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(-) Description

Title :  SHORT FORM HGFA WITH FIRST KUNITZ DOMAIN FROM HAI-1
 
Authors :  S. Shia, J. Stamos, D. Kirchhofer, B. Fan, J. Wu, R. T. Corpuz, L. Santell R. A. Lazarus, C. Eigenbrot
Date :  21 Dec 04  (Deposition) - 15 Feb 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,I
Keywords :  Hydrolase/Inhibitor, Hydrolase-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Shia, J. Stamos, D. Kirchhofer, B. Fan, J. Wu, R. T. Corpuz, L. Santell, R. A. Lazarus, C. Eigenbrot
Conformational Lability In Serine Protease Active Sites: Structures Of Hepatocyte Growth Factor Activator (Hgfa) Alone And With The Inhibitory Domain From Hgfa Inhibitor-1B
J. Mol. Biol. V. 346 1335 2005
PubMed-ID: 15713485  |  Reference-DOI: 10.1016/J.JMB.2004.12.048

(-) Compounds

Molecule 1 - HEPATOCYTE GROWTH FACTOR ACTIVATOR
    ChainsA
    EC Number3.4.21.-
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System PlasmidPACGP67A
    Expression System Taxid7108
    Expression System Vector TypeVIRUS
    FragmentSEQUENCE DATABASE RESIDUES 373-655
    GeneHGFAC
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHGF ACTIVATOR, HGFA
 
Molecule 2 - KUNITZ-TYPE PROTEASE INHIBITOR 1
    ChainsI
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPKD1
    Expression System Strain58F3
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentSEQUENCE DATABASE RESIDUES 245-303
    GeneSPINT1, HAI1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHEPATOCYTE GROWTH FACTOR ACTIVATOR INHIBITOR TYPE 1, HAI-1, KUNITZ DOMAIN FROM HAI-1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AI

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:451 , ARG I:265 , TYR I:280 , HOH I:327BINDING SITE FOR RESIDUE PO4 I 304

(-) SS Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1A:394 -A:521
2A:432 -A:448
3A:440 -A:510
4A:535 -A:604
5A:567 -A:583
6A:594 -A:622
7I:250 -I:300
8I:259 -I:283
9I:275 -I:296

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YC0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_024294R509HHGFA_HUMANPolymorphism16844401AR509H
2UniProtVAR_024295R644QHGFA_HUMANPolymorphism2498323AR644Q

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

(-) PROSITE Motifs  (5, 5)

Asymmetric/Biological Unit (5, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BPTI_KUNITZ_2PS50279 Pancreatic trypsin inhibitor (Kunitz) family profile.SPIT1_HUMAN250-300
391-441
  1I:250-300
-
2BPTI_KUNITZ_1PS00280 Pancreatic trypsin inhibitor (Kunitz) family signature.SPIT1_HUMAN278-296
419-437
  1I:278-296
-
3TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.HGFA_HUMAN408-646  1A:408-646
4TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.HGFA_HUMAN443-448  1A:443-448
5TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.HGFA_HUMAN592-603  1A:592-603

(-) Exons   (7, 7)

Asymmetric/Biological Unit (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003440511ENSE00001383728chr15:41136241-41136384144SPIT1_HUMAN-00--
1.2bENST000003440512bENSE00001372531chr15:41136688-41137227540SPIT1_HUMAN1-1591590--
1.3ENST000003440513ENSE00001100214chr15:41145322-41145449128SPIT1_HUMAN159-201430--
1.4ENST000003440514ENSE00001100225chr15:41145687-41145825139SPIT1_HUMAN202-248471I:238-248 (gaps)23
1.5bENST000003440515bENSE00001100217chr15:41145909-41146127219SPIT1_HUMAN248-321741I:248-30356
1.6ENST000003440516ENSE00001100211chr15:41146258-4114628427SPIT1_HUMAN321-330100--
1.7ENST000003440517ENSE00001100221chr15:41146595-41146720126SPIT1_HUMAN330-372430--
1.8ENST000003440518ENSE00001100216chr15:41146837-4114688751SPIT1_HUMAN372-389180--
1.9ENST000003440519ENSE00001100215chr15:41148090-41148260171SPIT1_HUMAN389-446580--
1.10ENST0000034405110ENSE00001100224chr15:41148474-4114852148SPIT1_HUMAN446-462170--
1.11bENST0000034405111bENSE00001865623chr15:41148968-411504051438SPIT1_HUMAN462-529680--

