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(-) Description

Title :  TAILORING SMALL MOLECULES FOR AN ALLOSTERIC SITE ON PROCASPASE-6: CPD1
 
Authors :  J. M. Murray, M. Steffek
Date :  09 Oct 13  (Deposition) - 18 Dec 13  (Release) - 22 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.06
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Procaspse-6, Caspase-6 Zymogen, Allosteric, Structure Based Drug Design, Cysteine Protease, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Murray, A. M. Giannetti, M. Steffek, P. Gibbons, B. R. Hearn, F. Cohen, C. Tam, C. Pozniak, B. Bravo, J. Lewcock, P. Jaishankar, C. Q. Ly, X. Zhao, Y. Tang, P. Chugha, M. R. Arkin, J. Flygare, A. R. Rensl
Tailoring Small Molecules For An Allosteric Site On Procaspase-6.
Chemmedchem V. 9 73 2014
PubMed-ID: 24259468  |  Reference-DOI: 10.1002/CMDC.201300424

(-) Compounds

Molecule 1 - CASPASE-6
    Chains: A, B
    EC Number: 3.4.22.59
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CASP6, MCH2, PROCASPASE-6
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CASP-6, APOPTOTIC PROTEASE MCH-2, CASPASE-6 SUBUNIT P18, CASPASE-6 SUBUNIT P11

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
12FQ1Ligand/Ion6-AMINO-2,8-DIMETHYLPYRIDO[2,3-D]PYRIMIDIN-7(8H)-ONE
2MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3PO42Ligand/IonPHOSPHATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:125 , GLN A:137 , TYR A:198 , LEU A:200 , TYR B:198 , LEU B:200BINDING SITE FOR RESIDUE 2FQ A 401
2AC2SOFTWAREARG A:64 , SER A:120 , HIS A:121 , GLN A:161 , ALA A:162 , ALA A:163 , ASP A:193 , ARG A:220BINDING SITE FOR RESIDUE PO4 A 402
3AC3SOFTWAREHIS A:41 , ALA A:109 , LYS A:154 , HOH A:532 , HOH A:555 , HOH A:621 , PHE B:88 , ASN B:89BINDING SITE FOR RESIDUE MPD A 403
4AC4SOFTWAREARG B:64 , SER B:120 , HIS B:121 , GLN B:161 , ALA B:162 , ALA B:163 , ASP B:193 , ARG B:220 , HOH B:518BINDING SITE FOR RESIDUE PO4 B 401
5AC5SOFTWARETYR A:216 , LYS A:273 , LYS B:144 , GLY B:145 , LYS B:156 , ALA B:204 , PHE B:206 , HOH B:603BINDING SITE FOR RESIDUE MPD B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4N5D)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:266 -Pro A:267

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4N5D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N5D)

(-) Exons   (0, 0)

(no "Exon" information available for 4N5D)

(-) 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:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains d4n5da_ A: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeee....hhhhh.....hhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh.......eeeeeeeeee..eee....eeehhhhhhhhhhhhhhhhh...eeeeeeee...............eeeee...........eeeee......eeeee...eehhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..................eeee............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n5d A  25 FYKREMFDPAEKYKMDHRRRGIALIFNHERFFWHLTLPERRGTCADRDNLTRRFSDLGFEVKCFNDLKAEELLLKIHEVSTVSHADADCFVCVFLSHGEGNHIYAYDAKIEIQTLTGLFKGDKCHSLVGKPKIFIIQAARGNQHDVPVIPDTNITEVDAASVYTLPAGADFLMCYSVAEGYYSHRETVNGSWYIQDLCEMLGKYGSSLEFTELLTLVNRKVSQRRVDFCKDPSAIGKKQVPCFASMLTKKLHFFPKS 292
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174|      195       205       215       225       235       245       255       265       275       285       
                                                                                                                                                                               174|                                                                                                          
                                                                                                                                                                                186                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:243
                                                                                                                                                                                                                                                                                   
               SCOP domains d4n5db_ B: automated matches                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeeeee....hhhhh.....hhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh....eeeeeeeeeeeee..eee....eeehhhhhhh.....hhhhh...eeeeeeee.......eeeee...........eeeee......eeeee...eehhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhh......eeee........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n5d B  30 MFDPAEKYKMDHRRRGIALIFNHERFFWHLTLPERRGTCADRDNLTRRFSDLGFEVKCFNDLKAEELLLKIHEVSTVSHADADCFVCVFLSHGEGNHIYAYDAKIEIQTLTGLFKGDKCHSLVGKPKIFIIQAARGNQTNITEVDAASVYTLPAGADFLMCYSVAEGYYSHRETVNGSWYIQDLCEMLGKYGSSLEFTELLTLVNRKVSQRRVDFCKDPSAIGKKQVPCFASMLTKKLHFFPK 291
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       188       198       208       218       228       238       248       258       268       278       288   
                                                                                                                                                                   167|                                                                                                        
                                                                                                                                                                    187
   Legend:   → Mismatch (orange background)
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  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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N5D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N5D)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asp A:266 - Pro A:267   [ RasMol ]  
 

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  4n5d
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  CASP6_HUMAN | P55212
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 Related Entries

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

UniProtKB/Swiss-Prot
        CASP6_HUMAN | P55212: 1mi9 2wdp 3k7e 3nkf 3nr2 3od5 3p45 3p4u 3qnw 3s70 3s8e 3v6l 3v6m 4ejf 4fxo 4hva 4iyr 4n6g 4n7j 4n7m 4nbk 4nbl 4nbn

(-) Related Entries Specified in the PDB File

4n6g 4n7j 4n7m 4nbk 4nbl 4nbn