Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN KALLIKREIN 7 IN COMPLEX WITH ALA-ALA-PHE-CHLOROMETHYLKETONE
 
Authors :  M. Debela, P. Hess, V. Magdolen, W. Bode, T. Steiner, P. Goettig
Date :  11 Aug 07  (Deposition) - 08 Jan 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Dimer, 37 Loop, Active Site Inhibitor, Chloromethyl Ketone, Alternative Splicing, Glycoprotein, Hydrolase, Protease, Secreted, Serine Protease, Zymogen (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Debela, P. Hess, V. Magdolen, N. M. Schechter, T. Steiner, R. Huber, W. Bode, P. Goettig
Chymotryptic Specificity Determinants In The 1. 0 A Structure Of The Zinc-Inhibited Human Tissue Kallikrein 7.
Proc. Natl. Acad. Sci. Usa V. 104 16086 2007
PubMed-ID: 17909180  |  Reference-DOI: 10.1073/PNAS.0707811104
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - KALLIKREIN-7
    ChainsA, B
    EC Number3.4.21.117
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainM15[PREP4]
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneKLK7, PRSS6, SCCE
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHK7, STRATUM CORNEUM CHYMOTRYPTIC ENZYME, HSCCE, SERINE PROTEASE 6

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1K7I2Ligand/IonL-ALANYL-N-[(1S,2R)-1-BENZYL-2-HYDROXYPROPYL]-L-ALANINAMIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1K7I1Ligand/IonL-ALANYL-N-[(1S,2R)-1-BENZYL-2-HYDROXYPROPYL]-L-ALANINAMIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1K7I1Ligand/IonL-ALANYL-N-[(1S,2R)-1-BENZYL-2-HYDROXYPROPYL]-L-ALANINAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:57 , HIS A:99 , CYS A:191 , ASN A:192 , GLY A:193 , SER A:195 , SER A:214 , TRP A:215 , GLY A:216 , CYS A:220 , HOH A:305 , HOH A:349BINDING SITE FOR RESIDUE K7I A 300
2AC2SOFTWAREHIS B:57 , HIS B:99 , CYS B:191 , ASN B:192 , GLY B:193 , SER B:195 , SER B:214 , TRP B:215 , GLY B:216 , CYS B:220 , HOH B:306 , HOH B:405BINDING SITE FOR RESIDUE K7I B 301

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:22 -A:157
2A:42 -A:58
3A:128 -A:232
4A:136 -A:201
5A:168 -A:182
6A:191 -A:220
7B:22 -B:157
8B:42 -B:58
9B:128 -B:232
10B:136 -B:201
11B:168 -B:182
12B:191 -B:220

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ser A:146 -Pro A:147
2Phe A:218 -Pro A:219
3Ser B:146 -Pro B:147
4Phe B:218 -Pro B:219

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QXG)

(-) PROSITE Motifs  (3, 6)

Asymmetric Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.KLK7_HUMAN30-250
 
  2A:16-243
B:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.KLK7_HUMAN66-71
 
  2A:53-58
B:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.KLK7_HUMAN199-210
 
  2A:189-200
B:189-200
Biological Unit 1 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.KLK7_HUMAN30-250
 
  1A:16-243
-
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.KLK7_HUMAN66-71
 
  1A:53-58
-
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.KLK7_HUMAN199-210
 
  1A:189-200
-
Biological Unit 2 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.KLK7_HUMAN30-250
 
  1-
B:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.KLK7_HUMAN66-71
 
  1-
B:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.KLK7_HUMAN199-210
 
  1-
B:189-200

(-) Exons   (4, 8)

Asymmetric Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2ENST000003918072ENSE00001509794chr19:51487071-5148702844KLK7_HUMAN-00--
1.3ENST000003918073ENSE00001261969chr19:51485713-51485583131KLK7_HUMAN1-25250--
1.4ENST000003918074ENSE00001123413chr19:51485170-51485023148KLK7_HUMAN25-74502A:16-61 (gaps)
B:16-61 (gaps)
46
46
1.5ENST000003918075ENSE00001621367chr19:51483743-51483496248KLK7_HUMAN74-157842A:61-149 (gaps)
B:61-149 (gaps)
89
89
1.6ENST000003918076ENSE00001683144chr19:51483180-51483044137KLK7_HUMAN157-202462A:149-192
B:149-192
46
46
1.7bENST000003918077bENSE00001261960chr19:51480947-514797291219KLK7_HUMAN203-253512A:193-246 (gaps)
B:193-246 (gaps)
55
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:224
 aligned with KLK7_HUMAN | P49862 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:224
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249    
          KLK7_HUMAN     30 IIDGAPCARGSHPWQVALLSGNQLHCGGVLVNERWVLTAAHCKMNEYTVHLGSDTLGDRRAQRIKASKSFRHPGYSTQTHVNDLMLVKLNSQARLSSMVKKVRLPSRCEPPGTTCTVSGWGTTTSPDVTFPSDLMCVDVKLISPQDCTKVYKDLLENSMLCAGIPDSKKNACNGDSGGPLVCRGTLQGLVSWGTFPCGQPNDPGVYTQVCKFTKWINDTMKKHR  253
               SCOP domains d2qxga_ A: automated matches                                                                                                                                                                                                     SCOP domains
               CATH domains 2qxgA01     2qxgA02 A:28-120,A:235-246 Trypsin-like serine proteases                                 2qxgA01 A:16-27,A:121-234 Trypsin-like serine proteases                                                        2qxgA02      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee..eeeeeeeeee..eeeehhhhh...eeeee..........eeeeeeeeee.............eeeee........................eeeeee...............eeeeeeeehhhhhhhhhhhhh...eeeee...............eeee..eeeeeeee...........eeeee...hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 30-250                                                                                                                                                                                   --- PROSITE (1)
                PROSITE (2) ------------------------------------TRYPSI-------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.4  PDB: A:16-61 (gaps) UniProt: 25-74 ----------------------------------------------------------------------------------Exon 1.6  PDB: A:149-192 UniProt: 157-202     Exon 1.7b  PDB: A:193-246 (gaps) UniProt: 203-253   Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.5  PDB: A:61-149 (gaps) UniProt: 74-157                                      ------------------------------------------------------------------------------------------------ Transcript 1 (2)
                2qxg A   16 IIDGAPCARGSHPWQVALLSGNQLHCGGVLVNERWVLTAAHCKMNEYTVHLGSDTLGDRRAQRIKASKSFRHPGYSTQTHVNDLMLVKLNSQARLSSMVKKVRLPSRCEPPGTTCTVSGWGTTTSPDVTFPSDLMCVDVKLISPQDCTKVYKDLLENSMLCAGIPDSKKNACNGDSGGPLVCRGTLQGLVSWGTFPCGQPNDPGVYTQVCKFTKWINDTMKKHR  246
                                    25        35||      46        56        66||      77|       89        99       109       119     ||130|      141       151       161       171       181     ||189       199   ||  213       222       232       242    
                                               36|                           67|      77|                                          125|  ||                                                   186A|              203|         220A                          
                                                38                            69       80                                           127  ||                                                    186B               208                                       
                                                                                                                                       130|                                                                                                                 
                                                                                                                                        132                                                                                                                 

