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(-) Description

Title :  PORCINE FACTOR IXA
 
Authors :  H. Brandstetter, M. Bauer, R. Huber, P. Lollar, W. Bode
Date :  19 Jul 95  (Deposition) - 17 Aug 96  (Release) - 20 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  C,L
Keywords :  Hemophilia/Egf, Blood Coagulation, Plasma, Serine Protease, Calcium- Binding, Hydrolase, Glycoprotein, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Brandstetter, M. Bauer, R. Huber, P. Lollar, W. Bode
X-Ray Structure Of Clotting Factor Ixa: Active Site And Module Structure Related To Xase Activity And Hemophilia B.
Proc. Natl. Acad. Sci. Usa V. 92 9796 1995
PubMed-ID: 7568220  |  Reference-DOI: 10.1073/PNAS.92.21.9796

(-) Compounds

Molecule 1 - FACTOR IXA
    ChainsC
    EC Number3.4.21.22
    EngineeredYES
    GenePETE
    OrganBLOOD
    Organism CommonPIG
    Organism ScientificSUS SCROFA
    Organism Taxid9823
    SynonymCHRISTMAS FACTOR
 
Molecule 2 - FACTOR IXA
    ChainsL
    EC Number3.4.21.22
    EngineeredYES
    GenePETE
    OrganBLOOD
    Organism CommonPIG
    Organism ScientificSUS SCROFA
    Organism Taxid9823
    SynonymCHRISTMAS FACTOR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit CL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric/Biological Unit (3, 14)
No.NameCountTypeFull Name
10G61Ligand/IonD-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO)METHYL]AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L-PROLINAMIDE
2BHD1Mod. Amino Acid(3S)-3-HYDROXY-L-ASPARTIC ACID
3CGU12Mod. Amino AcidGAMMA-CARBOXY-GLUTAMIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS C:57 , TYR C:99 , PHE C:174 , ASP C:189 , SER C:190 , CYS C:191 , GLN C:192 , GLY C:193 , SER C:195 , SER C:214 , TRP C:215 , GLY C:216 , GLU C:219 , ILE L:66BINDING SITE FOR RESIDUE 0G6 C 301

(-) SS Bonds  (11, 11)

Asymmetric/Biological Unit
No.Residues
1C:42 -C:58
2C:122 -L:132
3C:168 -C:182
4C:191 -C:220
5L:18 -L:23
6L:51 -L:62
7L:56 -L:71
8L:73 -L:82
9L:88 -L:99
10L:95 -L:109
11L:111 -L:124

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PFX)

(-) PROSITE Motifs  (10, 10)

Asymmetric/Biological Unit (10, 10)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLA_2PS50998 Gla domain profile.FA9_PIG2-48  1L:2-47
2GLA_1PS00011 Vitamin K-dependent carboxylation domain.FA9_PIG18-43  1L:17-42
3EGF_3PS50026 EGF-like domain profile.FA9_PIG48-84  1L:47-83
4EGF_CAPS01187 Calcium-binding EGF-like domain signature.FA9_PIG48-72  1L:47-71
5ASX_HYDROXYLPS00010 Aspartic acid and asparagine hydroxylation site.FA9_PIG63-74  1L:62-73
6EGF_1PS00022 EGF-like domain signature 1.FA9_PIG72-83  1L:71-82
7EGF_2PS01186 EGF-like domain signature 2.FA9_PIG72-83
110-125
  2L:71-82
L:109-124
8TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.FA9_PIG183-409  1C:16-237
9TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.FA9_PIG219-224  1C:53-58
10TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.FA9_PIG361-372  1C:189-200

(-) Exons   (0, 0)

(no "Exon" information available for 1PFX)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   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 C from PDB  Type:PROTEIN  Length:235
 aligned with FA9_PIG | P16293 from UniProtKB/Swiss-Prot  Length:409

