3IBC - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF CASPASE-7 INCOMPLEX WITH ACETYL-YVAD-CHO

Authors :   J. Agniswamy

Date :   15 Jul 09 (Deposition) - 01 Sep 09 (Release) - 10 Nov 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.75

Chains :   Asym./Biol. Unit : A,B,C,D,E,F

Keywords :   Protein-Peptide Complex, Alternative Splicing, Apoptosis, Cytoplasm, Hydrolase, Polymorphism, Protease, Thiol Protease, Zymogen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Agniswamy, B. Fang, I. T. Weber
Conformational Similarity In The Activation Of Caspase-3 And -7 Revealed By The Unliganded And Inhibited Structures Of Caspase-7.
Apoptosis V. 14 1135 2009
PubMed-ID: 19655253 | Reference-DOI: 10.1007/S10495-009-0388-9
(for further references see the PDB file header)

Molecule 1 - CASPASE-7
	Chains	:	A, C
	EC Number	:	3.4.22.60
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	P20 SUBUNIT
	Gene	:	CASP7, MCH3
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CASP-7, ICE-LIKE APOPTOTIC PROTEASE 3, ICE-LAP3, APOPTOTIC PROTEASE MCH-3, CMH-1, CASPASE-7 SUBUNIT P20, CASPASE-7 SUBUNIT P11

Molecule 2 - CASPASE-7
	Chains	:	B, D
	EC Number	:	3.4.22.60
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	P10 SUBUNIT
	Gene	:	CASP7, MCH3
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CASP-7, ICE-LIKE APOPTOTIC PROTEASE 3, ICE-LAP3, APOPTOTIC PROTEASE MCH-3, CMH-1, CASPASE-7 SUBUNIT P20, CASPASE-7 SUBUNIT P11

Molecule 3 - ACETYL-YVAD-CHO
	Chains	:	E, F
	Engineered	:	YES
	Other Details	:	THE PEPTIDE WAS OBTAINED BY CHEMICAL SYNTHESIS.
	Synthetic	:	YES

		1	2	3	4	5	6
Asymmetric/Biological Unit	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	ACE	2	Mod. Amino Acid	ACETYL GROUP

(no "Site" information available for 3IBC)

(no "SS Bond" information available for 3IBC)

(no "Cis Peptide Bond" information available for 3IBC)

Asymmetric/Biological Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_048618	D	255	E	CASP7_HUMAN	Polymorphism	2227310	B D	D	255 555	E

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CASPASE_P20	PS50208	Caspase family p20 domain profile.	CASP7_HUMAN	66-190	2	A:66-190 C:366-490
2	CASPASE_HIS	PS01121	Caspase family histidine active site.	CASP7_HUMAN	131-145	2	A:131-145 C:431-445
3	CASPASE_CYS	PS01122	Caspase family cysteine active site.	CASP7_HUMAN	177-188	2	A:177-188 C:477-488

Asymmetric/Biological Unit (5, 12)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2c	ENST00000369318	2c	ENSE00001832746	chr10:115439636-115439737	102	CASP7_HUMAN	-	0	0	-	-
1.4b	ENST00000369318	4b	ENSE00001749353	chr10:115457253-115457362	110	CASP7_HUMAN	1-37	37	0	-	-
1.6b	ENST00000369318	6b	ENSE00001096780	chr10:115480791-115480927	137	CASP7_HUMAN	37-83	47	2	A:57-83 - C:357-383 -	27 - 27 -
1.7d	ENST00000369318	7d	ENSE00001096775	chr10:115481410-115481538	129	CASP7_HUMAN	83-126	44	2	A:83-126 - C:383-426 -	44 - 44 -
1.8c	ENST00000369318	8c	ENSE00001096779	chr10:115485121-115485296	176	CASP7_HUMAN	126-184	59	2	A:126-184 - C:426-484 -	59 - 59 -
1.10b	ENST00000369318	10b	ENSE00001656181	chr10:115486064-115486193	130	CASP7_HUMAN	185-228	44	4	A:185-196 B:212-228 C:485-496 D:511-528	12 17 12 18
1.11c	ENST00000369318	11c	ENSE00001591443	chr10:115489070-115490662	1593	CASP7_HUMAN	228-303	76	2	- B:228-303 - D:528-603	- 76 - 76

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:140
 aligned with CASP7_HUMAN | P55210 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:140
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196
          CASP7_HUMAN    57 TYQYNMNFEKLGKCIIINNKNFDKVTGMGVRNGTDKDAEALFKCFRSLGFDVIVYNDCSCAKMQDLLKKASEEDHTNAACFACILLSHGEENVIYGKDGVTPIKDLTAHFRGDRCKTLLEKPKLFFIQACRGTELDDGIQ 196
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ibcA00 A:57-196  [code=3.40.50.1460, no name defined]                                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeee....hhhhh.....hhhhhhhhhhhhhhhhheeeeeee..hhhhhhhhhhhhhh........eeeeee..ee..eee....eeehhhhhhh.....hhhhh...eeeeee............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------CASPASE_P20  PDB: A:66-190 UniProt: 66-190                                                                                   ------ PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------CASPASE_HIS    -------------------------------CASPASE_CYS -------- PROSITE (2)
           Transcript 1 (1) Exon 1.6b  PDB: A:57-83    ------------------------------------------Exon 1.8c  PDB: A:126-184 UniProt: 126-184                 Exon 1.10b   Transcript 1 (1)
           Transcript 1 (2) --------------------------Exon 1.7d  PDB: A:83-126 UniProt: 83-126    ---------------------------------------------------------------------- Transcript 1 (2)
                 3ibc A  57 TYQYNMNFEKLGKCIIINNKNFDKVTGMGVRNGTDKDAEALFKCFRSLGFDVIVYNDCSCAKMQDLLKKASEEDHTNAACFACILLSHGEENVIYGKDGVTPIKDLTAHFRGDRCKTLLEKPKLFFIQACRGTELDDGIQ 196
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196

