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 :  CASPASE-3 SPECIFIC UNNATURAL AMINO ACID-BASED PEPTIDES
 
Authors :  C. J. Vickers, G. E. Gonzalez-Paez, D. W. Wolan
Date :  07 Mar 13  (Deposition) - 12 Jun 13  (Release) - 12 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.18
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protease, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. J. Vickers, G. E. Gonzalez-Paez, D. W. Wolan
Selective Detection Of Caspase-3 Versus Caspase-7 Using Activity-Based Probes With Key Unnatural Amino Acids.
Acs Chem. Biol. V. 8 1558 2013
PubMed-ID: 23614665  |  Reference-DOI: 10.1021/CB400209W

(-) Compounds

Molecule 1 - CASPASE-8
    Chains: A
    EC Number: 3.4.22.61
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET23B
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CASP8, CASP8 MCH5, MCH5
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CASP-8, APOPTOTIC CYSTEINE PROTEASE, APOPTOTIC PROTEASE MCH- 5, CAP4, FADD-HOMOLOGOUS ICE/CED-3-LIKE PROTEASE, FADD-LIKE ICE, FLICE, ICE-LIKE APOPTOTIC PROTEASE 5, MORT1-ASSOCIATED CED-3 HOMOLOG, MACH, CASPASE-8 SUBUNIT P18, CASPASE-8 SUBUNIT P10
 
Molecule 2 - CASPASE INHIBITOR
    Chains: B
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 7)

Asymmetric/Biological Unit (6, 7)
No.NameCountTypeFull Name
11MH1Mod. Amino Acid3-PYRIDIN-3-YL-L-ALANINE
21U81Mod. Amino Acid(3S)-3-AMINO-5-[(2,6-DIMETHYLBENZOYL)OXY]-4-OXOPENTANOIC ACID
3ACE1Mod. Amino AcidACETYL GROUP
4B3L1Mod. Amino Acid(3S)-3-AMINO-5-METHYLHEXANOIC ACID
5DTD2Ligand/IonDITHIANE DIOL
6HLX1Mod. Amino Acid5-METHYL-L-NORLEUCINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:392 , ASP A:454 , MET A:459BINDING SITE FOR RESIDUE DTD A 601
2AC2SOFTWARETYR A:334 , THR A:337 , GLU A:396 , PHE A:399 , LEU A:401 , THR A:469 , HOH A:874 , HOH A:876 , HOH A:913 , HOH A:1001BINDING SITE FOR RESIDUE DTD A 602
3AC3SOFTWAREARG A:258 , ARG A:260 , ASN A:261 , SER A:316 , HIS A:317 , GLY A:318 , GLN A:358 , CYS A:360 , SER A:411 , TYR A:412 , ARG A:413 , PRO A:415 , HOH B:601 , HOH B:602 , HOH B:603 , HOH B:604 , HOH B:605 , HOH B:607 , HOH B:608 , HOH B:609 , HOH B:611 , HOH B:613 , HOH B:614 , HOH B:615BINDING SITE FOR CHAIN B OF CASPASE INHIBITOR

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JJ7)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:231 -Pro A:232

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JJ7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JJ7)

(-) Exons   (0, 0)

(no "Exon" information available for 4JJ7)

(-) 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:241
                                                                                                                                                                                                                                                                                 
               SCOP domains d4jj7a_ A: automated matches                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeee...hhhhhhhhhhhh......hhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh.......eeeeee..ee..eee.....eeehhhhhhhhh...hhhhh...eeeeee.........................eeeee.........ee...eehhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.............eeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jj7 A 223 DKVYQMKSKPRGYCLIINNHNFAKAREKVPKLHSIRDRNGTHLDAGALTTTFEELHFEIKPHDDCTVEQIYEILKIYQLMDHSNMDCFICCILSHGDKGIIYGTDGQEAPIYELTSQFTGLKCPSLAGKPKVFFIQACQGDNYQKGIPVETDTRYIPDEADFLLGMATVNNCVSYRNPAEGTWYIQSLCQSLRERCPRGDDILTILTEVNYEVSNKDDKKNMGKQMPQPTFTLRKKLVFPS 478
                                   232       242       252       262       272       282       292       302       312       322       332       342       352       362       372 ||    397       407       417       427       437       447       457       467       477 
                                                                                                                                                                                 374|                                                                                        
                                                                                                                                                                                  390                                                                                        


Chain B from PDB  Type:PROTEIN  Length:6
                                      
               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
                 4jj7 B 501 xxDxxx 506
                            || |||
                          501-ACE|
                           502-1MH
                             504-B3L
                              505-HLX
                               506-1U8
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JJ7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JJ7)

(-) Gene Ontology  (70, 70)

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
    1MH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    1U8  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ACE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    B3L  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DTD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HLX  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Lys A:231 - Pro A:232   [ 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
  4jj7
    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
  CASP8_HUMAN | Q14790
    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)
  3.4.22.61
    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
  CASP8_HUMAN | Q14790
    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
        CASP8_HUMAN | Q14790: 1f9e 1i4e 1qdu 1qtn 2c2z 2fun 2k7z 2y1l 3h11 3kjn 3kjq 4prz 4ps1 4zbw 5jqe 5l08

(-) Related Entries Specified in the PDB File

1f9e CRYSTAL STRUCTURE OF THE CASPASE-8-Z-DEVD-CHO
1qdu CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE-8 WITH THE TRIPEPTIDE KETONE INHIBITOR ZEVD-DCBMK
1qtn CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE-8 WITH THE TETRAPEPTIDE INHIBITOR ACE-IETD-ALDEHYDE
4jj8
4jje