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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN KALLIKREIN 5 IN COMPLEX WITH LEUPEPTIN AND ZINC
 
Authors :  M. Debela, W. Bode, P. Goettig
Date :  07 May 07  (Deposition) - 11 Sep 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C#
Biol. Unit 1:  A,B,C#  (1x)
Biol. Unit 2:  A,B  (1x)
#:   chains that contain no standard or modified protein/DNA/RNA residue)
 
Keywords :  Zinc Inhibition, Stratum Corneum, Glcosylation, Hydrolase, Hydrolase- Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Debela, P. Goettig, V. Magdolen, R. Huber, N. M. Schechter, W. Bode
Structural Basis Of The Zinc Inhibition Of Human Tissue Kallikrein 5.
J. Mol. Biol. V. 373 1017 2007
PubMed-ID: 17881000  |  Reference-DOI: 10.1016/J.JMB.2007.08.042

(-) Compounds

Molecule 1 - KALLIKREIN-5
    ChainsA
    EC Number3.4.21.-
    EngineeredYES
    Expression System Vector TypeBACULOVIRUS
    GeneKLK5
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSTRATUM CORNEUM TRYPTIC ENZYME, KALLIKREIN-LIKE PROTEIN 2, KLK-L2
 
Molecule 2 - LEUPEPTIN
    ChainsB
    EngineeredYES
    Other DetailsCHEMICALLY SYNTHESIZED
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC#
Biological Unit 1 (1x)ABC#
Biological Unit 2 (1x)AB 
#:   chains that contain no standard or modified protein/DNA/RNA residue)
 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2AR71Mod. Amino AcidAMINO{[(4S)-4-AMINO-5,5-DIHYDROXYPENTYL]AMINO}METHANIMINIUM
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
4ZN3Ligand/IonZINC ION
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2AR71Mod. Amino AcidAMINO{[(4S)-4-AMINO-5,5-DIHYDROXYPENTYL]AMINO}METHANIMINIUM
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2AR71Mod. Amino AcidAMINO{[(4S)-4-AMINO-5,5-DIHYDROXYPENTYL]AMINO}METHANIMINIUM
3NAG-1Ligand/IonN-ACETYL-D-GLUCOSAMINE
4ZN-1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:96 , HIS A:99 , HOH A:2062 , HOH B:36 , LEU B:503BINDING SITE FOR RESIDUE ZN A 2000
2AC2SOFTWAREHIS A:25 , ASP A:117 , GLU A:240 , HOH A:2113BINDING SITE FOR RESIDUE ZN A 2001
3AC3SOFTWARESER A:95 , HIS A:96 , HIS A:150 , HOH A:2063 , HOH A:2112BINDING SITE FOR RESIDUE ZN A 2002
4AC4SOFTWARESER A:20 , LYS A:135 , ASN A:159 , SER A:246 , HOH A:2074 , HOH C:37 , HOH C:41BINDING SITE FOR CHAIN C OF POLYSACCHARIDE RESIDUES 159 TO 1001
5AC5SOFTWAREHIS A:57 , HIS A:99 , ASP A:189 , SER A:190 , CYS A:191 , GLN A:192 , SER A:195 , VAL A:213 , SER A:214 , TRP A:215 , GLY A:216 , ASP A:217 , ZN A:2000 , HOH B:12 , HOH B:48BINDING SITE FOR CHAIN B OF LEUPEPTIN

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:22 -A:157
2A:42 -A:58
3A:129 -A:232
4A:136 -A:201
5A:168 -A:182
6A:191 -A:220

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Arg A:36 -Pro A:37
2His A:96 -Pro A:97
3Ser A:146 -Pro A:147
4Tyr A:218 -Pro A:219

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_051854N153DKLK5_HUMANPolymorphism183854AD102D

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_051854N153DKLK5_HUMANPolymorphism183854AD102D

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_051854N153DKLK5_HUMANPolymorphism183854AD102D

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

(-) PROSITE Motifs  (3, 3)

Asymmetric Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.KLK5_HUMAN67-290  1A:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.KLK5_HUMAN104-109  1A:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.KLK5_HUMAN239-250  1A:189-200
Biological Unit 1 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.KLK5_HUMAN67-290  1A:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.KLK5_HUMAN104-109  1A:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.KLK5_HUMAN239-250  1A:189-200
Biological Unit 2 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.KLK5_HUMAN67-290  1A:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.KLK5_HUMAN104-109  1A:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.KLK5_HUMAN239-250  1A:189-200

(-) Exons   (4, 4)

