3S70 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF ACTIVE CASPASE-6 BOUND WITH AC-VEID-CHO SOLVED BY AS-SAD

Authors :   X. -D. Su, X. Liu, X. -J. Wang

Date :   26 May 11 (Deposition) - 11 Apr 12 (Release) - 11 Apr 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.62

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

Keywords :   Caspase-6, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Liu, H. Zhang, X. -J. Wang, L. -F. Li, X. -D. Su
Get Phases From Arsenic Anomalous Scattering: De Novo Sad Phasing Of Two Protein Structures Crystallized In Cacodylat Buffer
Plos One V. 6 24227 2011
PubMed-ID: 21912678 | Reference-DOI: 10.1371/JOURNAL.PONE.0024227

Molecule 1 - CASPASE-6
	Chains	:	A, C
	EC Number	:	3.4.22.59
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21B
	Expression System Strain	:	ROSETTA(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CASP6
	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 - ALDEHYDE INHIBITOR AC-VEID-CHO
	Chains	:	B, D
	Engineered	:	YES
	Other Details	:	CHEMICALLY SYNTHESIZED
	Synthetic	:	YES

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 14)

No.	Name	Count	Type	Full Name
1	ACE	2	Mod. Amino Acid	ACETYL GROUP
2	ACT	1	Ligand/Ion	ACETATE ION
3	ASA	2	Mod. Amino Acid	ASPARTIC ALDEHYDE
4	CAC	8	Ligand/Ion	CACODYLATE ION
5	MG	1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:264 , VAL B:1	BINDING SITE FOR RESIDUE CAC A 2
02	AC2	SOFTWARE	ARG A:164 , TYR A:210 , GLU A:214 , CYS A:277 , ALA A:279 , HOH A:464 , ALA C:279	BINDING SITE FOR RESIDUE CAC A 3
03	AC3	SOFTWARE	THR A:75 , VAL A:85 , CYS A:87 , CAC C:5	BINDING SITE FOR RESIDUE CAC A 6
04	AC4	SOFTWARE	ASN A:51 , CYS A:68 , ARG A:71 , ASN A:89 , GLU C:53 , ARG C:54 , ASP C:90	BINDING SITE FOR RESIDUE CAC A 7
05	AC5	SOFTWARE	ARG A:71 , GLU C:53 , ARG C:65 , GLY C:66 , HOH C:312 , HOH C:369 , HOH C:395	BINDING SITE FOR RESIDUE ACT A 1
06	AC6	SOFTWARE	ARG A:260 , HOH A:368 , ARG C:260	BINDING SITE FOR RESIDUE MG A 302
07	AC7	SOFTWARE	ALA A:279 , ARG C:164 , TYR C:210 , GLU C:214 , CYS C:277 , ALA C:279 , HOH C:410	BINDING SITE FOR RESIDUE CAC C 1
08	AC8	SOFTWARE	CYS C:264 , VAL D:1	BINDING SITE FOR RESIDUE CAC C 4
09	AC9	SOFTWARE	CAC A:6 , ASP A:72 , CYS C:68 , ALA C:69 , ASP C:72	BINDING SITE FOR RESIDUE CAC C 5
10	BC1	SOFTWARE	THR C:75 , VAL C:85 , CYS C:87	BINDING SITE FOR RESIDUE CAC C 8
11	BC2	SOFTWARE	CAC A:2 , ARG A:64 , HIS A:121 , GLN A:161 , CYS A:163 , TYR A:217 , SER A:218 , HIS A:219 , ARG A:220 , GLU A:221 , THR A:222 , HOH A:407 , HOH A:536 , HOH B:172 , HOH B:203 , HOH B:469 , HOH B:520 , HOH B:611 , HOH B:627	BINDING SITE FOR CHAIN B OF ALDEHYDE INHIBITOR AC-VEID-CHO
12	BC3	SOFTWARE	CAC C:4 , ARG C:64 , HIS C:121 , GLY C:122 , GLN C:161 , CYS C:163 , TYR C:217 , SER C:218 , HIS C:219 , ARG C:220 , GLU C:221 , THR C:222 , HOH D:109 , HOH D:156 , HOH D:194 , HOH D:305 , HOH D:375 , HOH D:495 , HOH D:534 , HOH D:598 , HOH D:675 , HOH D:677	BINDING SITE FOR CHAIN D OF ALDEHYDE INHIBITOR AC-VEID-CHO

(no "SS Bond" information available for 3S70)

(no "Cis Peptide Bond" information available for 3S70)

Asymmetric/Biological 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)

Asymmetric/Biological Unit (4, 8)

	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
4	CASPASE_P10	PS50207	Caspase family p10 domain profile.	CASP6_HUMAN	196-290	2	A:197-290 C:198-290

Asymmetric/Biological Unit (5, 10)

	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	2	A:162-215 (gaps) C:162-215 (gaps)	54 54
1.8d	ENST00000265164	8d	ENSE00001820381	chr4:110610724-110609898	827	CASP6_HUMAN	215-293	79	2	A:215-292 C:215-291	78 77

