2QLF - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF CASPASE-7 WITH INHIBITOR AC-DNLD-CHO

Authors :   J. Agniswamy, B. Fang, I. Weber

Date :   12 Jul 07 (Deposition) - 28 Aug 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Cysteine Protease, Apoptosis, Thiol Protease, Zymogen, Hydrolase- Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Agniswamy, B. Fang, I. T. Weber
Plasticity Of S2-S4 Specificity Pockets Of Executioner Caspase-7 Revealed By Structural And Kinetic Analysis.
Febs J. V. 274 4752 2007
PubMed-ID: 17697120 | Reference-DOI: 10.1111/J.1742-4658.2007.05994.X

Molecule 1 - CASPASE-7
	Chains	:	A, C
	EC Number	:	3.4.22.60
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET23B
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	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

Molecule 2 - CASPASE-7
	Chains	:	B, D
	EC Number	:	3.4.22.60
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET23B
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	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

Molecule 3 - INHIBITOR AC-DNLD-CHO
	Chains	:	E, F
	Engineered	:	YES
	Synthetic	:	YES

Molecule 4 - PEPTIDE QGHGE
	Chains	:	G
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4	5	6	7
Asymmetric/Biological Unit	:	A	B	C	D	E	F	G

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	ACE	2	Mod. Amino Acid	ACETYL GROUP
2	ASJ	2	Mod. Amino Acid	(3S)-3-AMINO-4-HYDROXYBUTANOIC ACID

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:87 , HIS A:144 , GLY A:145 , GLN A:184 , CYS A:186 , HOH B:38 , TYR B:230 , SER B:231 , TRP B:232 , ARG B:233 , SER B:234 , PRO B:235 , SER B:275 , GLN B:276 , PHE B:282 , HOH E:53	BINDING SITE FOR CHAIN E OF INHIBITOR AC-DNLD-CHO
2	AC2	SOFTWARE	ARG C:387 , HIS C:444 , GLY C:445 , GLN C:484 , CYS C:486 , HOH D:8 , TYR D:530 , SER D:531 , TRP D:532 , ARG D:533 , PRO D:535 , SER D:575 , GLN D:576	BINDING SITE FOR CHAIN F OF INHIBITOR AC-DNLD-CHO
3	AC3	SOFTWARE	GLN A:59 , GLN B:260 , TYR B:300 , GLN B:303 , GLN C:359 , GLN D:560 , TYR D:600 , SER D:602	BINDING SITE FOR CHAIN G OF PEPTIDE QGHGE

(no "SS Bond" information available for 2QLF)

(no "Cis Peptide Bond" information available for 2QLF)

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:58-83 - C:357-383 -	26 - 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:139
 aligned with CASP7_HUMAN | P55210 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:139
                                    67        77        87        97       107       117       127       137       147       157       167       177       187         
          CASP7_HUMAN    58 YQYNMNFEKLGKCIIINNKNFDKVTGMGVRNGTDKDAEALFKCFRSLGFDVIVYNDCSCAKMQDLLKKASEEDHTNAACFACILLSHGEENVIYGKDGVTPIKDLTAHFRGDRCKTLLEKPKLFFIQACRGTELDDGIQ 196
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qlfA00 A:58-196  [code=3.40.50.1460, no name defined]                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeee..............hhhhhhhhhhhhhhhhheeeeeee..hhhhhhhhhhhhhh.....eeeeeeeee..ee..eeee..eeeehhhhhhhhhhhhhhhhh...eeeeee...eee...... 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:58-83   ------------------------------------------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)
                 2qlf A  58 YQYNMNFEKLGKCIIINNKNFDKVTGMGVRNGTDKDAEALFKCFRSLGFDVIVYNDCSCAKMQDLLKKASEEDHTNAACFACILLSHGEENVIYGKDGVTPIKDLTAHFRGDRCKTLLEKPKLFFIQACRGTELDDGIQ 196
                                    67        77        87        97       107       117       127       137       147       157       167       177       187

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....ee..eee...eehhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhh......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)
                 2qlf 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 2qlfC00 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....eeehhhhhhh.....hhhhh...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)
                 2qlf 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 (1) Peptidase_C14-2qlfD01 D:511-601                                                            -- Pfam domains (1)
           Pfam domains (2) Peptidase_C14-2qlfD02 D:511-601                                                            -- Pfam domains (2)
           Pfam domains (3) Peptidase_C14-2qlfD03 D:511-601                                                            -- Pfam domains (3)
           Pfam domains (4) Peptidase_C14-2qlfD04 D:511-601                                                            -- Pfam domains (4)
         Sec.struct. author ........eeeee....ee..eee...eehhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....hhhhh......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)
                 2qlf 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
                 2qlf E 701 xDNLx 705
                            |   |
                          701-ACE
                              705-ASJ

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
                 2qlf F 801 xDNLx 805
                            |   |
                            |   |
                          801-ACE
                              805-ASJ

Chain G from PDB  Type:PROTEIN  Length:5
                                     
               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
                 2qlf G 810 QGHGE 814

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 2QLF)

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	2qlfC00	C:357-496
1b	2qlfA00	A:58-196

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_CD (53)

Family: Peptidase_C14 (53)

Homo sapiens (Human) (51)

1a	Peptidase_C14-2qlfD01	D:511-601
1b	Peptidase_C14-2qlfD02	D:511-601
1c	Peptidase_C14-2qlfD03	D:511-601
1d	Peptidase_C14-2qlfD04	D:511-601

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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	2qlf
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

PROSITE Motifs (3, 6)

Exons (5, 12)

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