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(-) Description

Title :  MODELS OF THE SERINE PROTEASE DOMAIN OF THE HUMAN ANTITHROMBOTIC PLASMA FACTOR ACTIVATED PROTEIN C AND ITS ZYMOGEN
 
Authors :  C. L. Fisher, J. S. Greengard, J. H. Griffin
Date :  13 Jun 94  (Deposition) - 31 Jul 94  (Release) - 31 Jul 94  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,_#
#:   chains that contain no standard or modified protein/DNA/RNA residue)
 
Keywords :  Serine Proteinase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. L. Fisher, J. S. Greengard, J. H. Griffin
Models Of The Serine Protease Domain Of The Human Antithrombotic Plasma Factor Activated Protein C And Its Zymogen.
Protein Sci. V. 3 588 1994
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN C
    ChainsA
    EC Number3.4.21.69
    EngineeredYES

 Structural Features

(-) Chains, Units

  
Theoretical Model 
#:   chains that contain no standard or modified protein/DNA/RNA residue)
 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Theoretical Model (3, 3)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2CA1Ligand/IonCALCIUM ION
3NH21Mod. Amino AcidAMINO GROUP

(-) Sites  (1, 1)

Theoretical Model (1, 1)
No.NameEvidenceResiduesDescription
1CATnot definedHIS A:211 , ASP A:257 , SER A:360

(-) SS Bonds  (4, 4)

Theoretical Model
No.Residues
1A:141 -A:277
2A:196 -A:212
3A:331 -A:345
4A:356 -A:384

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PCT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (58, 58)

Theoretical Model (58, 58)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_074299C175YPROC_HUMANPolymorphism199469474AC133Y
02UniProtVAR_006660A178PPROC_HUMANDisease (THPH4)  ---AA136P
03UniProtVAR_074300F181VPROC_HUMANPolymorphism199469470AF139V
04UniProtVAR_006661C183RPROC_HUMANPolymorphism748920874AC141R
05UniProtVAR_006662R189WPROC_HUMANPolymorphism146922325AR147W
06UniProtVAR_006663R194CPROC_HUMANPolymorphism371071104AR152C
07UniProtVAR_006664P210LPROC_HUMANDisease (THPH3)121918145AP168L
08UniProtVAR_006666R211QPROC_HUMANPolymorphism28933987AR169Q
09UniProtVAR_006665R211WPROC_HUMANDisease (THPH3)28933986AR169W
10UniProtVAR_006667R220PPROC_HUMANUnclassified  ---AR178P
11UniProtVAR_006669R220QPROC_HUMANDisease (THPH3)121918153AR178Q
12UniProtVAR_006668R220WPROC_HUMANDisease (THPH3)121918152AR178W
13UniProtVAR_074301S223RPROC_HUMANPolymorphism199469483AS181R
14UniProtVAR_006670Q226HPROC_HUMANPolymorphism121918155AQ184H
15UniProtVAR_074302A240GPROC_HUMANUnclassified  ---AA198G
16UniProtVAR_006671I243TPROC_HUMANDisease (THPH3)774584131AI201T
17UniProtVAR_006672H244YPROC_HUMANPolymorphism759557871AH202Y
18UniProtVAR_006673H253QPROC_HUMANUnclassified  ---AH211Q
19UniProtVAR_006674L265FPROC_HUMANPolymorphism121918156AL223F
20UniProtVAR_006675R271QPROC_HUMANUnclassified  ---AR229Q
21UniProtVAR_006676R271WPROC_HUMANPolymorphism767112991AR229W
22UniProtVAR_006677R272CPROC_HUMANDisease (THPH3)121918154AR230C
23UniProtVAR_006679P289LPROC_HUMANDisease (THPH4)121918151AP247L
24UniProtVAR_006680S294NPROC_HUMANPolymorphism200721675AS252N
25UniProtVAR_074303D297HPROC_HUMANDisease (THPH3)199469471AD255H
26UniProtVAR_006681N298DPROC_HUMANUnclassified  ---AN256D
27UniProtVAR_006682A301TPROC_HUMANUnclassified  ---AA259T
28UniProtVAR_006683A301VPROC_HUMANPolymorphism121918144AA259V
29UniProtVAR_006684A309TPROC_HUMANPolymorphism121918146AA267T
30UniProtVAR_006685S312LPROC_HUMANPolymorphism121918160AS270L
31UniProtVAR_006686S312PPROC_HUMANUnclassified  ---AS270P
32UniProtVAR_074304P317SPROC_HUMANUnclassified  ---AP275S
33UniProtVAR_006687P321LPROC_HUMANDisease (THPH3)  ---AP279L
34UniProtVAR_006688G324RPROC_HUMANDisease (THPH3)  ---AG282R
35UniProtVAR_074305E327VPROC_HUMANPolymorphism199469480AE285V
36UniProtVAR_006689R328CPROC_HUMANDisease (THPH3)201907715AR286C
37UniProtVAR_006690R328HPROC_HUMANDisease (THPH4)  ---AR286H
38UniProtVAR_006691G334SPROC_HUMANDisease (THPH4)121918150AG292S
39UniProtVAR_006692T340MPROC_HUMANDisease (THPH3)766261022AT298M
40UniProtVAR_006693G343DPROC_HUMANUnclassified  ---AG301D
41UniProtVAR_074306T357APROC_HUMANUnclassified  ---AT315A
42UniProtVAR_006695V367APROC_HUMANDisease (THPH4)767730328AV325A
43UniProtVAR_006696P369LPROC_HUMANDisease (THPH3)  ---AP327L
44UniProtVAR_006697M385IPROC_HUMANUnclassified  ---AM343I
45UniProtVAR_006698A388TPROC_HUMANUnclassified  ---AA346T
46UniProtVAR_006699A388VPROC_HUMANUnclassified  ---AA346V
47UniProtVAR_006700G392RPROC_HUMANDisease (THPH3)756467027AG350R
48UniProtVAR_006701R394WPROC_HUMANPolymorphism759316085AR352W
49UniProtVAR_006702D401NPROC_HUMANDisease (THPH3)142742242AD359N
50UniProtVAR_006703G418DPROC_HUMANDisease (THPH4)  ---AG376D
51UniProtVAR_074307V420LPROC_HUMANDisease (THPH3)199469472AV378L
52UniProtVAR_006704G423SPROC_HUMANDisease (THPH3)  ---AG381S
53UniProtVAR_006705C426YPROC_HUMANDisease (THPH3)  ---AC384Y
54UniProtVAR_006706G433SPROC_HUMANUnclassified  ---AG391S
55UniProtVAR_006707T436NPROC_HUMANDisease (THPH3)  ---AT394N
56UniProtVAR_006708Y441HPROC_HUMANDisease (THPH3)753436021AY399H
57UniProtVAR_006709W444CPROC_HUMANDisease (THPH3)121918142AW402C
58UniProtVAR_006710I445MPROC_HUMANPolymorphism121918157AI403M