Asymmetric Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003363341bENSE00001377703chr19:51456344-51456003342KLK5_HUMAN-00--
1.2ENST000003363342ENSE00001116578chr19:51455924-5145584184KLK5_HUMAN1-25250--
1.3ENST000003363343ENSE00001116579chr19:51453372-51453111262KLK5_HUMAN25-112881A:16-6146
1.4ENST000003363344ENSE00001188457chr19:51452371-51452115257KLK5_HUMAN112-198871A:61-149 (gaps)90
1.5ENST000003363345ENSE00001116575chr19:51452029-51451896134KLK5_HUMAN198-242451A:149-192 (gaps)46
1.6ENST000003363346ENSE00001116576chr19:51447042-51446561482KLK5_HUMAN243-293511A:193-246 (gaps)55

(-) Sequences/Alignments

Asymmetric 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:227
 aligned with KLK5_HUMAN | Q9Y337 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:227
                                    76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       
          KLK5_HUMAN     67 IINGSDCDMHTQPWQAALLLRPNQLYCGAVLVHPQWLLTAAHCRKKVFRVRLGHYSLSPVYESGQQMFQGVKSIPHPGYSHPGHSNNLMLIKLNRRIRPTKDVRPINVSSHCPSAGTKCLVSGWGTTKSPQVHFPKVLQCLNISVLSQKRCEDAYPRQIDDTMFCAGDKAGRDSCQGDSGGPVVCNGSLQGLVSWGDYPCARPNRPGVYTNLCKFTKWIQETIQANS  293
               SCOP domains d2psya_ A: automated matches                                                                                                                                                                                                        SCOP domains
               CATH domains 2psyA01     2psyA02 A:28-120,A:235-246 Trypsin-like serine proteases                                     2psyA01 A:16-27,A:121-234 Trypsin-like serine proteases                                                       2psyA02      CATH domains
               Pfam domains Trypsin-2psyA01 A:16-238                                                                                                                                                                                                   -------- Pfam domains
         Sec.struct. author ....ee........eeeee.....eeeeeeeee..eeeehhhhh....eeee.............eeeeeeeeee.............eeeee........................eeeeee...............eeeeee..hhhhhhhhh.......eeee...............eeee..eeeeeeee...........eeeee...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------D-------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 67-290                                                                                                                                                                                      --- PROSITE (1)
                PROSITE (2) -------------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.3  PDB: A:16-61 UniProt: 25-112        -------------------------------------------------------------------------------------Exon 1.5  PDB: A:149-192 (gaps)              Exon 1.6  PDB: A:193-246 (gaps) UniProt: 243-293    Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------Exon 1.4  PDB: A:61-149 (gaps) UniProt: 112-198                                        ----------------------------------------------------------------------------------------------- Transcript 1 (2)
                2psy A   16 IINGSDCDMHTQPWQAALLLRPNQLYCGAVLVHPQWLLTAAHCRKKVFRVRLGHYSLSPVYESGQQMFQGVKSIPHPGYSHPGHSNDLMLIKLNRRIRPTKDVRPINVSSHCPSAGTKCLVSGWGTTKSPQVHFPKVLQCLNISVLSQKRCEDAYPRQIDDTMFCAGDKAGRDSCQGDSGGPVVCNGSLQGLVSWGDYPCARPNRPGVYTNLCKFTKWIQETIQANS  246
                                    25        35        45        55        65 ||     75        85        95       105       115       125|      137       147       157       167       177      186A       196       210       220 |     229       239       
                                                                              67|   74A                                                125|                                           174A|       186A               204|         221A                         
                                                                               69                                                       128                                             176                           209                                      

Chain B from PDB  Type:PROTEIN  Length:4
                                     
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                2psy B  501 xLLx  504
                            |  |
                          501-ACE
                             504-AR7

   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 Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (KLK5_HUMAN | Q9Y337)
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: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:0008544    epidermis development    The process whose specific outcome is the progression of the epidermis over time, from its formation to the mature structure. The epidermis is the outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species.
    GO:0045745    positive regulation of G-protein coupled receptor protein signaling pathway    Any process that activates or increases the frequency, rate or extent of G-protein coupled receptor protein signaling pathway activity.
    GO:0002803    positive regulation of antibacterial peptide production    Any process that activates or increases the frequency, rate, or extent of antibacterial peptide production.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0097209    epidermal lamellar body    A specialized secretory organelle found in keratinocytes and involved in the formation of an impermeable, lipid-containing membrane that serves as a water barrier and is required for correct skin barrier function.
    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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        KLK5_HUMAN | Q9Y3372psx

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