1ZIV - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CATALYTIC DOMAIN OF HUMAN CALPAIN-9

Authors :   J. R. Walker, T. Davis, E. M. Newman, F. Mackenzie, A. Dong, J. Choe, C. Arrowsmith, M. Sundstrom, A. Edwards, A. Bochkarev, S. Dhe- Paganon, Structural Genomics Consortium (Sgc)

Date :   27 Apr 05 (Deposition) - 05 Jul 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.31

Chains :   Asym./Biol. Unit : A

Keywords :   Cysteine Protease, Papain, Calcium-Dependent, Thiol Protease, Structural Genomics Consortium, Sgc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. L. Davis, J. R. Walker, P. J. Finerty, F. Mackenzie, E. M. Newman, S. Dhe-Paganon
The Crystal Structures Of Human Calpains 1 And 9 Imply Diverse Mechanisms Of Action And Auto-Inhibition.
J. Mol. Biol. V. 366 216 2007
PubMed-ID: 17157313 | Reference-DOI: 10.1016/J.JMB.2006.11.037
(for further references see the PDB file header)

Molecule 1 - CALPAIN 9
	Chains	:	A
	EC Number	:	3.4.22.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET28-LIC
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	CALPAIN CATALYTIC DOMAIN
	Gene	:	CAPN9, NCL4
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DIGESTIVE TRACT-SPECIFIC CALPAIN, NCL-4, CG36 PROTEIN

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	BME	2	Ligand/Ion	BETA-MERCAPTOETHANOL
2	CA	2	Ligand/Ion	CALCIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:284 , ASP A:291 , LEU A:312 , ASP A:314 , GLU A:316	BINDING SITE FOR RESIDUE CA A 1
2	AC2	SOFTWARE	LEU A:81 , GLY A:83 , ASP A:88 , GLU A:167 , HOH A:389	BINDING SITE FOR RESIDUE CA A 2
3	AC3	SOFTWARE	GLY A:95 , CYS A:97 , LEU A:100 , GLU A:174 , HOH A:376	BINDING SITE FOR RESIDUE BME A 3
4	AC4	SOFTWARE	GLU A:197 , THR A:200 , GLY A:202 , VAL A:203 , CYS A:334 , ASN A:335	BINDING SITE FOR RESIDUE BME A 4

(no "SS Bond" information available for 1ZIV)

(no "Cis Peptide Bond" information available for 1ZIV)

Asymmetric/Biological Unit (8, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_022188	A	102	V	CAN9_HUMAN	Polymorphism	12562749	A	A	102	V
2	UniProt	VAR_022189	S	122	R	CAN9_HUMAN	Polymorphism	28359608	A	S	122	R
3	UniProt	VAR_022190	D	164	N	CAN9_HUMAN	Polymorphism	28359632	A	D	164	N
4	UniProt	VAR_022191	I	234	T	CAN9_HUMAN	Polymorphism	28359644	A	I	234	T
5	UniProt	VAR_022192	A	239	T	CAN9_HUMAN	Polymorphism	28359647	A	A	239	T
6	UniProt	VAR_022193	R	277	W	CAN9_HUMAN	Polymorphism	28359655	A	R	277	W
7	UniProt	VAR_022194	K	322	Q	CAN9_HUMAN	Polymorphism	1933631	A	K	322	Q
8	UniProt	VAR_022195	H	327	Q	CAN9_HUMAN	Polymorphism	28359684	A	H	327	Q

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

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CALPAIN_CAT	PS50203	Cysteine proteinase, calpain-type, catalytic domain profile.	CAN9_HUMAN	42-337	1	A:42-337
2	THIOL_PROTEASE_CYS	PS00139	Eukaryotic thiol (cysteine) proteases cysteine active site.	CAN9_HUMAN	91-102	1	A:91-102

Asymmetric/Biological Unit (9, 9)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000271971	1a	ENSE00001070036	chr1:230883130-230883455	326	CAN9_HUMAN	1-71	71	1	A:28-71 (gaps)	44
1.2	ENST00000271971	2	ENSE00000921431	chr1:230891083-230891152	70	CAN9_HUMAN	72-95	24	1	A:72-95	24
1.3	ENST00000271971	3	ENSE00000961374	chr1:230895258-230895376	119	CAN9_HUMAN	95-134	40	1	A:95-134	40
1.4	ENST00000271971	4	ENSE00000961375	chr1:230898399-230898532	134	CAN9_HUMAN	135-179	45	1	A:135-179	45
1.5	ENST00000271971	5	ENSE00000961376	chr1:230903287-230903455	169	CAN9_HUMAN	179-235	57	1	A:179-235	57
1.6	ENST00000271971	6	ENSE00000961377	chr1:230904926-230905009	84	CAN9_HUMAN	236-263	28	1	A:236-263	28
1.7	ENST00000271971	7	ENSE00000961378	chr1:230907760-230907845	86	CAN9_HUMAN	264-292	29	1	A:264-292	29
1.8	ENST00000271971	8	ENSE00000961379	chr1:230910300-230910377	78	CAN9_HUMAN	292-318	27	1	A:292-318	27
1.9	ENST00000271971	9	ENSE00000961380	chr1:230914719-230914879	161	CAN9_HUMAN	318-372	55	1	A:318-337	20
1.10	ENST00000271971	10	ENSE00000961381	chr1:230915925-230916082	158	CAN9_HUMAN	372-424	53	0	-	-
1.11	ENST00000271971	11	ENSE00000961382	chr1:230916246-230916454	209	CAN9_HUMAN	425-494	70	0	-	-
1.12	ENST00000271971	12	ENSE00000961383	chr1:230921727-230921763	37	CAN9_HUMAN	494-506	13	0	-	-
1.13	ENST00000271971	13	ENSE00000961384	chr1:230923268-230923348	81	CAN9_HUMAN	507-533	27	0	-	-
1.14	ENST00000271971	14	ENSE00000961385	chr1:230925878-230925935	58	CAN9_HUMAN	534-553	20	0	-	-
1.15a	ENST00000271971	15a	ENSE00000961386	chr1:230927610-230927674	65	CAN9_HUMAN	553-574	22	0	-	-
1.16	ENST00000271971	16	ENSE00000961387	chr1:230928172-230928240	69	CAN9_HUMAN	575-597	23	0	-	-
1.17	ENST00000271971	17	ENSE00000961388	chr1:230928596-230928674	79	CAN9_HUMAN	598-624	27	0	-	-
1.18	ENST00000271971	18	ENSE00000961389	chr1:230930909-230931025	117	CAN9_HUMAN	624-663	40	0	-	-
1.19	ENST00000271971	19	ENSE00001416134	chr1:230933908-230933966	59	CAN9_HUMAN	663-682	20	0	-	-
1.20b	ENST00000271971	20b	ENSE00001414530	chr1:230937316-230937518	203	CAN9_HUMAN	683-690	8	0	-	-

