3P4U - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ACTIVE CASPASE-6 IN COMPLEX WITH AC-VEID-CHO INHIBITOR

Authors :   I. Mueller, M. B. A. C. Lamers, A. J. Ritchie, C. Dominguez, I. Munoz, M. M A. Kiselyov

Date :   07 Oct 10 (Deposition) - 28 Sep 11 (Release) - 02 Dec 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,E  (1x)
Biol. Unit 2: C,D,F  (1x)

Keywords :   Protease, Caspase, Huntington'S Disease, Competitive Inhibition, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. Mueller, M. B. A. C. Lamers, A. J. Ritchie, C. Dominguez, I. Munoz, M. Maillard, A. Kiselyov
Crystal Structures Of Active And Inhibitor-Bound Human Casp
To Be Published
PubMed: search

Molecule 1 - CASPASE-6
	Chains	:	A, C
	EC Number	:	3.4.22.59
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	ROSETTA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP REISIDUES 24-179
	Gene	:	CASP6, MCH2
	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

Molecule 2 - CASPASE-6
	Chains	:	B, D
	EC Number	:	3.4.22.59
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	ROSETTA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 193-293
	Gene	:	CASP6, MCH2
	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

Molecule 3 - AC-VEID-CHO INHIBITOR
	Chains	:	E, F
	Engineered	:	YES
	Other Details	:	SYNTHETIC CONSTRUCT
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 12)

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
3	CAS	8	Mod. Amino Acid	S-(DIMETHYLARSENIC)CYSTEINE

Biological Unit 1 (3, 6)

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

Biological Unit 2 (3, 6)

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

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:64 , ARG A:65 , HIS A:121 , GLY A:122 , GLN A:161 , CYS A:163 , TYR B:217 , SER B:218 , HIS B:219 , ARG B:220 , GLU B:221 , THR B:222 , CAS B:264	BINDING SITE FOR CHAIN E OF AC-VEID-CHO
2	AC2	SOFTWARE	ARG C:64 , HIS C:121 , GLN C:161 , CYS C:163 , HOH C:311 , TYR D:217 , SER D:218 , HIS D:219 , ARG D:220 , GLU D:221 , THR D:222 , CAS D:264 , HOH D:422	BINDING SITE FOR CHAIN F OF AC-VEID-CHO

(no "SS Bond" information available for 3P4U)

(no "Cis Peptide Bond" information available for 3P4U)

Asymmetric Unit (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_029242	E	35	K	CASP6_HUMAN	Polymorphism	11574697	A/C	E	35	K
2	UniProt	VAR_016130	A	109	T	CASP6_HUMAN	Polymorphism	5030674	A/C	A	109	T

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

Biological Unit 1 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_029242	E	35	K	CASP6_HUMAN	Polymorphism	11574697	A	E	35	K
2	UniProt	VAR_016130	A	109	T	CASP6_HUMAN	Polymorphism	5030674	A	A	109	T

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

Biological Unit 2 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_029242	E	35	K	CASP6_HUMAN	Polymorphism	11574697	C	E	35	K
2	UniProt	VAR_016130	A	109	T	CASP6_HUMAN	Polymorphism	5030674	C	A	109	T

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

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CASPASE_P20	PS50208	Caspase family p20 domain profile.	CASP6_HUMAN	43-167	2	A:43-167 C:43-167
2	CASPASE_HIS	PS01121	Caspase family histidine active site.	CASP6_HUMAN	108-122	2	A:108-122 C:108-122
3	CASPASE_CYS	PS01122	Caspase family cysteine active site.	CASP6_HUMAN	154-165	2	A:154-165 C:154-165

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CASPASE_P20	PS50208	Caspase family p20 domain profile.	CASP6_HUMAN	43-167	1	A:43-167 -
2	CASPASE_HIS	PS01121	Caspase family histidine active site.	CASP6_HUMAN	108-122	1	A:108-122 -
3	CASPASE_CYS	PS01122	Caspase family cysteine active site.	CASP6_HUMAN	154-165	1	A:154-165 -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CASPASE_P20	PS50208	Caspase family p20 domain profile.	CASP6_HUMAN	43-167	1	- C:43-167
2	CASPASE_HIS	PS01121	Caspase family histidine active site.	CASP6_HUMAN	108-122	1	- C:108-122
3	CASPASE_CYS	PS01122	Caspase family cysteine active site.	CASP6_HUMAN	154-165	1	- C:154-165