Chain B from PDB  Type:PROTEIN  Length:92
 aligned with CASP7_HUMAN | P55210 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:92
                                   221       231       241       251       261       271       281       291       301  
          CASP7_HUMAN   212 KIPVEADFLFAYSTVPGYYSWRSPGRGSWFVQALCSILEEHGKDLEIMQILTRVNDRVARHFESQSDDPHFHEKKQIPCVVSMLTKELYFSQ 303
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee........eee...eehhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..................eeee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.10b       --------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------Exon 1.11c  PDB: B:228-303 UniProt: 228-303                                  Transcript 1 (2)
                 3ibc B 212 KIPVEADFLFAYSTVPGYYSWRSPGRGSWFVQALCSILEEHGKDLEIMQILTRVNDRVARHFESQSDDPHFHEKKQIPCVVSMLTKELYFSQ 303
                                   221       231       241       251       261       271       281       291       301

Chain C from PDB  Type:PROTEIN  Length:140
 aligned with CASP7_HUMAN | P55210 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:140
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196
          CASP7_HUMAN    57 TYQYNMNFEKLGKCIIINNKNFDKVTGMGVRNGTDKDAEALFKCFRSLGFDVIVYNDCSCAKMQDLLKKASEEDHTNAACFACILLSHGEENVIYGKDGVTPIKDLTAHFRGDRCKTLLEKPKLFFIQACRGTELDDGIQ 196
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ibcC00 C:357-496  [code=3.40.50.1460, no name defined]                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeee....hhhhh.....hhhhhhhhhhhhhhhhheeeeeee..hhhhhhhhhhhhhhh.......eeeeee..ee..eee....eeehhhhhhhhhhhhhhhhh...eeeeee...eee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------CASPASE_P20  PDB: C:366-490 UniProt: 66-190                                                                                  ------ PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------CASPASE_HIS    -------------------------------CASPASE_CYS -------- PROSITE (2)
           Transcript 1 (1) Exon 1.6b  PDB: C:357-383  ------------------------------------------Exon 1.8c  PDB: C:426-484 UniProt: 126-184                 Exon 1.10b   Transcript 1 (1)
           Transcript 1 (2) --------------------------Exon 1.7d  PDB: C:383-426 UniProt: 83-126   ---------------------------------------------------------------------- Transcript 1 (2)
                 3ibc C 357 TYQYNMNFEKLGKCIIINNKNFDKVTGMGVRNGTDKDAEALFKCFRSLGFDVIVYNDCSCAKMQDLLKKASEEDHTNAACFACILLSHGEENVIYGKDGVTPIKDLTAHFRGDRCKTLLEKPKLFFIQACRGTELDDGIQ 496
                                   366       376       386       396       406       416       426       436       446       456       466       476       486       496

Chain D from PDB  Type:PROTEIN  Length:93
 aligned with CASP7_HUMAN | P55210 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:93
                                   220       230       240       250       260       270       280       290       300   
          CASP7_HUMAN   211 YKIPVEADFLFAYSTVPGYYSWRSPGRGSWFVQALCSILEEHGKDLEIMQILTRVNDRVARHFESQSDDPHFHEKKQIPCVVSMLTKELYFSQ 303
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee....ee..eee...eehhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..................eeee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------E------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.10b        --------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------Exon 1.11c  PDB: D:528-603 UniProt: 228-303                                  Transcript 1 (2)
                 3ibc D 511 YKIPVEADFLFAYSTVPGYYSWRSPGRGSWFVQALCSILEEHGKDLEIMQILTRVNDRVARHFESQSDDPHFHEKKQIPCVVSMLTKELYFSQ 603
                                   520       530       540       550       560       570       580       590       600

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
                 3ibc E 701 xYVAD 705
                            |    
                          701-ACE

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
                 3ibc F 801 xYVAD 805
                            |    
                            |    
                          801-ACE

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 '\|'

(no "SCOP Domain" information available for 3IBC)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1460, no name defined] (93)

Human (Homo sapiens) (87)

1a	3ibcA00	A:57-196
1b	3ibcC00	C:357-496

(no "Pfam Domain" information available for 3IBC)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (CASP7_HUMAN | P55210)

molecular function
	GO:0004197	cysteine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
	GO:0097200	cysteine-type endopeptidase activity involved in execution phase of apoptosis	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile, and contributing to the execution phase of apoptosis.
	GO:0008234	cysteine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0008635	activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c	Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process and is mediated by cytochrome c.
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0006921	cellular component disassembly involved in execution phase of apoptosis	The breakdown of structures such as organelles, proteins, or other macromolecular structures during apoptosis.
	GO:0097194	execution phase of apoptosis	A stage of the apoptotic process that starts with the controlled breakdown of the cell through the action of effector caspases or other effector molecules (e.g. cathepsins, calpains etc.). Key steps of the execution phase are rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric/Biological Unit
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Description

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Ligands, Modified Residues, Ions (1, 2)

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