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (3, 3)

Theoretical Model (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.PROC_HUMAN212-450  1A:170-408
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.PROC_HUMAN249-254  1A:207-212
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.PROC_HUMAN396-407  1A:354-365

(-) Exons   (4, 4)

Theoretical Model (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002340711aENSE00001747079chr2:128176003-12817606866PROC_HUMAN-00--
1.2eENST000002340712eENSE00000857263chr2:128177498-12817758891PROC_HUMAN1-24240--
1.3aENST000002340713aENSE00001019166chr2:128178859-128179025167PROC_HUMAN24-79560--
1.4aENST000002340714aENSE00001657237chr2:128180493-12818051725PROC_HUMAN80-8890--
1.4hENST000002340714hENSE00000775732chr2:128180610-128180747138PROC_HUMAN88-134470--
1.4kENST000002340714kENSE00001019181chr2:128180850-128180984135PROC_HUMAN134-179461A:132-1376
1.5bENST000002340715bENSE00000775730chr2:128183661-128183803143PROC_HUMAN179-226481A:137-18448
1.6ENST000002340716ENSE00000775729chr2:128184681-128184798118PROC_HUMAN227-266401A:185-22440
1.7dENST000002340717dENSE00001853552chr2:128185933-128186822890PROC_HUMAN266-4611961A:224-409186

(-) Sequences/Alignments

Theoretical Model
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:278
 aligned with PROC_HUMAN | P04070 from UniProtKB/Swiss-Prot  Length:461