2.1aENST000003827741aENSE00001493344chr4:3443614-3443845232HGFA_HUMAN1-39390--
2.2ENST000003827742ENSE00000699356chr4:3444459-3444639181HGFA_HUMAN40-100610--
2.3ENST000003827743ENSE00000699357chr4:3444777-344487397HGFA_HUMAN100-132330--
2.4ENST000003827744ENSE00000699358chr4:3445068-344514780HGFA_HUMAN132-159280--
2.5ENST000003827745ENSE00000699359chr4:3445766-3445888123HGFA_HUMAN159-200420--
2.6aENST000003827746aENSE00000699360chr4:3446038-3446169132HGFA_HUMAN200-244450--
2.7ENST000003827747ENSE00001267259chr4:3446350-3446460111HGFA_HUMAN244-281380--
2.8ENST000003827748ENSE00001267254chr4:3446546-3446720175HGFA_HUMAN281-339590--
2.9aENST000003827749aENSE00000699364chr4:3446992-344707786HGFA_HUMAN339-368300--
2.10bENST0000038277410bENSE00000699365chr4:3447769-3448021253HGFA_HUMAN368-452851A:393-452 (gaps)60
2.11ENST0000038277411ENSE00000699367chr4:3449219-3449358140HGFA_HUMAN452-499481A:452-49948
2.12ENST0000038277412ENSE00000699371chr4:3449622-3449762141HGFA_HUMAN499-546481A:499-54648
2.13bENST0000038277413bENSE00000699372chr4:3449855-3450003149HGFA_HUMAN546-595501A:546-59550
2.14cENST0000038277414cENSE00001493333chr4:3450964-3451211248HGFA_HUMAN596-655601A:596-64651

(-) 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 A from PDB  Type:PROTEIN  Length:247
 aligned with HGFA_HUMAN | Q04756 from UniProtKB/Swiss-Prot  Length:655

    Alignment length:254
                                   402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642    
           HGFA_HUMAN   393 ACGRRHKKRTFLRPRIIGGSSSLPGSHPWLAAIYIGDSFCAGSLVHTCWVVSAAHCFSHSPPRDSVSVVLGQHFFNRTTDVTQTFGIEKYIPYTLYSVFNPSDHDLVLIRLKKKGDRCATRSQFVQPICLPEPGSTFPAGHKCQIAGWGHLDENVSGYSSSLREALVPLVADHKCSSPEVYGADISPNMLCAGYFDCKSDACQGDSGGPLACEKNGVAYLYGIISWGDGCGRLHKPGVYTRVANYVDWINDRIR 646
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------1yc0A01     1yc0A02 A:420-519,A:634-646 Trypsin-like serine proteases                                           1yc0A01 A:408-419,A:520-633 Trypsin-like serine proteases                                                         1yc0A02       CATH domains
               Pfam domains ---------------Trypsin-1yc0A01 A:408-641                                                                                                                                                                                                                 ----- Pfam domains
         Sec.struct. author ........-------....ee........eeeeee..eeeeeeeee..eeeehhhhhh...hhh.eeeee............eee.eeeeee..............eeeee..............................eeeeee...............eeeeee..hhhhhh....hhhhh...eeee................eeeeee..eeeeeeeeee..........eeeee...hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------H--------------------------------------------------------------------------------------------------------------------------------------Q-- SAPs(SNPs)
                PROSITE (1) ---------------TRYPSIN_DOM  PDB: A:408-646 UniProt: 408-646                                                                                                                                                                                                    PROSITE (1)
                PROSITE (2) --------------------------------------------------TRYPSI-----------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ------------------------------------------- PROSITE (2)
           Transcript 2 (1) Exon 2.10b  PDB: A:393-452 (gaps) UniProt: 368-452          ----------------------------------------------Exon 2.12  PDB: A:499-546 UniProt: 499-546      -------------------------------------------------Exon 2.14c  PDB: A:596-646 UniProt: 596-655         Transcript 2 (1)
           Transcript 2 (2) -----------------------------------------------------------Exon 2.11  PDB: A:452-499 UniProt: 452-499      ----------------------------------------------Exon 2.13b  PDB: A:546-595 UniProt: 546-595       --------------------------------------------------- Transcript 2 (2)
                 1yc0 A 393 ACGRRHKK-------IIGGSSSLPGSHPWLAAIYIGDSFCAGSLVHTCWVVSAAHCFSHSPPRDSVSVVLGQHFFNRTTDVTQTFGIEKYIPYTLYSVFNPSDHDLVLIRLKKKGDRCATRSQFVQPICLPEPGSTFPAGHKCQIAGWGHLDENVSGYSSSLREALVPLVADHKCSSPEVYGADISPNMLCAGYFDCKSDACQGDSGGPLACEKNGVAYLYGIISWGDGCGRLHKPGVYTRVANYVDWINDRIR 646
                                   | -     | 412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642    
                                 400     408                                                                                                                                                                                                                                              