Asymmetric Unit (5, 12)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000265164	1b	ENSE00001018825	chr4:110624629-110624512	118	CASP6_HUMAN	1-14	14	0	-	-
1.3	ENST00000265164	3	ENSE00000935048	chr4:110619498-110619456	43	CASP6_HUMAN	14-28	15	0	-	-
1.4b	ENST00000265164	4b	ENSE00000935047	chr4:110618924-110618778	147	CASP6_HUMAN	28-77	50	2	A:31-77 - C:31-77 -	47 - 47 -
1.5b	ENST00000265164	5b	ENSE00000935046	chr4:110617642-110617566	77	CASP6_HUMAN	77-103	27	2	A:77-103 - C:77-103 -	27 - 27 -
1.6c	ENST00000265164	6c	ENSE00000935045	chr4:110615856-110615681	176	CASP6_HUMAN	103-161	59	2	A:103-161 - C:103-161 -	59 - 59 -
1.7c	ENST00000265164	7c	ENSE00000935044	chr4:110612165-110612006	160	CASP6_HUMAN	162-215	54	4	A:162-175 B:198-215 C:162-175 D:198-215	14 18 14 18
1.8d	ENST00000265164	8d	ENSE00001820381	chr4:110610724-110609898	827	CASP6_HUMAN	215-293	79	2	- B:215-291 - D:215-291	- 77 - 77

Asymmetric 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:145
 aligned with CASP6_HUMAN | P55212 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:145
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170     
          CASP6_HUMAN    31 FDPAEKYKMDHRRRGIALIFNHERFFWHLTLPERRGTCADRDNLTRRFSDLGFEVKCFNDLKAEELLLKIHEVSTVSHADADCFVCVFLSHGEGNHIYAYDAKIEIQTLTGLFKGDKCHSLVGKPKIFIIQACRGNQHDVPVIPL 175
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeeee....hhhhh.....hhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh.......eeeeee..ee..eee....eeehhhhhhh.....hhhhh...eeeeee.........ee... Sec.struct. author
                 SAPs(SNPs) ----K-------------------------------------------------------------------------T------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ------------CASPASE_P20  PDB: A:43-167 UniProt: 43-167                                                                                   -------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------CASPASE_HIS    -------------------------------CASPASE_CYS ---------- PROSITE (2)
           Transcript 1 (1) Exon 1.4b  PDB: A:31-77 UniProt: 28-77         -------------------------Exon 1.6c  PDB: A:103-161 UniProt: 103-161                 Exon 1.7c      Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------Exon 1.5b  PDB: A:77-103   ------------------------------------------------------------------------ Transcript 1 (2)
                 3p4u A  31 FDPAEKYKMDHRRRGIALIFNHERFFWHLTLPERRGTcADRDNLTRRFSDLGFEVKcFNDLKAEELLLKIHEVSTVSHADADCFVCVFLSHGEGNHIYAYDAKIEIQTLTGLFKGDKCHSLVGKPKIFIIQACRGNQHDVPVIPL 175
                                    40        50        60       |70        80      | 90       100       110       120       130       140       150       160       170     
                                                                68-CAS             87-CAS

Chain B from PDB  Type:PROTEIN  Length:94
 aligned with CASP6_HUMAN | P55212 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:94
                                   207       217       227       237       247       257       267       277       287    
          CASP6_HUMAN   198 YTLPAGADFLMCYSVAEGYYSHRETVNGSWYIQDLCEMLGKYGSSLEFTELLTLVNRKVSQRRVDFCKDPSAIGKKQVPCFASMLTKKLHFFPK 291
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....eeeee........eee...eehhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhh......eeee........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.7c         ---------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------Exon 1.8d  PDB: B:215-291 UniProt: 215-293 [INCOMPLETE]                       Transcript 1 (2)
                 3p4u B 198 YTLPAGADFLMCYSVAEGYYSHRETVNGSWYIQDLCEMLGKYGSSLEFTELLTLVNRKVSQRRVDFcKDPSAIGKKQVPcFASMLTKKLHFFPK 291
                                   207       217       227       237       247       257      |267       277       287    
                                                                                            264-CAS      277-CAS

