1TL9 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   HIGH RESOLUTION CRYSTAL STRUCTURE OF CALPAIN I PROTEASE CORE IN COMPLEX WITH LEUPEPTIN

Authors :   T. Moldoveanu, R. L. Campbell, D. Cuerrier, P. L. Davies

Date :   09 Jun 04 (Deposition) - 02 Nov 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Covalently-Linked Inhibitor At The Active Site Cysteine Forms A Hemithioacetal, Hydrolase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Moldoveanu, R. L. Campbell, D. Cuerrier, P. L. Davies
Crystal Structures Of Calpain-E64 And -Leupeptin Inhibitor Complexes Reveal Mobile Loops Gating The Active Site
J. Mol. Biol. V. 343 1313 2004
PubMed-ID: 15491615 | Reference-DOI: 10.1016/J.JMB.2004.09.016
(for further references see the PDB file header)

Molecule 1 - CALPAIN 1, LARGE [CATALYTIC] SUBUNIT
	Chains	:	A
	EC Number	:	3.4.22.52
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET24D
	Expression System Strain	:	BL21 DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 27-356
	Gene	:	CAPN1, CLS1
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	CALCIUM-ACTIVATED NEUTRAL PROTEINASE, CANP, MU-TYPE, MUCANP, MICROMOLAR-CALPAIN

Molecule 2 - LEUPEPTIN INHIBITOR
	Chains	:	B
	Engineered	:	YES
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 4)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP
2	AR7	1	Mod. Amino Acid	AMINO{[(4S)-4-AMINO-5,5-DIHYDROXYPENTYL]AMINO}METHANIMINIUM
3	CA	2	Ligand/Ion	CALCIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:99 , GLY A:101 , ASP A:106 , GLU A:185 , HOH A:389 , HOH A:465	BINDING SITE FOR RESIDUE CA A 1
2	AC2	SOFTWARE	GLU A:302 , ASP A:309 , MET A:329 , ASP A:331 , GLU A:333 , HOH A:401	BINDING SITE FOR RESIDUE CA A 2
3	AC3	SOFTWARE	GLN A:57 , ASP A:59 , GLU A:72 , GLN A:109 , GLY A:113 , ASP A:114 , CYS A:115 , TRP A:116 , SER A:206 , GLY A:207 , GLY A:208 , GLU A:261 , GLY A:271 , HOH A:531 , HOH A:589 , HOH B:182 , HOH B:258	BINDING SITE FOR CHAIN B OF LEUPEPTIN INHIBITOR

(no "SS Bond" information available for 1TL9)

(no "Cis Peptide Bond" information available for 1TL9)

(no "SAP(SNP)/Variant" information available for 1TL9)

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.	CAN1_RAT	55-354	1	A:55-353
2	THIOL_PROTEASE_CYS	PS00139	Eukaryotic thiol (cysteine) proteases cysteine active site.	CAN1_RAT	109-120	1	A:109-120

(no "Exon" information available for 1TL9)

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:321
 aligned with CAN1_RAT | P97571 from UniProtKB/Swiss-Prot  Length:713

    Alignment length:321
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352 
             CAN1_RAT    33 NAIKYLGQDYENLRARCLQNGVLFQDDAFPPVSHSLGFKELGPNSSKTYGIKWKRPTELLSNPQFIVDGATRTDICQGALGDCWLLAAIASLTLNETILHRVVPYGQSFQEGYAGIFHFQLWQFGEWVDVVVDDLLPTKDGKLVFVHSAQGNEFWSALLEKAYAKVNGSYEALSGGCTSEAFEDFTGGVTEWYDLQKAPSDLYQIILKALERGSLLGCSINISDIRDLEAITFKNLVRGHAYSVTDAKQVTYQGQRVNLIRMRNPWGEVEWKGPWSDNSYEWNKVDPYEREQLRVKMEDGEFWMSFRDFIREFTKLEICNL 353
               SCOP domains d1tl9a_ A: Calpain large subunit, catalytic domain (domain II)                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------Peptidase_C2-1tl9A01 A:55-353                                                                                                                                                                                                                                                                               Pfam domains
         Sec.struct. author ..ee.hhhhhhhhhhhhhhh...........hhhhhh.......hhhhh..eeehhhhhh..........hhhhh......hhhhhhhhhhhh.hhhhhhhhh............eeeeeeee..eeeeeeee..eeee..ee..........hhhhhhhhhhhhhhh.hhhhh..hhhhhhhhhhh..eeeee.hhh..hhhhhhhhhhhhh.eeeee....hhhhh.............eeeeeeeeeee..eeeeeeeee...............hhhhhhhhhhhhhhhh......eeeeehhhhhhhh.eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------CALPAIN_CAT  PDB: A:55-353 UniProt: 55-354                                                                                                                                                                                                                                                                  PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------THIOL_PROTEA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tl9 A  33 NAIKYLGQDYENLRARCLQNGVLFQDDAFPPVSHSLGFKELGPNSSKTYGIKWKRPTELLSNPQFIVDGATRTDICQGALGDCWLLAAIASLTLNETILHRVVPYGQSFQEGYAGIFHFQLWQFGEWVDVVVDDLLPTKDGKLVFVHSAQGNEFWSALLEKAYAKVNGSYEALSGGCTSEAFEDFTGGVTEWYDLQKAPSDLYQIILKALERGSLLGCSINISDIRDLEAITFKNLVRGHAYSVTDAKQVTYQGQRVNLIRMRNPWGEVEWKGPWSDNSYEWNKVDPYEREQLRVKMEDGEFWMSFRDFIREFTKLEICNL 353
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352

Chain B from PDB  Type:PROTEIN  Length:4
                                    
               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
                 1tl9 B 355 xLLx 358
                            |  |
                          355-ACE
                             358-AR7

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)

Norway rat (Rattus norvegicus), mu-type [TaxId: 10116] (10)

d1tl9a_

(no "CATH Domain" information available for 1TL9)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_CA (169)

Family: Peptidase_C2 (15)

Rattus norvegicus (Rat) (10)

Peptidase_C2-1tl9A01

A:55-353

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CAN1_RAT | P97571)

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:0008092	cytoskeletal protein binding	Interacting selectively and non-covalently with any protein component of any cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton).
	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.
	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:0016540	protein autoprocessing	Processing which a protein carries out itself. This involves actions such as the autolytic removal of residues to generate the mature form of the protein.
	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: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.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		ACE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		AR7	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1tl9)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1tl9
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	CAN1_RAT \| P97571
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.4.22.52
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	CAN1_RAT \| P97571
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	CAN1_RAT \| P97571	:	1kxr 1qxp 1tlo 2g8e 2g8j 2nqg 2nqi 2r9c 2r9f

1dfo	CRYSTAL STRUCTURE OF THE RAT CALPAIN II HETERODIMER
1kfu	CRYSTAL STRUCTURE OF THE HUMAN CALPAIN II HETERODIMER FORM II
1kfx	CRYSTAL STRUCTURE OF THE HUMAN CALPAIN II HETERODIMER FORM I
1kxr	CRYSTAL STRUCTURE OF THE CALPAIN I PROTEASE CORE IN THE PRESENCE OF CALCIUM
1mdw	CRYSTAL STRUCTURE OF THE CALPAIN II PROTEASE CORE IN THE PRESENCE OF CALCIUM
1nx0	CALPAIN DOMAIN VI COMPLEXED WITH CALPASTATIN INHIBITORY DOMAIN C
1tlo	HIGH RESOLUTION CRYSTAL STRUCTURE OF CALPAIN I PROTEASE CORE IN COMPLEX WITH E64

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (14, 14)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File