Chain B from PDB  Type:PROTEIN  Length:224
 aligned with KLK7_HUMAN | P49862 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:224
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249    
          KLK7_HUMAN     30 IIDGAPCARGSHPWQVALLSGNQLHCGGVLVNERWVLTAAHCKMNEYTVHLGSDTLGDRRAQRIKASKSFRHPGYSTQTHVNDLMLVKLNSQARLSSMVKKVRLPSRCEPPGTTCTVSGWGTTTSPDVTFPSDLMCVDVKLISPQDCTKVYKDLLENSMLCAGIPDSKKNACNGDSGGPLVCRGTLQGLVSWGTFPCGQPNDPGVYTQVCKFTKWINDTMKKHR  253
               SCOP domains d2qxgb_ B: automated matches                                                                                                                                                                                                     SCOP domains
               CATH domains 2qxgB01     2qxgB02 B:28-120,B:235-246 Trypsin-like serine proteases                                 2qxgB01 B:16-27,B:121-234 Trypsin-like serine proteases                                                        2qxgB02      CATH domains
           Pfam domains (1) Trypsin-2qxgB01 B:16-238                                                                                                                                                                                                -------- Pfam domains (1)
           Pfam domains (2) Trypsin-2qxgB02 B:16-238                                                                                                                                                                                                -------- Pfam domains (2)
         Sec.struct. author ....ee........eeeeee..eeeeeeeeee..eeeehhhhh...eeeee..........eeeeeeeeee.............eeeee........................eeeeee...............eeeeeeeehhhhhhhhhhhhh...eeeee...............eeee..eeeeeeee...........eeeee...hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: B:16-243 UniProt: 30-250                                                                                                                                                                                   --- PROSITE (1)
                PROSITE (2) ------------------------------------TRYPSI-------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.4  PDB: B:16-61 (gaps) UniProt: 25-74 ----------------------------------------------------------------------------------Exon 1.6  PDB: B:149-192 UniProt: 157-202     Exon 1.7b  PDB: B:193-246 (gaps) UniProt: 203-253   Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.5  PDB: B:61-149 (gaps) UniProt: 74-157                                      ------------------------------------------------------------------------------------------------ Transcript 1 (2)
                2qxg B   16 IIDGAPCARGSHPWQVALLSGNQLHCGGVLVNERWVLTAAHCKMNEYTVHLGSDTLGDRRAQRIKASKSFRHPGYSTQTHVNDLMLVKLNSQARLSSMVKKVRLPSRCEPPGTTCTVSGWGTTTSPDVTFPSDLMCVDVKLISPQDCTKVYKDLLENSMLCAGIPDSKKNACNGDSGGPLVCRGTLQGLVSWGTFPCGQPNDPGVYTQVCKFTKWINDTMKKHR  246
                                    25        35||      46        56        66||      77|       89        99       109       119     ||130|      141       151       161       171       181     ||189       199   ||  213       222       232       242    
                                               36|                           67|      77|                                          125|  ||                                                   186A|              203|         220A                          
                                                38                            69       80                                           127  ||                                                    186B               208                                       
                                                                                                                                       130|                                                                                                                 
                                                                                                                                        132                                                                                                                 

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
1a2qxgA01A:16-27,A:121-234
1b2qxgB01B:16-27,B:121-234
1c2qxgA02A:28-120,A:235-246
1d2qxgB02B:28-120,B:235-246

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (KLK7_HUMAN | P49862)
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:0004222    metalloendopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    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: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:0022617    extracellular matrix disassembly    A process that results in the breakdown of the extracellular matrix.
    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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    K7I  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Phe A:218 - Pro A:219   [ RasMol ]  
    Phe B:218 - Pro B:219   [ RasMol ]  
    Ser A:146 - Pro A:147   [ RasMol ]  
    Ser B:146 - Pro B:147   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2qxg
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  KLK7_HUMAN | P49862
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.21.117
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  KLK7_HUMAN | P49862
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        KLK7_HUMAN | P498622qxh 2qxi 2qxj 3bsq 5fah

(-) Related Entries Specified in the PDB File

2qxh 2qxi 2qxj