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(-) Description

Title :  STRUCTURE OF MATURE HUMAN TISSUE KALLIKREIN (HUMAN KALLIKREIN 1 OR KLK1) AT 1.70 ANGSTROM RESOLUTION WITH VACANT ACTIVE SITE
 
Authors :  G. Laxmikanthan, S. I. Blaber, M. J. Bernett, M. Blaber
Date :  16 Mar 04  (Deposition) - 25 Jan 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Serine Protease, Klk1, Hk1, Human Kallikrein 1, Human Tissue Kallikrein 1, Tissue Kallikrein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Laxmikanthan, S. I. Blaber, M. J. Bernett, I. A. Scarisbrick, M. A. Juliano, M. Blaber
1. 70 A X-Ray Structure Of Human Apo Kallikrein 1: Structura Changes Upon Peptide Inhibitor/Substrate Binding
Proteins V. 58 802 2005
PubMed-ID: 15651049  |  Reference-DOI: 10.1002/PROT.20368

(-) Compounds

Molecule 1 - KALLIKREIN 1
    ChainsA
    EC Number3.4.21.35
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System PlasmidPBAC3
    Expression System StrainSF9
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    GeneKLK1
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTISSUE KALLIKREIN, KIDNEY/PANCREAS/SALIVARY GLAND KALLIKREIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2CA2Ligand/IonCALCIUM ION
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:95BINDING SITE FOR RESIDUE NAG A 401
2AC2SOFTWARELYS A:169 , HIS A:172 , HOH A:619 , HOH A:937BINDING SITE FOR RESIDUE CA A 300
3AC3SOFTWAREASN A:245 , HOH A:684 , HOH A:767 , HOH A:776 , HOH A:882 , HOH A:912BINDING SITE FOR RESIDUE CA A 301
4AC4SOFTWARETRP A:20 , CYS A:22 , GLU A:23 , SER A:26 , GLN A:27 , HOH A:950BINDING SITE FOR RESIDUE ACY A 501

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:157
2A:42 -A:58
3A:136 -A:201
4A:168 -A:182
5A:191 -A:220

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val A:218 -Pro A:219

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Asymmetric/Biological Unit (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_014567R77HKLK1_HUMANPolymorphism5515AR70H
2UniProtVAR_006625E145QKLK1_HUMANPolymorphism5516AE128Q
3UniProtVAR_006626K186EKLK1_HUMANPolymorphism5517AK169E
4UniProtVAR_014568V193EKLK1_HUMANPolymorphism5518AV176E

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.KLK1_HUMAN25-259  1A:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.KLK1_HUMAN61-66  1A:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.KLK1_HUMAN208-219  1A:189-200

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003014201ENSE00001116553chr19:51327043-5132695985KLK1_HUMAN1-16160--
1.2ENST000003014202ENSE00001116552chr19:51325127-51324968160KLK1_HUMAN16-69541A:16-61 (gaps)46
1.3bENST000003014203bENSE00001116550chr19:51323699-51323410290KLK1_HUMAN69-166981A:61-149 (gaps)101
1.4ENST000003014204ENSE00001116551chr19:51323291-51323155137KLK1_HUMAN166-211461A:149-19246
1.5ENST000003014205ENSE00001116549chr19:51322605-51322404202KLK1_HUMAN212-262511A:193-246 (gaps)55

(-) 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:236
 aligned with KLK1_HUMAN | P06870 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:238
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254        
          KLK1_HUMAN     25 IVGGWECEQHSQPWQAALYHFSTFQCGGILVHRQWVLTAAHCISDNYQLWLGRHNLFDDENTAQFVHVSESFPHPGFNMSLLENHTRQADEDYSHDLMLLRLTEPADTITDAVKVVELPTEEPEVGSTCLASGWGSIEPENFSFPDDLQCVDLKILPNDECKKAHVQKVTDFMLCVGHLEGGKDTCVGDSGGPLMCDGVLQGVTSWGYVPCGTPNKPSVAVRVLSYVKWIEDTIAENS  262
               SCOP domains d1spja_ A: automated matches                                                                                                                                                                                                                   SCOP domains
               CATH domains 1spjA01     1spjA02 A:28-120,A:233-245 Trypsin-like serine proteases                                               1spjA01 A:16-27,A:121-232 Trypsin-like serine proteases                                                      1spjA02      - CATH domains
               Pfam domains Trypsin-1spjA01 A:16-238                                                                                                                                                                                                              -------- Pfam domains
         Sec.struct. author ....ee........eeeeee..eeeeeeeeee..eeeehhhhh...eeeee............eee.eeeeee....hhhhhh.--...........eeeee.........................eeeeee...............eeeeeeeehhhhhhhhh.......eeeee...............eeee..eeeeeeee...........eeeee...hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------H-------------------------------------------------------------------Q----------------------------------------E------E--------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 25-259                                                                                                                                                                                                 --- PROSITE (1)
                PROSITE (2) ------------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: A:16-61 (gaps) UniProt: 16-69 ------------------------------------------------------------------------------------------------Exon 1.4  PDB: A:149-192 UniProt: 166-211     Exon 1.5  PDB: A:193-246 (gaps) UniProt: 212-262    Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.3b  PDB: A:61-149 (gaps) UniProt: 69-166                                                   ------------------------------------------------------------------------------------------------ Transcript 1 (2)
                1spj A   16 IVGGWECEQHSQPWQAALYHFSTFQCGGILVHRQWVLTAAHCISDNYQLWLGRHNLFDDENTAQFVHVSESFPHPGFNMSLLEN--RQADEDYSHDLMLLRLTEPADTITDAVKVVELPTEEPEVGSTCLASGWGSIEPENFSFPDDLQCVDLKILPNDECKKAHVQKVTDFMLCVGHLEGGKDTCVGDSGGPLMCDGVLQGVTSWGYVPCGTPNKPSVAVRVLSYVKWIEDTIAENS  246
                                    25        35||      46        56    ||  67        77        87       95B||||  ||96       106       115       125|      137       147       157       167       177      186A|      195      |209       219 |     228       238        
                                               36|                     61|                              95A|||||  |||                114A        125|                                                       186A|             202|          220A                          
                                                38                      63                               95B||||  |||                             128                                                        186B              207                                        
                                                                                                          95C|||  |||                                                                                                                                                     
                                                                                                           95D||  |||                                                                                                                                                     
                                                                                                            95E|  |||                                                                                                                                                     
                                                                                                             95F  |||                                                                                                                                                     
                                                                                                                95I||                                                                                                                                                     
                                                                                                                 95J|                                                                                                                                                     
                                                                                                                  95K                                                                                                                                                     

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  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  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (KLK1_HUMAN | P06870)
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: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:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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