4JJ8 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CASPASE-3 SPECIFIC UNNATURAL AMINO ACID PEPTIDES

Authors :   C. J. Vickers, G. E. Gonzalez-Paez, D. W. Wolan

Date :   07 Mar 13 (Deposition) - 12 Jun 13 (Release) - 19 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.94

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

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

Reference :   C. J. Vickers, G. E. Gonzalez-Paez, D. W. Wolan
Selective Detection Of Caspase-3 Versus Caspase-7 Using Activity-Based Probes With Key Unnatural Amino Acids.
Acs Chem. Biol. V. 8 1558 2013
PubMed-ID: 23614665 | Reference-DOI: 10.1021/CB400209W

Molecule 1 - CASPASE-7
	Chains	:	A, B
	EC Number	:	3.4.22.60
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET23B
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	CASP7, CASPASE-7 MCH-3, MCH3
	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 SUBUNIT P20, CASPASE-7 SUBUNIT P11

Molecule 2 - CASPASE INHIBITOR
	Chains	:	C, D
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 10)

No.	Name	Count	Type	Full Name
1	1MH	2	Mod. Amino Acid	3-PYRIDIN-3-YL-L-ALANINE
2	1U8	2	Mod. Amino Acid	(3S)-3-AMINO-5-[(2,6-DIMETHYLBENZOYL)OXY]-4-OXOPENTANOIC ACID
3	ACE	2	Mod. Amino Acid	ACETYL GROUP
4	B3L	2	Mod. Amino Acid	(3S)-3-AMINO-5-METHYLHEXANOIC ACID
5	HLX	2	Mod. Amino Acid	5-METHYL-L-NORLEUCINE

Biological Unit 1 (5, 5)

No.	Name	Count	Type	Full Name
1	1MH	1	Mod. Amino Acid	3-PYRIDIN-3-YL-L-ALANINE
2	1U8	1	Mod. Amino Acid	(3S)-3-AMINO-5-[(2,6-DIMETHYLBENZOYL)OXY]-4-OXOPENTANOIC ACID
3	ACE	1	Mod. Amino Acid	ACETYL GROUP
4	B3L	1	Mod. Amino Acid	(3S)-3-AMINO-5-METHYLHEXANOIC ACID
5	HLX	1	Mod. Amino Acid	5-METHYL-L-NORLEUCINE

Biological Unit 2 (5, 5)

No.	Name	Count	Type	Full Name
1	1MH	1	Mod. Amino Acid	3-PYRIDIN-3-YL-L-ALANINE
2	1U8	1	Mod. Amino Acid	(3S)-3-AMINO-5-[(2,6-DIMETHYLBENZOYL)OXY]-4-OXOPENTANOIC ACID
3	ACE	1	Mod. Amino Acid	ACETYL GROUP
4	B3L	1	Mod. Amino Acid	(3S)-3-AMINO-5-METHYLHEXANOIC ACID
5	HLX	1	Mod. Amino Acid	5-METHYL-L-NORLEUCINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:87 , HIS A:144 , GLY A:145 , GLN A:184 , CYS A:186 , TYR A:230 , SER A:231 , ARG A:233 , PRO A:235 , PHE A:282	BINDING SITE FOR CHAIN C OF CASPASE INHIBITOR
2	AC2	SOFTWARE	ARG B:87 , ASN B:88 , 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 , PHE B:282	BINDING SITE FOR CHAIN D OF CASPASE INHIBITOR

(no "SS Bond" information available for 4JJ8)

(no "Cis Peptide Bond" information available for 4JJ8)

(no "SAP(SNP)/Variant" information available for 4JJ8)

(no "PROSITE Motif" information available for 4JJ8)

(no "Exon" information available for 4JJ8)

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:231
                                                                                                                                                                                                                                                                       
               SCOP domains d4jj8a_ A: automated matches                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeee....hhhhh.....hhhhhhhhhhhhhhhhh.eeeeee..hhhhhhhhhhhhhhh....eeeeeeeee..ee..eee....eeehhhhhhhhh...hhhhh...eeeeee...eee.............eeeee....ee...ee...eehhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....hhhhh......eeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jj8 A  57 TYQYNMNFEKLGKCIIINNKNFDKVTGMGVRNGTDKDAEALFKCFRSLGFDVIVYNDCSCAKMQDLLKKASEEDHTNAACFACILLSHGEENVIYGKDGVTPIKDLTAHFRGDRCKTLLEKPKLFFIQACRGTELDDGIQKIPVEADFLFAYSTVPGYYSWRSPGRGSWFVQALCSILEEHGKDLEIMQILTRVNDRVARHFESQSDDPHFHEKKQIPCVVSMLTKELYFS 302
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196|      221       231       241       251       261       271       281       291       301 
                                                                                                                                                                     196|                                                                                          
                                                                                                                                                                      212

Chain B from PDB  Type:PROTEIN  Length:231
                                                                                                                                                                                                                                                                       
               SCOP domains d4jj8b_ B: automated matches                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeee....hhhhh.....hhhhhhhhhhhhhhhhh.eeeeee..hhhhhhhhhhhhhh.....eeeeeeeee..ee..eee....eeehhhhhhhhh...hhhhh...eeeeee...eee.............eeeee....ee...ee...eehhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....hhhhh......eeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jj8 B  57 TYQYNMNFEKLGKCIIINNKNFDKVTGMGVRNGTDKDAEALFKCFRSLGFDVIVYNDCSCAKMQDLLKKASEEDHTNAACFACILLSHGEENVIYGKDGVTPIKDLTAHFRGDRCKTLLEKPKLFFIQACRGTELDDGIQKIPVEADFLFAYSTVPGYYSWRSPGRGSWFVQALCSILEEHGKDLEIMQILTRVNDRVARHFESQSDDPHFHEKKQIPCVVSMLTKELYFS 302
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196|      221       231       241       251       261       271       281       291       301 
                                                                                                                                                                     196|                                                                                          
                                                                                                                                                                      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
                 4jj8 C 701 xxDxxx 706
                            || |||
                          701-ACE|
                           702-1MH
                             704-B3L
                              705-HLX
                               706-1U8

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
                 4jj8 D 801 xxDxxx 806
                            || |||
                            || |||
                          801-ACE|
                           802-1MH
                             804-B3L
                              805-HLX
                               806-1U8

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Caspase-like (92)

Superfamily: Caspase-like (92)

Family: Caspase catalytic domain (76)

Protein domain: automated matches (12)

Human (Homo sapiens) [TaxId: 9606] (11)

1a	d4jj8a_	A:
1b	d4jj8b_	B:

(no "CATH Domain" information available for 4JJ8)

(no "Pfam Domain" information available for 4JJ8)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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		HLX	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4jj8)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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1f1j	CRYSTAL STRUCTURE OF CASPASE-7 IN COMPLEX WITH ACETYL-ASP- GLU-VAL-ASP-CHO
2ql5	CRYSTAL STRUCTURE OF CASPASE-7 WITH INHIBITOR AC-DMQD-CHO
3ibc	CRYSTAL STRUCTURE OF CASPASE-7 INCOMPLEX WITH ACETYL-YVAD- CHO
4jj7	CASPASE-8 IN COMPLEX WITH CASPASE-3 SPECIFIC UNNATURAL AMINO ACID PEPTIDE
4jje

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 10)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (1, 2)

CATH Domains (0, 0)

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Gene Ontology (15, 15)

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