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:241
 aligned with CASP6_HUMAN | P55212 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:262
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290  
          CASP6_HUMAN    31 FDPAEKYKMDHRRRGIALIFNHERFFWHLTLPERRGTCADRDNLTRRFSDLGFEVKCFNDLKAEELLLKIHEVSTVSHADADCFVCVFLSHGEGNHIYAYDAKIEIQTLTGLFKGDKCHSLVGKPKIFIIQACRGNQHDVPVIPLDVVDNQTEKLDTNITEVDAASVYTLPAGADFLMCYSVAEGYYSHRETVNGSWYIQDLCEMLGKYGSSLEFTELLTLVNRKVSQRRVDFCKDPSAIGKKQVPCFASMLTKKLHFFPKS 292
               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...---------------------...ee....eeeee........eee...eehhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhh......eeee............ Sec.struct. author
                 SAPs(SNPs) ----K-------------------------------------------------------------------------T--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------CASPASE_P20  PDB: A:43-167 UniProt: 43-167                                                                                   ----------------------------CASPASE_P10  PDB: A:197-290 UniProt: 196-290                                                   -- 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  PDB: A:162-215 (gaps) UniProt: 162-215     ----------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------Exon 1.5b  PDB: A:77-103   ---------------------------------------------------------------------------------------------------------------Exon 1.8d  PDB: A:215-292 UniProt: 215-293 [INCOMPLETE]                        Transcript 1 (2)
                 3s70 A  31 FDPAEKYKMDHRRRGIALIFNHERFFWHLTLPERRGTCADRDNLTRRFSDLGFEVKCFNDLKAEELLLKIHEVSTVSHADADCFVCVFLSHGEGNHIYAYDAKIEIQTLTGLFKGDKCHSLVGKPKIFIIQACRGNQHDVPVIPL---------------------VYTLPAGADFLMCYSVAEGYYSHRETVNGSWYIQDLCEMLGKYGSSLEFTELLTLVNRKVSQRRVDFCKDPSAIGKKQVPCFASMLTKKLHFFPKS 292
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170    |    -         -      |200       210       220       230       240       250       260       270       280       290  
                                                                                                                                                                          175                   197

Chain B 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
                 3s70 B   0 xVEId   4
                            |   |
                            0-ACE
                                4-ASA

Chain C from PDB  Type:PROTEIN  Length:239
 aligned with CASP6_HUMAN | P55212 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:261
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290 
          CASP6_HUMAN    31 FDPAEKYKMDHRRRGIALIFNHERFFWHLTLPERRGTCADRDNLTRRFSDLGFEVKCFNDLKAEELLLKIHEVSTVSHADADCFVCVFLSHGEGNHIYAYDAKIEIQTLTGLFKGDKCHSLVGKPKIFIIQACRGNQHDVPVIPLDVVDNQTEKLDTNITEVDAASVYTLPAGADFLMCYSVAEGYYSHRETVNGSWYIQDLCEMLGKYGSSLEFTELLTLVNRKVSQRRVDFCKDPSAIGKKQVPCFASMLTKKLHFFPK 291
               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...----------------------..ee....eeeee........eee...eehhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhh......eeee........... Sec.struct. author
                 SAPs(SNPs) ----K-------------------------------------------------------------------------T-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------CASPASE_P20  PDB: C:43-167 UniProt: 43-167                                                                                   ----------------------------CASPASE_P10  PDB: C:198-290 UniProt: 196-290                                                   - 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  PDB: C:162-215 (gaps) UniProt: 162-215     ---------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------Exon 1.5b  PDB: C:77-103   ---------------------------------------------------------------------------------------------------------------Exon 1.8d  PDB: C:215-291 UniProt: 215-293 [INCOMPLETE]                       Transcript 1 (2)
                 3s70 C  31 FDPAEKYKMDHRRRGIALIFNHERFFWHLTLPERRGTCADRDNLTRRFSDLGFEVKCFNDLKAEELLLKIHEVSTVSHADADCFVCVFLSHGEGNHIYAYDAKIEIQTLTGLFKGDKCHSLVGKPKIFIIQACRGNQHDVPVIPL----------------------YTLPAGADFLMCYSVAEGYYSHRETVNGSWYIQDLCEMLGKYGSSLEFTELLTLVNRKVSQRRVDFCKDPSAIGKKQVPCFASMLTKKLHFFPK 291
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170    |    -         -       200       210       220       230       240       250       260       270       280       290 
                                                                                                                                                                          175                    198

Chain D 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
                 3s70 D   0 xVEId   4
                            |   |
                            |   |
                            0-ACE
                                4-ASA

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 3S70)

(no "CATH Domain" information available for 3S70)

(no "Pfam Domain" information available for 3S70)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,C (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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
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	3s70
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(no "Related Entries Specified in the PDB File" available for 3S70)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 14)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 4)

PROSITE Motifs (4, 8)

Exons (5, 10)

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Gene Ontology (16, 16)

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