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 :  CRYSTAL STRUCTURE OF STREPTOMYCES CAESPITOSUS SERMETSTATIN IN COMPLEX WITH BACILLUS LICHENIFORMIS SUBTILISIN
 
Authors :  S. Trillo-Muyo, S. Martinez-Rodriguez, J. L. Arolas, F. X. Gomis-Ruth
Date :  09 Nov 12  (Deposition) - 05 Dec 12  (Release) - 27 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Streptomyces Subtilisin Inhibitor Fold, Subtilisin Carlsberg, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Trillo-Muyo, S. Martinez-Rodriguez, J. L. Arolas, F. X. Gomis-Rut
Mechanism Of Action Of A Janus-Faced Single-Domain Protein Inhibitor Simultaneously Targeting Two Peptidase Classes
Chem Sci V. 4 791 2013
PubMed: search  |  Reference-DOI: 10.1039/C2SC21712K

(-) Compounds

Molecule 1 - KERA
    Chains: A, C
    EC Number: 3.4.21.62
    Fragment: MATURE PROTEASE
    Organism Scientific: BACILLUS LICHENIFORMIS
    Organism Taxid: 1402
    Synonym: SUBTILISIN
 
Molecule 2 - NEUTRAL PROTEINASE INHIBITOR SCNPI
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET32A
    Expression System Strain: ORIGAMI
    Expression System Taxid: 562
    Expression System Vector Type: PET
    Gene: SCNPI
    Organism Scientific: STREPTOMYCES CAESPITOSUS
    Organism Taxid: 53502
    Synonym: SERMETSTATIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (10, 18)

Asymmetric/Biological Unit (10, 18)
No.NameCountTypeFull Name
11AX1Ligand/Ion(2R,2'R)-3,3'-OXYDIPROPANE-1,2-DIOL
2ACT1Ligand/IonACETATE ION
3CA4Ligand/IonCALCIUM ION
4CAC1Ligand/IonCACODYLATE ION
5CL1Ligand/IonCHLORIDE ION
6GOL2Ligand/IonGLYCEROL
7IPA3Ligand/IonISOPROPYL ALCOHOL
8K2Ligand/IonPOTASSIUM ION
9PO41Ligand/IonPHOSPHATE ION
10ZN2Ligand/IonZINC ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:2 , ASP A:41 , LEU A:75 , ASN A:77 , THR A:79 , VAL A:81BINDING SITE FOR RESIDUE CA A 301
02AC2SOFTWAREALA A:169 , TYR A:171 , VAL A:174 , HOH A:420 , HOH A:423BINDING SITE FOR RESIDUE CA A 302
03AC3SOFTWAREHIS A:238 , GLN A:275 , HOH A:476 , GLU C:112BINDING SITE FOR RESIDUE ZN A 303
04AC4SOFTWARETYR A:209BINDING SITE FOR RESIDUE CL A 304
05AC5SOFTWAREASN A:25 , GLY A:118 , MET A:119 , ASP A:120 , ARG A:145 , GLY A:146 , VAL A:147 , PO4 A:306 , HOH A:525BINDING SITE FOR RESIDUE 1AX A 305
06AC6SOFTWAREASP A:120 , GLY A:146 , PRO A:239 , LEU A:241 , 1AX A:305BINDING SITE FOR RESIDUE PO4 A 306
07AC7SOFTWAREARG A:186 , TYR A:262 , TYR A:263 , HOH A:504BINDING SITE FOR RESIDUE GOL A 307
08AC8SOFTWAREALA A:37 , HIS A:39 , LEU A:42 , ASN A:43 , HOH A:449 , HOH A:543BINDING SITE FOR RESIDUE IPA A 308
09AC9SOFTWAREHIS B:3 , CAC B:504 , HOH B:645 , ASP C:120BINDING SITE FOR RESIDUE ZN B 501
10BC1SOFTWAREHIS B:93 , ASN B:104 , HOH B:652BINDING SITE FOR RESIDUE K B 502
11BC2SOFTWAREHIS B:93 , HOH B:629BINDING SITE FOR RESIDUE K B 503
12BC3SOFTWAREALA B:2 , HIS B:3 , ASN B:85 , ARG B:87 , ZN B:501 , HOH B:645 , GLY C:118 , ASP C:120BINDING SITE FOR RESIDUE CAC B 504
13BC4SOFTWAREGLN C:2 , ASP C:41 , LEU C:75 , ASN C:77 , THR C:79 , VAL C:81BINDING SITE FOR RESIDUE CA C 301
14BC5SOFTWAREALA C:169 , TYR C:171 , VAL C:174 , HOH C:401 , HOH C:447BINDING SITE FOR RESIDUE CA C 302
15BC6SOFTWARELYS C:27 , TYR C:91 , ASN C:117 , HOH C:414BINDING SITE FOR RESIDUE ACT C 303
16BC7SOFTWAREARG C:186 , TYR C:262BINDING SITE FOR RESIDUE GOL C 304
17BC8SOFTWAREASN C:62 , TYR C:209 , TYR D:72BINDING SITE FOR RESIDUE IPA C 305
18BC9SOFTWAREHIS D:93 , THR D:94 , ASN D:104BINDING SITE FOR RESIDUE IPA D 201

