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- PDB-1aut: Human activated protein C -

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Basic information

Entry
Database: PDB / ID: 1aut
TitleHuman activated protein C
Components(ACTIVATED PROTEIN C) x 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEINASE / PLASMA CALCIUM BINDING / GLYCOPROTEIN / HYDROLASE-HYDROLASE INHIBITOR complex / BLOOD CLOTTING
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 / Laminin / Coagulation Factor Xa inhibitory site / Laminin / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / 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 / Laminin / Coagulation Factor Xa inhibitory site / Laminin / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / 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
AuthorsMather, T. / Oganessyan, V. / Hof, P. / Bode, W. / Huber, R. / Foundling, S. / Esmon, C.
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
DepositionJun 8, 1996Processing site: BNL
Revision 1.0Aug 20, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Jun 20, 2012Group: Non-polymer description
Revision 1.4Feb 27, 2013Group: Other
Revision 1.5Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_src_syn / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.details / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: ACTIVATED PROTEIN C
L: ACTIVATED PROTEIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2763
Polymers40,8222
Non-polymers4541
Water2,630146
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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

#1: Protein ACTIVATED PROTEIN C / AUTOPROTHROMBIN IIA


Mass: 28091.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GLA-DOMAIN REMOVED BY CHYMOTRYPSIN / Source: (natural) Homo sapiens (human) / Organ: PLASMA / Tissue: PLASMA / References: UniProt: P04070, protein C (activated)
#2: Protein ACTIVATED PROTEIN C / AUTOPROTHROMBIN IIA


Mass: 12730.634 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GLA-DOMAIN REMOVED BY CHYMOTRYPSIN / Source: (natural) Homo sapiens (human) / Organ: PLASMA / Tissue: PLASMA / References: UniProt: P04070, protein C (activated)
#3: Chemical ChemComp-0G6 / D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide / PPACK


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 453.986 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H34ClN6O3 / Details: MAI IS DEOXO-METHYLARGININE SYNTHETIC PEPTIDE / References: D-Phe-Pro-Arg-CH2Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE UNBOUND FORM OF THE INHIBITOR IS D-PHE-PRO-ARG-CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN ...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
Sequence detailsTHE CHYMOTRYPSIN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED HERE, BASED ON THE TOPOLOGICAL ...THE CHYMOTRYPSIN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED HERE, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF CHYMOTRYPSIN (W.BODE ET AL., 1989, EMBO J.8, 3467-3475).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 61 %
Crystal growpH: 4.7 / Details: 0.1 M CITRATE, 20% ISOPROPANOL 2% PEG 20000 PH 4.7
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 %PEG100001reservoir
220 %isopropanol1reservoir
30.1 Mcitrate1reservoir

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Data collection

DiffractionMean temperature: 285 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 5, 1995
RadiationMonochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→8 Å / Num. obs: 12294 / % possible obs: 92.4 % / Observed criterion σ(I): 3 / Redundancy: 2 % / Rmerge(I) obs: 0.126
Reflection shellResolution: 2.8→2.9 Å / % possible all: 85.5
Reflection shell
*PLUS
% possible obs: 85.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
MAIN95model building
PROLSQrefinement
MAINV. 95phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FACTOR XA POLY-ALA

Resolution: 2.8→8 Å / σ(F): 2
Details: THE FOLLOWING SEGMENTS ARE DISORDERED AND ARE MODELED STEREOCHEMICALLY TO PRESERVE CHAIN CONTINUITY: C 60 - C 62, C 148 - C 151, L 70 - L 77. HIS L 107 IS IN A TIGHT TURN AND HAS TORSION ...Details: THE FOLLOWING SEGMENTS ARE DISORDERED AND ARE MODELED STEREOCHEMICALLY TO PRESERVE CHAIN CONTINUITY: C 60 - C 62, C 148 - C 151, L 70 - L 77. HIS L 107 IS IN A TIGHT TURN AND HAS TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS. THE STRAIN IS STABILIZED BY A HYDROGEN BOND TO ASN L 102. RESIDUE BHD L 71 HAS BEEN SHOWN TO BE BETA-HYDROXYLATED ALTHOUGH IT IS IN A DISORDERED SEGMENT OF THIS STRUCTURE. THE HYDROXYL GROUP IS NOT VISIBLE.
RfactorNum. reflection
Rwork0.184 -
obs-11715
Displacement parametersBiso mean: 26.7 Å2
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2635 0 30 146 2811
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d2.0720.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.5
X-RAY DIFFRACTIONp_mcangle_it2
X-RAY DIFFRACTIONp_scbond_it2
X-RAY DIFFRACTIONp_scangle_it2.5
X-RAY DIFFRACTIONp_plane_restr0.01
X-RAY DIFFRACTIONp_chiral_restr0.1
X-RAY DIFFRACTIONp_singtor_nbd0.2
X-RAY DIFFRACTIONp_multtor_nbd0.2
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2
X-RAY DIFFRACTIONp_planar_tor10
X-RAY DIFFRACTIONp_staggered_tor15
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor45
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS

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