Chain C from PDB  Type:PROTEIN  Length:145
 aligned with CASP6_HUMAN | P55212 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:145
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170     
          CASP6_HUMAN    31 FDPAEKYKMDHRRRGIALIFNHERFFWHLTLPERRGTCADRDNLTRRFSDLGFEVKCFNDLKAEELLLKIHEVSTVSHADADCFVCVFLSHGEGNHIYAYDAKIEIQTLTGLFKGDKCHSLVGKPKIFIIQACRGNQHDVPVIPL 175
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeeee....hhhhh.....hhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh.......eeeeee..ee..eee....eeehhhhhhhhh...hhhhh...eeeeee.........ee... Sec.struct. author
                 SAPs(SNPs) ----K-------------------------------------------------------------------------T------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ------------CASPASE_P20  PDB: C:43-167 UniProt: 43-167                                                                                   -------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------CASPASE_HIS    -------------------------------CASPASE_CYS ---------- PROSITE (2)
           Transcript 1 (1) Exon 1.4b  PDB: C:31-77 UniProt: 28-77         -------------------------Exon 1.6c  PDB: C:103-161 UniProt: 103-161                 Exon 1.7c      Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------Exon 1.5b  PDB: C:77-103   ------------------------------------------------------------------------ Transcript 1 (2)
                 3p4u C  31 FDPAEKYKMDHRRRGIALIFNHERFFWHLTLPERRGTcADRDNLTRRFSDLGFEVKcFNDLKAEELLLKIHEVSTVSHADADCFVCVFLSHGEGNHIYAYDAKIEIQTLTGLFKGDKCHSLVGKPKIFIIQACRGNQHDVPVIPL 175
                                    40        50        60       |70        80      | 90       100       110       120       130       140       150       160       170     
                                                                68-CAS             87-CAS

Chain D from PDB  Type:PROTEIN  Length:94
 aligned with CASP6_HUMAN | P55212 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:94
                                   207       217       227       237       247       257       267       277       287    
          CASP6_HUMAN   198 YTLPAGADFLMCYSVAEGYYSHRETVNGSWYIQDLCEMLGKYGSSLEFTELLTLVNRKVSQRRVDFCKDPSAIGKKQVPCFASMLTKKLHFFPK 291
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....eeeee........eee...eehhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhh......eeee........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.7c         ---------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------Exon 1.8d  PDB: D:215-291 UniProt: 215-293 [INCOMPLETE]                       Transcript 1 (2)
                 3p4u D 198 YTLPAGADFLMCYSVAEGYYSHRETVNGSWYIQDLCEMLGKYGSSLEFTELLTLVNRKVSQRRVDFcKDPSAIGKKQVPcFASMLTKKLHFFPK 291
                                   207       217       227       237       247       257      |267       277       287    
                                                                                            264-CAS      277-CAS

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
                 3p4u E 701 xVEIx 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
                 3p4u F 801 xVEIx 805
                            |   |
                            |   |
                          801-ACE
                              805-ASJ

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 3P4U)

(no "CATH Domain" information available for 3P4U)

(no "Pfam Domain" information available for 3P4U)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (CASP6_HUMAN | P55212)

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:0097153	cysteine-type endopeptidase activity involved in apoptotic process	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 apoptotic process.
	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:0004175	endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
	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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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: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:0030855	epithelial cell differentiation	The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0042981	regulation of apoptotic process	Any process that modulates the occurrence or rate of cell death by apoptotic process.
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.

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3p45	APO-CASPASE-6 AT PHYSIOLOGICAL PH

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 4)

PROSITE Motifs (3, 6)

Exons (5, 12)

Sequences/Alignments

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SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (16, 16)

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Related Entries

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Related Entries Specified in the PDB File