    Alignment length:278
                                   183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443        
           PROC_HUMAN   174 QCHPAVKFPCGRPWKRMEKKRSHLKRDTEDQEDQVDPRLIDGKMTRRGDSPWQVVLLDSKKKLACGAVLIHPSWVLTAAHCMDESKKLLVRLGEYDLRRWEKWELDLDIKEVFVHPNYSKSTTDNDIALLHLAQPATLSQTIVPICLPDSGLAERELNQAGQETLVTGWGYHSSREKEAKRNRTFVLNFIKIPVVPHNECSEVMSNMVSENMLCAGILGDRQDACEGDSGGPMVASFHGTWFLVGLVSWGEGCGLLHNYGVYTKVSRYLDWIHGHIRD 451
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ............................hhhhh..................eeeeeee...eeeeeeeeee..eeee...........eeee............eeeeeeeeeee...........eeeeee.................hhhhhh......eeeeeee....hhhh...........eeeeeeee.hhhhhhhh......eeeee...............eeeeeee..eeeeeeeeee..........----hhhhhhhhhhhhhh. Sec.struct. author (1)
     Sec.struct. author (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------eeeeee------------- Sec.struct. author (2)
             SAPs(SNPs) (1) -Y--P--V-R-----W----C---------------LQ--------P--R--H-------------G--TY--------Q-----------F-----QC----------------L----N--HD--T-------T--L----S---L--R--VC-----S-----M--D-------------A---------A-L---------------I--T---R-W------N----------------D-L--S--Y------S--N----H--CM------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------W--------Q--------------------------------------------------W-----------------------------V----------P---------------H-----------------------------------------------------------V--------------------------------------------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ----------------------------------------------W--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (3)
                PROSITE (1) --------------------------------------TRYPSIN_DOM  PDB: A:170-408 UniProt: 212-450                                                                                                                                                                                                   - PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.4k  -----------------------------------------------Exon 1.6  PDB: A:185-224                ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----Exon 1.5b  PDB: A:137-184 UniProt: 179-226      ---------------------------------------Exon 1.7d  PDB: A:224-409 UniProt: 266-461 [INCOMPLETE]                                                                                                                                    Transcript 1 (2)
                 2pct A 132 xCHPAVKFPCGRPWKRMEKKRSHLKRDTEDQEDQVDPRLIDGKMTRRGDSPWQVVLLDSKKKLACGAVLIHPSWVLTAAHCMDESKKLLVRLGEYDLRRWEKWELDLDIKEVFVHPNYSKSTTDNDIALLHLAQPATLSQTIVPICLPDSGLAERELNQAGQETLVTGWGYHSSREKEAKRNRTFVLNFIKIPVVPHNECSEVMSNMVSENMLCAGILGDRQDACEGDSGGPMVASFHGTWFLVGLVSWGEGCGLLHNYGVYTKVSRYLDWIHGHIRx 409
                            |      141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       |
                            |                                                                                                                                                                                                                                                                                  409-NH2
                          132-ACE                                                                                                                                                                                                                                                                                 

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2PCT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2PCT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2PCT)

(-) Gene Ontology  (24, 24)

Theoretical Model(hide GO term definitions)
Chain A   (PROC_HUMAN | P04070)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0006888    ER to Golgi vesicle-mediated transport    The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
    GO:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    GO:0007599    hemostasis    The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
    GO:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0030195    negative regulation of blood coagulation    Any process that stops, prevents, or reduces the frequency, rate or extent of blood coagulation.
    GO:0050819    negative regulation of coagulation    Any process that stops, prevents, or reduces the frequency, rate or extent of coagulation.
    GO:0050728    negative regulation of inflammatory response    Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response.
    GO:0017187    peptidyl-glutamic acid carboxylation    The gamma-carboxylation of peptidyl-glutamic acid; catalyzed by the vitamin K dependent gamma-glutamyl carboxylase.
    GO:1903142    positive regulation of establishment of endothelial barrier    Any process that activates or increases the frequency, rate or extent of establishment of endothelial barrier.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0006465    signal peptide processing    The proteolytic removal of a signal peptide from a protein during or after transport to a specific location in the cell.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005796    Golgi lumen    The volume enclosed by the membranes of any cisterna or subcompartment of the Golgi apparatus, including the cis- and trans-Golgi networks.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        PROC_HUMAN | P040701aut 1lqv 1pcu 3f6u 3jtc 4dt7

(-) Related Entries Specified in the PDB File

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