    Alignment length:235
                                                                                                                                                                                                                                                            409        
                                   192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402      |  -     
             FA9_PIG    183 IVGGENAKPGQFPWQVLLNGKIDAFCGGSIINEKWVVTAAHCIEPGVKITVVAGEYNTEETEPTEQRRNVIRAIPHHSYNATVNKYSHDIALLELDEPLTLNSYVTPICIADKEYTNIFLKFGSGYVSGWGRVFNRGRSATILQYLKVPLVDRATCLRSTKVTIYSNMFCAGFHEGGKDSCLGDSGGPHVTEVEGTSFLTGIISWGEECAVKGKYGIYTKVSRYVNW--------    -
               SCOP domains d1pfxc_ C: Coagulation factor IXa, protease domain                                                                                                                                                                                          SCOP domains
               CATH domains 1pfxC01     1pfxC02 C:28-120,C:233-245 Trypsin-like serine proteases                                       1pfxC01 C:16-27,C:121-232 Trypsin-like serine proteases                                                            1pfxC02       CATH domains
               Pfam domains Trypsin-1pfxC01 C:16-237                                                                                                                                                                                                           -------- Pfam domains
         Sec.struct. author ....ee........eeeee......eeeeeee..eeeehhhhh......eeee............eeeeeeeeee...............eeeee................hhhhhhhhhh..eeeeee..............eeeeeeeehhhhhhhhh.......eeee.................eeeee..eeee..eeee..........eeeehhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: C:16-237 UniProt: 183-409                                                                                                                                                                                        -------- PROSITE (1)
                PROSITE (2) ------------------------------------TRYPSI----------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER --------------------------------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1pfx C   16 IVGGENAKPGQFPWQVLLNGKIDAFCGGSIINEKWVVTAAHCIEPGVKITVVAGEYNTEETEPTEQRRNVIRAIPHHSYNATVNKYSHDIALLELDEPLTLNSYVTPICIADKEYTNIFLKFGSGYVSGWGRVFNRGRSATILQYLKVPLVDRATCLRSTKFTIYSNMFCAGFHEGGKDSCQGDSGGPHVTEVEGTSFLTGIISWGEECAVKGKYGIYTKVSRYVNWIKEKTKLT  245
                                    25        35||      46        56    |   65        75        85        95||     103       113       123      |131       141   ||  152       162       172       182  |    190       200       210      |221|      230       240     
                                               36|                    60A                                 95A|                               129A|             145|                                  184A 188A                          217|  |                        
                                                38                                                         95B                                129B              147                                                                      219  |                        
                                                                                                                                                                                                                                           221A                        

Chain L from PDB  Type:PROTEIN  Length:146
 aligned with FA9_PIG | P16293 from UniProtKB/Swiss-Prot  Length:409

    Alignment length:147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       
             FA9_PIG      1 YNSGKLEESFVRGNLERECIEEKCSFEEAREVFENTEKTNEFWKQYVDGDQCEPNPCLNGGLCKDDINSYECWCQVGFEGKNCELDATCNIKNGRCKQFCKTGADSKVLCSCTTGYRLAPDQKSCKPAVPFPCGRVSVSHSPTTLTR  147
               SCOP domains d1pfxl3  L:1-46 Coagulation factor IX (IXa)    d1pfxl1 L:47-86 Factor IX (IXa)         d1pfxl2 L:87-146 Factor IX (IXa)                             SCOP domains
               CATH domains 1pfxL01  L:1-46 Coagulation Factor IX          1pfxL02 L:47-86 Laminin                 1pfxL03 L:87-127 Laminin                 ------------------- CATH domains
               Pfam domains ---------Gla-1pfxL02 L:9-47                     ---EGF-1pfxL01 L:51-81            ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ........-....hhhhhh.....hhhhhhhhhh.hhhhhhhhhh................eeee....eeee....ee.....ee....hhhhhh..ee.........ee....eee......eee........hhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -GLA_2  PDB: L:2-47 UniProt: 2-48               --------------ASX_HYDROXYL-----------------------------------EGF_2           ---------------------- PROSITE (1)
                PROSITE (2) -----------------GLA_1  PDB: L:17-42       ----EGF_3  PDB: L:47-83 UniProt: 48-84   --------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -----------------------------------------------EGF_CA  PDB: L:47-71     GF_2       ---------------------------------------------------------------- PROSITE (3)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1pfx L    1 YNSGKLee-FVRGNLeReCIeeKCSFeeAReVFeNTeKTNeFWKQYVDGDQCEPNPCLNGGLCKdDINSYECWCQVGFEGKNCELDATCNIKNGRCKQFCKTGADSKVLCSCTTGYRLAPDQKSCKPAVPFPCGRVSVSHSPTTLTR  146
                                  || 9     | |19||    ||29|  |  | 39|       49        59    |   69        79        89        99       109       119       129       139       
                                  7-CGU    | |  ||    ||  |  |  |   |                      64-BHD                                                                              
                                   8-CGU  15-CGU||    ||  |  |  |   |                                                                                                          
                                            17-CGU    ||  |  |  |   |                                                                                                          
                                               20-CGU ||  |  |  |   |                                                                                                          
                                                21-CGU||  |  |  |   |                                                                                                          
                                                     26-CGU  |  |   |                                                                                                          
                                                      27-CGU |  |   |                                                                                                          
                                                         30-CGU |   |                                                                                                          
                                                            33-CGU  |                                                                                                          

   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  (3, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (3, 5)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: EGF (60)
(-)
Family: EGF (31)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain C,L   (FA9_PIG | P16293)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0004175    endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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: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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0031638    zymogen activation    The proteolytic processing of an inactive enzyme to an active form.
cellular component
    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)

UniProtKB/Swiss-Prot
        FA9_PIG | P162931x7a

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1PFX)