Chain I from PDB  Type:PROTEIN  Length:66
 aligned with SPIT1_HUMAN | O43278 from UniProtKB/Swiss-Prot  Length:529

    Alignment length:78
                                   235       245       255       265       275       285       295        
          SPIT1_HUMAN   226 SSDHPEDTANVTVTVLSTKQTEDYCLASNKVGRCRGSFPRWYYDPTEQICKSFVYGGCLGNKNNYLREEECILACRGV 303
               SCOP domains d1yc            0i_ I: automated matches                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
               Pfam domains -----------------------Kunitz_BPTI-1yc0I01 I:249-301                        -- Pfam domains
         Sec.struct. author ..hh------------hhhhhhhhhh...........eeeeeee....eeeeeee...........hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ------------------------BPTI_KUNITZ_2  PDB: I:250-300 UniProt: 250-300     --- PROSITE (1)
                PROSITE (2) ----------------------------------------------------BPTI_KUNITZ_1      ------- PROSITE (2)
           Transcript 1 (1) Exon 1.4 [INCOMPLETE]  ------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------Exon 1.5b  PDB: I:248-303 UniProt: 248-321 [INCOMPLETE]  Transcript 1 (2)
                 1yc0 I 238 QHQH------------QMHQTEDYCLASNKVGRCRGSFPRWYYDPTEQICKSFVYGGCLGNKNNYLREEECILACRGV 303
                               |     -      |245       255       265       275       285       295        
                             241          242                                                             

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (22, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (HGFA_HUMAN | Q04756)
molecular function
    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: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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
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.

Chain I   (SPIT1_HUMAN | O43278)
molecular function
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
    GO:0004867    serine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
    GO:0060670    branching involved in labyrinthine layer morphogenesis    The process in which the branches of the fetal placental villi are generated and organized. The villous part of the placenta is called the labyrinth layer.
    GO:0071773    cellular response to BMP stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a bone morphogenetic protein (BMP) stimulus.
    GO:0001892    embryonic placenta development    The embryonically driven process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin.
    GO:0030198    extracellular matrix organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
    GO:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
    GO:2000178    negative regulation of neural precursor cell proliferation    Any process that stops, prevents, or reduces the frequency, rate or extent of neural precursor cell proliferation.
    GO:0010466    negative regulation of peptidase activity    Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
    GO:0001843    neural tube closure    The last step in the formation of the neural tube, where the paired neural folds are brought together and fuse at the dorsal midline.
    GO:0060674    placenta blood vessel development    The process whose specific outcome is the progression of a blood vessel of the placenta over time, from its formation to the mature structure.
    GO:0045687    positive regulation of glial cell differentiation    Any process that activates or increases the frequency, rate or extent of glia cell differentiation.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HGFA_HUMAN | Q047561ybw 2r0k 2r0l 2wub 2wuc 3k2u
        SPIT1_HUMAN | O432782msx 4isl 4isn 4iso 5ezd 5h7v

(-) Related Entries Specified in the PDB File

1ybw SHORT FORM HGFA ALONE