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(-) Description

Title :  HUMAN PROCASPASE-7 BOUND TO AC-DEVD-CMK
 
Authors :  N. D. Thomsen, J. A. Wells
Date :  20 Mar 13  (Deposition) - 08 May 13  (Release) - 05 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Protease, Proenzyme, Protein-Peptide Complex, Irreversible Inhibitor, Activity Based Probe, Caspase, Apoptosis, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. D. Thomsen, J. T. Koerber, J. A. Wells
Structural Snapshots Reveal Distinct Mechanisms Of Procaspase-3 And -7 Activation.
Proc. Natl. Acad. Sci. Usa V. 110 8477 2013
PubMed-ID: 23650375  |  Reference-DOI: 10.1073/PNAS.1306759110

(-) Compounds

Molecule 1 - PROCASPASE-7
    Chains: A, B
    EC Number: 3.4.22.60
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: ADDGENE PLASMID 29653
    Expression System Strain: BL21(DE3) PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: PROTEASE DOMAIN (UNP RESIDUES 57-303)
    Gene: CASP7, MCH3
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CASP-7, APOPTOTIC PROTEASE MCH-3, CMH-1, ICE-LIKE APOPTOTIC PROTEASE 3, ICE-LAP3, CASPASE-7
 
Molecule 2 - AC-DEVD-CMK
    Chains: C, D
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
10QE2Mod. Amino AcidCHLOROMETHANE
2ACE2Mod. Amino AcidACETYL GROUP
3AKZ2Mod. Amino Acid(3S)-3-AMINO-4,4-DIHYDROXYBUTANOIC ACID
4CL2Ligand/IonCHLORIDE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:76 , GLY A:89 , THR A:90 , ASP A:91BINDING SITE FOR RESIDUE CL A 401
2AC2SOFTWARELYS B:76 , ASN B:88 , GLY B:89 , THR B:90 , ASP B:91BINDING SITE FOR RESIDUE CL B 401
3AC3SOFTWAREARG A:87 , HIS A:144 , GLY A:145 , GLN A:184 , CYS A:186 , TYR A:230 , SER A:231 , TRP A:232 , ARG A:233 , SER A:234 , PRO A:235 , TRP A:240BINDING SITE FOR CHAIN C OF AC-DEVD-CMK
4AC4SOFTWAREARG B:87 , HIS B:144 , GLY B:145 , GLN B:184 , CYS B:186 , TYR B:230 , SER B:231 , TRP B:232 , ARG B:233 , PRO B:235 , SER B:275 , GLN B:276 , HOH D:201 , HOH D:202BINDING SITE FOR CHAIN D OF AC-DEVD-CMK

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:100 -A:246
2B:100 -B:246

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4JR1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JR1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JR1)

(-) Exons   (0, 0)

(no "Exon" information available for 4JR1)

(-) 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 d4jr1a_ A: Caspase-7                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeee....hhhhh.....hhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhh........eeeeee..ee..eee....eeehhhhhhhhh...hhhhh...eeeeee......................eeeee.........ee...eehhhhhhhhhhhhhh...hhhhhhhhhhhhhhh......eeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jr1 A  56 ATYQYNMNFEKLGKCIIINNKNFDKVTGMGVRNGTDKDAEALFKCFRSLGFDVIVYNDCSCAKMQDLLKKASEEDHTNAACFACILLSHGEENVIYGKDGVTPIKDLTAHFRGDRCKTLLEKPKLFFIQACRGTINDTDANPRYKIPVEADFLFAYSTVPGYYSWRSPGRGSWFVQALCSILEEHGKDLEIMQILTRVNDRVARHFKQIPCVVSMLTKELYFS 302
                                    65        75        85        95       105       115       125       135       145       155       165       175       185   ||  207       217       227       237       247       257       267     ||289       299   
                                                                                                                                                               189|                                                                    273|                
                                                                                                                                                                202                                                                     286                


Chain B from PDB  Type:PROTEIN  Length:228
                                                                                                                                                                                                                                                                    
               SCOP domains d4jr1b_ B: Caspase-7                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeeeeeeee..............hhhhhhhhhhhhhhhhheeeeeee..hhhhhhhhhhhhhh.....eeeeeeeee..ee..eeee..eeeehhhhhhhhh...hhhhh...eeeeee...............eeeee.........ee...eehhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....hhhhh......eeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4jr1 B  56 ATYQYNMNFEKLGKCIIINNKNFDKVTGMGVRNGTDKDAEALFKCFRSLGFDVIVYNDCSCAKMQDLLKKASEEDHTNAACFACILLSHGEENVIYGKDGVTPIKDLTAHFRGDRCKTLLEKPKLFFIQACRGTELDKIPVEADFLFAYSTVPGYYSWRSPGRGSWFVQALCSILEEHGKDLEIMQILTRVNDRVARHFESQSDDPHFHEKKQIPCVVSMLTKELYFS 302
                                    65        75        85        95       105       115       125       135       145       155       165       175       185      |214       224       234       244       254       264       274       284       294        
                                                                                                                                                                  192|                                                                                          
                                                                                                                                                                   212                                                                                          


Chain C 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
                 4jr1 C   1 xDEVdx   6
                            |   ||
                            1-ACE|
                                5-AKZ
                                 6-0QE


Chain D 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
                 4jr1 D   1 xDEVdx   6
                            |   ||
                            |   ||
                            1-ACE|
                                5-AKZ
                                 6-0QE
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JR1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JR1)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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  CASP7_HUMAN | P55210
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  3.4.22.60
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 Related Entries

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

UniProtKB/Swiss-Prot
        CASP7_HUMAN | P55210: 1f1j 1gqf 1i4o 1i51 1k86 1k88 1kmc 1mia 1shj 1shl 2ql5 2ql7 2ql9 2qlb 2qlf 2qlj 3edr 3h1p 3ibc 3ibf 3r5k 4fdl 4fea 4hq0 4hqr 4jb8 4jj8 4jr2 4lsz 4zvo 4zvp 4zvq 4zvr 4zvs 4zvt 4zvu 5ic6 5k20

(-) Related Entries Specified in the PDB File

4jqy 4jqz 4jr0 4jr2