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

(-) Description

Title :  ATOMIC RESOLUTION CRYSTAL STRUCTURE OF KALLIKREIN-RELATED PEPTIDASE 4 COMPLEXED WITH A MODIFIED SFTI INHIBITOR FCQR(N)
 
Authors :  O. V. Ilyichova, J. E. Swedberg, S. J. De Veer, K. C. Sit, J. M. Harris, A.
Date :  25 Apr 13  (Deposition) - 30 Apr 14  (Release) - 09 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Bowman-Birk Inhibitor, Protease, Protease Inhibitor, Hydrolase- Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. V. Ilyichova, J. E. Swedberg, S. J. De Veer, K. C. Sit, J. M. Harris, A. M. Buckle
Atomic Resolution Crystal Structures Of Kallikrein-Related Peptidase 4 : Sfti Inhibitor Complexes
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - KALLIKREIN-4
    Chains: A
    EC Number: 3.4.21.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET12A-PROPSA-HK4
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RELATED PEPTIDASE 4, UNP RESIDUES 31-253
    Gene: KLK4
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ENAMEL MATRIX SERINE PROTEINASE 1, KALLIKREIN-LIKE PROTEIN 1, KLK-L1, PROSTASE, SERINE PROTEASE 17
 
Molecule 2 - TRYPSIN INHIBITOR 1
    Chains: B
    Engineered: YES
    Mutation: YES
    Organism Common: COMMON SUNFLOWER
    Organism Scientific: HELIANTHUS ANNUUS
    Organism Taxid: 4232
    Other Details: MODIFIED SUNFLOWER TRYPSIN INHIBITOR
    Synonym: SFTI-1
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4KEL)

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:40 , PHE A:41 , CYS A:42 , HIS A:57 , TYR A:94 , LEU A:99 , MET A:151 , TYR A:172 , LEU A:175 , ASP A:189 , SER A:190 , CYS A:191 , ASN A:192 , GLY A:193 , ASP A:194 , SER A:195 , SER A:214 , PHE A:215 , GLY A:216 , LYS A:217 , ALA A:218 , CYS A:220 , HOH A:322 , HOH A:348 , HOH B:101 , HOH B:102 , HOH B:103 , HOH B:104 , HOH B:105 , HOH B:106 , HOH B:108BINDING SITE FOR CHAIN B OF TRYPSIN INHIBITOR 1

(-) SS Bonds  (7, 7)

Asymmetric/Biological 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:3 -B:11

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Arg A:96 -Pro A:97
2Asp A:173 -Pro A:174
3Ala A:218 -Pro A:219
4Ile B:7 -Pro B:8

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4KEL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KEL)

(-) Exons   (0, 0)

(no "Exon" information available for 4KEL)

(-) 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:223
                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee..eeeeeeeeee..eeeehhhhh...eeeee.............eeeee.eeee.............eeee.........................eeeeee.............eeeeee..hhhhhhhhh.......eeeee...............eeee..eeeeeeeeee........eeeeee...hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4kel A   16 IINGEDCSPHSQPWQAALVMENELFCSGVLVHPQWVLSAAHCFQNSYTIGLGLHSLEADQEPGSQMVEASLSVRHPEYNRPLLANDLMLIKLDESVSESDTIRSISIASQCPTAGNSCLVSGWGLLANGRMPTVLQCVNVSVVSEEVCSKLYDPLYHPSMFCAGGGQDQKDSCNGDSGGPLICNGYLQGLVSFGKAPCGQVGVPGVYTNLCKFTEWIEKTVQA  244
                                    25        35  ||    46        56        66||     |76        86        96       106       116       127  ||   138       150       160       170       180      |188       198    || 212       221       231       241   
                                                 38|                         67|   74A                                                125|  ||            147|                                 186A|              203|         220A                        
                                                  40                          69                                                       127  ||             150                                  186B               208                                     
                                                                                                                                          130|                                                                                                             
                                                                                                                                           132                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:14
                                               
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author .eee.....ee... Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                4kel B    1 GFCQRSIPPICFPN   14
                                    10
   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  (0, 0)

(no "SCOP Domain" information available for 4KEL)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4KEL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KEL)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
(no "Ligands, Modified Residues, Ions" information available for 4kel)
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:218 - Pro A:219   [ RasMol ]  
    Arg A:96 - Pro A:97   [ RasMol ]  
    Asp A:173 - Pro A:174   [ RasMol ]  
    Ile B:7 - Pro B:8   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4kel
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  KLK4_HUMAN | Q9Y5K2
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  SFTI1_HELAN | Q4GWU5
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.21.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  KLK4_HUMAN | Q9Y5K2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  SFTI1_HELAN | Q4GWU5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        KLK4_HUMAN | Q9Y5K2: 2bdg 2bdh 2bdi 4k1e 4k8y 4kga
        SFTI1_HELAN | Q4GWU5: 1jbl 1jbn 1o8y 1o8z 1sfi 1t9e 2ab9 3p8f 4abi 4abj 4hgc 4k1e 4k8y 4xoj

(-) Related Entries Specified in the PDB File

2bdg 2bdh 2bdi 4k1e 4k8y 4kga