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(-) Description

Title :  HUMAN PROCASPASE-3 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 :  1.80
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-3
    Chains: A, B
    EC Number: 3.4.22.56
    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 34-277)
    Gene: CASP3, CPP32
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CASP-3, APOPAIN, CYSTEINE PROTEASE CPP32, CPP-32, PROTEIN YAMA, SREBP CLEAVAGE ACTIVITY 1, SCA-1, CASPASE-3
 
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:53 , GLY A:66 , THR A:67 , ASP A:68BINDING SITE FOR RESIDUE CL A 301
2AC2SOFTWARELYS B:53 , GLY B:66 , THR B:67 , ASP B:68BINDING SITE FOR RESIDUE CL B 301
3AC3SOFTWAREARG A:64 , SER A:120 , HIS A:121 , GLY A:122 , GLN A:161 , CYS A:163 , SER A:205 , TRP A:206 , ARG A:207 , ASN A:208 , SER A:209 , SER A:249 , PHE A:250 , HOH A:447 , HOH A:584 , HOH A:612 , HOH C:201 , HOH C:202 , HOH C:203 , HOH C:204 , HOH C:205 , HOH C:206BINDING SITE FOR CHAIN C OF AC-DEVD-CMK
4AC4SOFTWAREARG B:64 , SER B:120 , HIS B:121 , GLY B:122 , GLN B:161 , CYS B:163 , SER B:205 , TRP B:206 , ARG B:207 , ASN B:208 , SER B:209 , TRP B:214 , SER B:249 , PHE B:250 , HOH B:460 , HOH B:494 , HOH B:568 , HOH D:201 , HOH D:202 , HOH D:203 , HOH D:204 , HOH D:205BINDING SITE FOR CHAIN D OF AC-DEVD-CMK

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JR0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4JR0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JR0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JR0)

(-) Exons   (0, 0)

(no "Exon" information available for 4JR0)

(-) 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:226
                                                                                                                                                                                                                                                                  
               SCOP domains d4jr0a_ A: Apopain (caspase-3, cpp32)                                                                                                                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeee....hhhhh.....hhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhh.....eeeeeeeee..ee..eeee..eeeehhhhhhh.....hhhhh...eeeeee............eeeee.........ee...eehhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....hhhhh......eeee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jr0 A  33 ADNSYKMDYPEMGLCIIINNKNFHKSTGMTSRSGTDVDAANLRETFRNLKYEVRNKNDLTREEIVELMRDVSKEDHSKRSSFVCVLLSHGEEGIIFGTNGPVDLKKITNFFRGDRCRSLTGKPKLFIIQACRGTKIPVEADFLYAYSTAPGYYSWRNSKDGSWFIQSLCAMLKQYADKLEFMHILTRVNRKVATEFESFSFDATFHAKKQIPCIVSMLTKELYFYH 277
                                    42        52        62        72        82        92       102       112       122       132       142       152       162   ||  191       201       211       221       231       241       251       261       271      
                                                                                                                                                               166|                                                                                           
                                                                                                                                                                186                                                                                           


Chain B from PDB  Type:PROTEIN  Length:226
                                                                                                                                                                                                                                                                  
               SCOP domains d4jr0b_ B: Apopain (caspase-3, cpp32)                                                                                                                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeeee....hhhhh.....hhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh....eeeeeeeee..ee..eeee..eeeehhhhhhhhh...hhhhh...eeeeee...........eeeee.........ee...eehhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....hhhhh......eeee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jr0 B  32 NADNSYKMDYPEMGLCIIINNKNFHKSTGMTSRSGTDVDAANLRETFRNLKYEVRNKNDLTREEIVELMRDVSKEDHSKRSSFVCVLLSHGEEGIIFGTNGPVDLKKITNFFRGDRCRSLTGKPKLFIIQACRGTIPVEADFLYAYSTAPGYYSWRNSKDGSWFIQSLCAMLKQYADKLEFMHILTRVNRKVATEFESFSFDATFHAKKQIPCIVSMLTKELYFYH 277
                                    41        51        61        71        81        91       101       111       121       131       141       151       161    || 191       201       211       221       231       241       251       261       271      
                                                                                                                                                                166|                                                                                          
                                                                                                                                                                 187                                                                                          


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
                 4jr0 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
                 4jr0 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 4JR0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JR0)

(-) Gene Ontology  (78, 78)

Asymmetric/Biological Unit(hide GO term definitions)

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  CASP3_HUMAN | P42574
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 Related Entries

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

UniProtKB/Swiss-Prot
        CASP3_HUMAN | P42574: 1cp3 1gfw 1i3o 1nme 1nmq 1nms 1pau 1qx3 1re1 1rhj 1rhk 1rhm 1rhq 1rhr 1rhu 2c1e 2c2k 2c2m 2c2o 2cdr 2cjx 2cjy 2cnk 2cnl 2cnn 2cno 2dko 2h5i 2h5j 2h65 2j30 2j31 2j32 2j33 2xyg 2xyh 2xyp 2xzd 2xzt 2y0b 3deh 3dei 3dej 3dek 3edq 3gjq 3gjr 3gjs 3gjt 3h0e 3itn 3kjf 3pcx 3pd0 3pd1 4dcj 4dco 4dcp 4eha 4ehd 4ehf 4ehh 4ehk 4ehl 4ehn 4jje 4jqy 4jqz 4pry 4ps0 4qtx 4qty 4qu0 4qu5 4qu8 4qu9 4qua 4qub 4qud 4que 4qug 4quh 4qui 4quj 4qul 5i9b 5i9t 5iab 5iae 5iag 5iaj 5iak 5ian 5iar 5ias 5ibc 5ibp 5ibr 5ic4

(-) Related Entries Specified in the PDB File

4jqy 4jqz 4jr1 4jr2