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
(-)Biological Unit 3
(-)Biological Unit 4
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)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  CASPASE-8 SPECIFIC UNNATURAL AMINO ACID PEPTIDES
 
Authors :  D. W. Wolan, C. J. Vickers, G. E. Gonzalez-Paez
Date :  06 Mar 14  (Deposition) - 21 Jan 15  (Release) - 21 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,E  (1x)
Biol. Unit 2:  B,F  (1x)
Biol. Unit 3:  C,G  (1x)
Biol. Unit 4:  D,H  (1x)
Keywords :  Protease, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. J. Vickers, G. E. Gonzalez-Paez, K. M. Litwin, J. C. Umotoy, E. A. Coutsias, D. W. Wolan
Selective Inhibition Of Initiator Versus Executioner Caspases Using Small Peptides Containing Unnatural Amino Acids.
Acs Chem. Biol. V. 9 2194 2014
PubMed-ID: 25079698  |  Reference-DOI: 10.1021/CB5004256

(-) Compounds

Molecule 1 - CASPASE-8
    Chains: A, B, C, D
    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: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 217-479
    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 - (BAL)LQ(HYP)(1U8) PEPTIDE
    Chains: E, F, G, H
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): A   E   
Biological Unit 2 (1x):  B   F  
Biological Unit 3 (1x):   C   G 
Biological Unit 4 (1x):    D   H

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 16)

Asymmetric Unit (4, 16)
No.NameCountTypeFull Name
11U84Mod. Amino Acid(3S)-3-AMINO-5-[(2,6-DIMETHYLBENZOYL)OXY]-4-OXOPENTANOIC ACID
2BAL4Mod. Amino AcidBETA-ALANINE
3DTT4Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
4HYP4Mod. Amino Acid4-HYDROXYPROLINE
Biological Unit 1 (4, 4)
No.NameCountTypeFull Name
11U81Mod. Amino Acid(3S)-3-AMINO-5-[(2,6-DIMETHYLBENZOYL)OXY]-4-OXOPENTANOIC ACID
2BAL1Mod. Amino AcidBETA-ALANINE
3DTT1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
4HYP1Mod. Amino Acid4-HYDROXYPROLINE
Biological Unit 2 (4, 4)
No.NameCountTypeFull Name
11U81Mod. Amino Acid(3S)-3-AMINO-5-[(2,6-DIMETHYLBENZOYL)OXY]-4-OXOPENTANOIC ACID
2BAL1Mod. Amino AcidBETA-ALANINE
3DTT1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
4HYP1Mod. Amino Acid4-HYDROXYPROLINE
Biological Unit 3 (4, 4)
No.NameCountTypeFull Name
11U81Mod. Amino Acid(3S)-3-AMINO-5-[(2,6-DIMETHYLBENZOYL)OXY]-4-OXOPENTANOIC ACID
2BAL1Mod. Amino AcidBETA-ALANINE
3DTT1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
4HYP1Mod. Amino Acid4-HYDROXYPROLINE
Biological Unit 4 (4, 4)
No.NameCountTypeFull Name
11U81Mod. Amino Acid(3S)-3-AMINO-5-[(2,6-DIMETHYLBENZOYL)OXY]-4-OXOPENTANOIC ACID
2BAL1Mod. Amino AcidBETA-ALANINE
3DTT1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
4HYP1Mod. Amino Acid4-HYDROXYPROLINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:337 , GLU A:396 , THR A:469 , HOH A:669BINDING SITE FOR RESIDUE DTT A 501
2AC2SOFTWARETHR B:337 , GLU B:396 , THR B:469 , HOH B:632 , HOH B:643BINDING SITE FOR RESIDUE DTT B 501
3AC3SOFTWARETHR C:337 , GLU C:396 , THR C:469 , HOH C:626 , HOH D:743BINDING SITE FOR RESIDUE DTT C 501
4AC4SOFTWAREHOH C:680 , THR D:337 , GLU D:396 , THR D:469 , HOH D:647BINDING SITE FOR RESIDUE DTT D 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PS1)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Lys A:231 -Pro A:232
2Lys B:231 -Pro B:232
3Lys C:231 -Pro C:232
4Lys D:231 -Pro D:232

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PS1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PS1)

(-) Exons   (0, 0)

(no "Exon" information available for 4PS1)

(-) 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:238
                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeee...hhhhhhhhhhhh......hhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhh........eeeeee..ee..eee.....eeehhhhhhhhh...hhhhh...eeeeee......................eeeee........eee...eehhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhh.....eeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ps1 A 222 LDKVYQMKSKPRGYCLIINNHNFAKAREKVPKLHSIRDRNGTHLDAGALTTTFEELHFEIKPHDDCTVEQIYEILKIYQLMDHSNMDCFICCILSHGDKGIIYGTDGQEAPIYELTSQFTGLKCPSLAGKPKVFFIQACQGDNYQKGIPVTRYIPDEADFLLGMATVNNCVSYRNPAEGTWYIQSLCQSLRERCPRGDDILTILTEVNYEVSNKDDKKNMGKQMPQPTFTLRKKLVFP 477
                                   231       241       251       261       271       281       291       301       311       321       331       341       351       361       371|      399       409       419       429       439       449       459       469        
                                                                                                                                                                               371|                                                                                       
                                                                                                                                                                                390                                                                                       


