENTRY 1AUT.

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.006data extraction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1AUT

1aut


Resolution: 2.8→35.25 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.873 / WRfactor Rfree: 0.232 / WRfactor Rwork: 0.163 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.873 / SU B: 10.741 / SU ML: 0.214 / SU R Cruickshank DPI: 1.093 / SU Rfree: 0.343 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.093 / ESU R Free: 0.344 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1236 10.1 %RANDOM
Rwork0.161 ---
obs0.169 12292 92.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 89.78 Å2 / Biso mean: 27.307 Å2 / Biso min: 4.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.8→35.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2639 0 32 147 2818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0212561
X-RAY DIFFRACTIONr_angle_refined_deg2.5671.9563482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5635315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.00623.796108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.99615394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.481513
X-RAY DIFFRACTIONr_chiral_restr0.1650.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021950
X-RAY DIFFRACTIONr_nbd_refined0.2730.21149
X-RAY DIFFRACTIONr_nbtor_refined0.3330.21663
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2120
X-RAY DIFFRACTIONr_metal_ion_refined0.4020.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2630.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3660.29
X-RAY DIFFRACTIONr_mcbond_it1.2051.51579
X-RAY DIFFRACTIONr_mcangle_it2.25822519
X-RAY DIFFRACTIONr_scbond_it3.25531041
X-RAY DIFFRACTIONr_scangle_it5.3214.5963
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 93 -
Rwork0.242 718 -
all-811 -
obs--84.13 %

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