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1B:31 -B:46
2B:69 -B:99
3D:31 -D:46
4D:69 -D:99

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr A:167 -Pro A:168
2Pro A:210 -Thr A:211
3Tyr C:167 -Pro C:168
4Pro C:210 -Thr C:211

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HX2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HX2)

(-) Exons   (0, 0)

(no "Exon" information available for 4HX2)

(-) 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:274
                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4hx2a_ A: automated matches                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh.......eeeeee...........eeeeee............hhhhhhhhhhhh..............eeeeee.......eehhhhhhhhhhhhhh...eeee.ee....hhhhhhhhhhhhhh..eeeee......................eeeeee...............eeeeee...eeeee...eeeee.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.....hhhhhh....hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hx2 A   1 AQTVPYGIPLIKADKVQAQGFKGANVKVAVLDTGIQASHPDLNVVGGASFVAGEAYNTDGNGHGTHVAGTVAALDNTTGVLGVAPSVSLYAVKVLNSSGSGSYSGIVSGIEWATTNGMDVINMSLGGASGSTAMKQAVDNAYARGVVVVAAAGNSGSSGNTNTIGYPAKYDSVIAVGAVDSNSNRASFSSVGAELEVMAPGAGVYSTYPTNTYATLNGTSMASPHVAGAAALILSKHPNLSASQVRNRLSSTATYLGSSFYYGKGLINVEAAAQ 275
                                    10        20        30        40        50    ||  61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271    
                                                                                 55|                                                                                                                                                                                                                          
                                                                                  57                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:114
                                                                                                                                                  
               SCOP domains d4hx2b_ B: automated matches                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeeee.......eeeeeeeeee...ee....hhhhhhhhhhhh..hhhhhhh.....eeee.....eeeeeeeee..eeeeeeeee.hhhhhhhhhh.hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 4hx2 B  -1 GSAHGPSAMVFTVIQGSGEPTDTVLRATTLSCAYTAEGTHPAPRAACDALNATDGELNRLLAAPDPSLVCPMYFDPVTVTADGVLNGRRVAWKHTFSNTCVMSANLNSNPVYAF 113
                            ||       9        19        29        39        49        59        69        79        89        99       109    
                           -1|                                                                                                                
                             1                                                                                                                


Chain C from PDB  Type:PROTEIN  Length:274
                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4hx2c_ C: automated matches                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh.......eeeeee...........eeeeee............hhhhhhhhhhhh..............eeeeee.......eehhhhhhhhhhhhhh...eeee.ee....hhhhhhhhhhhhhh..eeeee......................eeeeee...............eeeeee...eeeee...eeeee.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.....hhhhhh....hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hx2 C   1 AQTVPYGIPLIKADKVQAQGFKGANVKVAVLDTGIQASHPDLNVVGGASFVAGEAYNTDGNGHGTHVAGTVAALDNTTGVLGVAPSVSLYAVKVLNSSGSGSYSGIVSGIEWATTNGMDVINMSLGGASGSTAMKQAVDNAYARGVVVVAAAGNSGSSGNTNTIGYPAKYDSVIAVGAVDSNSNRASFSSVGAELEVMAPGAGVYSTYPTNTYATLNGTSMASPHVAGAAALILSKHPNLSASQVRNRLSSTATYLGSSFYYGKGLINVEAAAQ 275
                                    10        20        30        40        50    ||  61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271    
                                                                                 55|                                                                                                                                                                                                                          
                                                                                  57                                                                                                                                                                                                                          


Chain D from PDB  Type:PROTEIN  Length:110
                                                                                                                                              
               SCOP domains d4hx2d_ D: automated matches                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee.......eeeeeeeeee...ee....hhhhhhhhhhhh..hhhhhhh.....eeee.....eeeeeeeee..eeeeeeeee.hhhhhhhhhh.hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 4hx2 D   4 GPSAMVFTVIQGSGEPTDTVLRATTLSCAYTAEGTHPAPRAACDALNATDGELNRLLAAPDPSLVCPMYFDPVTVTADGVLNGRRVAWKHTFSNTCVMSANLNSNPVYAF 113
                                    13        23        33        43        53        63        73        83        93       103       113
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HX2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HX2)

(-) Gene Ontology  (10, 10)

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
    1AX  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CAC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    IPA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    K  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Pro A:210 - Thr A:211   [ RasMol ]  
    Pro C:210 - Thr C:211   [ RasMol ]  
    Tyr A:167 - Pro A:168   [ RasMol ]  
    Tyr C:167 - Pro C:168   [ 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
  4hx2
    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
  Q9FDF2_BACLI | Q9FDF2
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  Q9FDS0_STRCS | Q9FDS0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  3.4.21.62
    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
  Q9FDF2_BACLI | Q9FDF2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q9FDS0_STRCS | Q9FDS0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9FDF2_BACLI | Q9FDF2: 4gi3
        Q9FDS0_STRCS | Q9FDS0: 4hwx 4hx3

(-) Related Entries Specified in the PDB File

4hwx CRYSTAL STRUCTURE OF SERMETSTATIN
4hx3