Chain B from PDB  Type:PROTEIN  Length:238
                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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........eee...eehhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhh.....eeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ps1 B 222 LDKVYQMKSKPRGYCLIINNHNFAKAREKVPKLHSIRDRNGTHLDAGALTTTFEELHFEIKPHDDCTVEQIYEILKIYQLMDHSNMDCFICCILSHGDKGIIYGTDGQEAPIYELTSQFTGLKCPSLAGKPKVFFIQACQGDNYQKGIPVERYIPDEADFLLGMATVNNCVSYRNPAEGTWYIQSLCQSLRERCPRGDDILTILTEVNYEVSNKDDKKNMGKQMPQPTFTLRKKLVFP 477
                                   231       241       251       261       271       281       291       301       311       321       331       341       351       361       371||     399       409       419       429       439       449       459       469        
                                                                                                                                                                                372|                                                                                      
                                                                                                                                                                                 391                                                                                      


Chain C from PDB  Type:PROTEIN  Length:237
                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeee...hhhhhhhhhhhh......hhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhh........eeeeee..ee..eee.....eeehhhhhhhhh...hhhhh...eeeeee.....................eeeee........eee...eehhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh............eeee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ps1 C 223 DKVYQMKSKPRGYCLIINNHNFAKAREKVPKLHSIRDRNGTHLDAGALTTTFEELHFEIKPHDDCTVEQIYEILKIYQLMDHSNMDCFICCILSHGDKGIIYGTDGQEAPIYELTSQFTGLKCPSLAGKPKVFFIQACQGDNYQKGIPVRYIPDEADFLLGMATVNNCVSYRNPAEGTWYIQSLCQSLRERCPRGDDILTILTEVNYEVSNKDDKKNMGKQMPQPTFTLRKKLVFPS 478
                                   232       242       252       262       272       282       292       302       312       322       332       342       352       362       391       401       411       421       431       441       451       461       471       
                                                                                                                                                                              371|                                                                                       
                                                                                                                                                                               391                                                                                       


Chain D from PDB  Type:PROTEIN  Length:236
                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeee...hhhhhhhhhhhh......hhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhh........eeeeee..ee..eee.....eeehhhhhhhhh...hhhhh...eeeeee.......ee............eeeee........eee...eehhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhh.ee...eeee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ps1 D 223 DKVYQMKSKPRGYCLIINNHNFAKAREKVPKLHSIRDRNGTHLDAGALTTTFEELHFEIKPHDDCTVEQIYEILKIYQLMDHSNMDCFICCILSHGDKGIIYGTDGQEAPIYELTSQFTGLKCPSLAGKPKVFFIQACQGDNYQKGIPVRYIPDEADFLLGMATVNNCVSYRNPAEGTWYIQSLCQSLRERCPRGDDILTILTEVNYEVSNKDDKKNMGKQMPQPTFTLRKKLVFP 477
                                   232       242       252       262       272       282       292       302       312       322       332       342       352       362       391       401       411       421       431       441       451       461       471      
                                                                                                                                                                              371|                                                                                      
                                                                                                                                                                               391                                                                                      


Chain E from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..ee. Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 4ps1 E 401 xLQpx 405
                            |  ||
                          401-BAL
                             404-HYP
                              405-1U8


Chain F from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..ee. Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 4ps1 F 401 xLQpx 405
                            |  ||
                            |  ||
                          401-BAL
                             404-HYP
                              405-1U8


Chain G from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..ee. Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 4ps1 G 401 xLQpx 405
                            |  ||
                            |  ||
                          401-BAL
                             404-HYP
                              405-1U8


Chain H from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..ee. Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 4ps1 H 401 xLQpx 405
                            |  ||
                            |  ||
                          401-BAL
                             404-HYP
                              405-1U8
   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  (0, 0)

(no "SCOP Domain" information available for 4PS1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PS1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PS1)

(-) Gene Ontology  (70, 70)

Asymmetric Unit(hide GO term definitions)

 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
    1U8  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    BAL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DTT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HYP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Lys A:231 - Pro A:232   [ RasMol ]  
    Lys B:231 - Pro B:232   [ RasMol ]  
    Lys C:231 - Pro C:232   [ RasMol ]  
    Lys D:231 - Pro D:232   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format | Biol. Unit 4 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
  4ps1
    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 4jj7 4prz 4zbw 5jqe 5l08

(-) Related Entries Specified in the PDB File

4jj7 CASPASE-8 IN COMPLEX WITH CASPASE-3 SPECIFIC PEPTIDE
4jj8 CASPASE-7 IN COMPLEX WITH CASPASE-3 SPECIFIC PEPTIDE
4jje CASPASE-3 IN COMPLEX WITH CASPASE-3 SPECIFIC PEPTIDE
4pry CASPASE-3 IN COMPLEX WITH AC-LETD-CHO
4prz CASPASE-8 IN COMPLEX WITH AC-LETD-AOMK
4ps0 CASPASE-3 IN COMPLEX WITH CASPASE-8 SPECIFIC PEPTIDE