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:308
 aligned with CAN9_HUMAN | O14815 from UniProtKB/Swiss-Prot  Length:690

    Alignment length:310
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337
           CAN9_HUMAN    28 SFEQMRQECLQRGTLFEDADFPASNSSLFYSERPQIPFVWKRPGEIVKNPEFILGGATRTDICQGELGDCWLLAAIASLTLNQKALARVIPQDQSFGPGYAGIFHFQFWQHSEWLDVVIDDRLPTFRDRLVFLHSADHNEFWSALLEKAYAKLNGSYEALKGGSAIEAMEDFTGGVAETFQTKEAPENFYEILEKALKRGSLLGCFIDTRSAAESEARTPFGLIKGHAYSVTGIDQVSFRGQRIELIRIRNPWGQVEWNGSWSDSSPEWRSVGPAEQKRLCHTALDDGEFWMAFKDFKAHFDKVEICNLT 337
               SCOP domains d1ziva1 A:28-337 Calpain large   subunit, catalytic domain (domain II)                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------Peptidase_C2-1ziv  A01 A:42-337                                                                                                                                                                                                                                                                          Pfam domains
         Sec.struct. author hhhhhhhhhhhh...........hhhhh...--.....eeehhhhh...........hhhhh........hhhhhhhhhhhhhhhhhhhh............eeeeeee....eeeeeee..eee...............hhhhhhhhhhhhhhh.hhhhh..hhhhhhhhhhh...eeee.hhh..hhhhhhhhhhhhh.eeeee....hhhhh.............eeeeeeeeeee..eeeeeeeee...............hhhhhhhhhhhhhhh........eeeeehhhhhhhh.eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------V-------------------R-----------------------------------------N---------------------------------------------------------------------T----T-------------------------------------W--------------------------------------------Q----Q---------- SAPs(SNPs)
                PROSITE (1) --------------CALPAIN_CAT  PDB: A:42-337 UniProt: 42-337                                                                                                                                                                                                                                                               PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------THIOL_PROTEA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1a  PDB: A:28-71 (gaps) UniProt: 1-71Exon 1.2  PDB: A:72-95  ---------------------------------------Exon 1.4  PDB: A:135-179 UniProt: 135-179    --------------------------------------------------------Exon 1.6  PDB: A:236-263    Exon 1.7  PDB: A:264-292     -------------------------Exon 1.9             Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------Exon 1.3  PDB: A:95-134 UniProt: 95-134 --------------------------------------------Exon 1.5  PDB: A:179-235 UniProt: 179-235                --------------------------------------------------------Exon 1.8  PDB: A:292-318   ------------------- Transcript 1 (2)
                 1ziv A  28 SFEQMRQECLQRGTLFEDADFPASNSSLFYS--PQIPFVWKRPGEIVKNPEFILGGATRTDICQGELGDCWLLAAIASLTLNQKALARVIPQDQSFGPGYAGIFHFQFWQHSEWLDVVIDDRLPTFRDRLVFLHSADHNEFWSALLEKAYAKLNGSYEALKGGSAIEAMEDFTGGVAETFQTKEAPENFYEILEKALKRGSLLGCFIDTRSAAESEARTPFGLIKGHAYSVTGIDQVSFRGQRIELIRIRNPWGQVEWNGSWSDSSPEWRSVGPAEQKRLCHTALDDGEFWMAFKDFKAHFDKVEICNLT 337
                                    37        47        57|  |    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337
                                                         58 61

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Cysteine proteinases (392)

Superfamily: Cysteine proteinases (392)

Family: Calpain large subunit, catalytic domain (domain II) (19)

Protein domain: Calpain large subunit, catalytic domain (domain II) (19)

Human (Homo sapiens), calpain 9 [TaxId: 9606] (1)

d1ziva1

A:28-337

(no "CATH Domain" information available for 1ZIV)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_CA (169)

Family: Peptidase_C2 (15)

Homo sapiens (Human) (5)

Peptidase_C2-1zivA01

A:42-337

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CAN9_HUMAN | O14815)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0004198	calcium-dependent cysteine-type endopeptidase activity	Catalysis of the hydrolysis of nonterminal peptide bonds in a polypeptide chain by a mechanism using a cysteine residue at the enzyme active center, and requiring the presence of calcium.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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.
biological process
	GO:0007586	digestion	The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

Asymmetric/Biological Unit
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(no "Related Entries Specified in the PDB File" available for 1ZIV)

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (8, 8)

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Exons (9, 9)

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