1NP8 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   18-K C-TERMINALLY TRUNUCATED SMALL SUBUNIT OF CALPAIN

Authors :   E. K. Leinala, J. S. Arthur, P. Grochulski, P. L. Davies, J. S. Elce, Z. Jia

Date :   17 Jan 03 (Deposition) - 18 Nov 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Dimer In Solution, Oligomer In Crystal, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. K. Leinala, J. S. Arthur, P. Grochulski, P. L. Davies, J. S. Elce, Z. Jia
A Second Binding Site Revealed By C-Terminal Truncation Of Calpain Small Subunit, A Penta-Ef-Hand Protein
Proteins: V. 53 649 2003 Struct. , Funct. , Genet.
PubMed-ID: 14579356 | Reference-DOI: 10.1002/PROT.10453
(for further references see the PDB file header)

Molecule 1 - CALCIUM-DEPENDENT PROTEASE, SMALL SUBUNIT
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 87-245
	Gene	:	CAPNS1 OR CAPN4 OR CSS1
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	CALPAIN REGULATORY SUBUNIT, CALCIUM-ACTIVATED NEUTRAL PROTEINASE, CANP, FRAGMENT

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 13)

No.	Name	Count	Type	Full Name
1	CD	13	Ligand/Ion	CADMIUM ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:68 , ASP A:70 , THR A:72 , LYS A:74 , GLU A:79 , HOH A:778	BINDING SITE FOR RESIDUE CD A 700
02	AC2	SOFTWARE	ASP A:100 , HOH A:769 , HOH A:771 , HOH A:774 , GLU B:615	BINDING SITE FOR RESIDUE CD A 701
03	AC3	SOFTWARE	ASP A:98 , ASP A:100 , SER A:102 , THR A:104 , GLU A:109 , HOH A:720	BINDING SITE FOR RESIDUE CD A 702
04	AC4	SOFTWARE	ALA A:25 , ASP A:28 , GLU A:30 , GLU A:35 , HOH A:726 , HOH A:772	BINDING SITE FOR RESIDUE CD A 703
05	AC5	SOFTWARE	ASP A:53 , ASP A:141 , ASP A:143 , ASN A:144 , HOH A:729 , HOH A:773	BINDING SITE FOR RESIDUE CD A 704
06	AC6	SOFTWARE	ASP A:27 , GLU A:115 , HOH A:768 , HOH A:776 , ASP B:600	BINDING SITE FOR RESIDUE CD A 705
07	AC7	SOFTWARE	HOH B:112 , ASP B:568 , ASP B:570 , THR B:572 , LYS B:574 , GLU B:579	BINDING SITE FOR RESIDUE CD B 707
08	AC8	SOFTWARE	HOH B:138 , ASP B:598 , ASP B:600 , SER B:602 , THR B:604 , GLU B:609	BINDING SITE FOR RESIDUE CD B 708
09	AC9	SOFTWARE	HOH B:142 , HOH B:186 , ALA B:525 , ASP B:528 , GLU B:530 , GLU B:535	BINDING SITE FOR RESIDUE CD B 709
10	BC1	SOFTWARE	HOH B:119 , ASP B:553 , ASP B:641 , ASP B:643 , ASN B:644	BINDING SITE FOR RESIDUE CD B 710
11	BC2	SOFTWARE	HIS A:47 , ASP A:49 , HOH A:777 , LYS B:519	BINDING SITE FOR RESIDUE CD A 711
12	BC3	SOFTWARE	HOH A:770 , HIS B:547 , ASP B:549 , LYS B:595	BINDING SITE FOR RESIDUE CD B 712
13	BC4	SOFTWARE	HOH B:148 , HOH B:198 , HIS B:624 , MET B:628	BINDING SITE FOR RESIDUE CD B 713

(no "SS Bond" information available for 1NP8)

(no "Cis Peptide Bond" information available for 1NP8)

(no "SAP(SNP)/Variant" information available for 1NP8)

Asymmetric/Biological Unit (2, 10)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	CPNS1_RAT	154-166 184-196	4	A:68-80 B:568-580 A:98-110 B:598-610
2	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	CPNS1_RAT	171-206 141-169 236-270	6	A:85-120 B:585-620 A:55-83 B:555-583 A:150-159 B:650-659

(no "Exon" information available for 1NP8)

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:149
 aligned with CPNS1_RAT | Q64537 from UniProtKB/Swiss-Prot  Length:270

    Alignment length:149
                                   106       116       126       136       146       156       166       176       186       196       206       216       226       236         
            CPNS1_RAT    97 SEEERQFRKLFVQLAGDDMEVSATELMNILNKVVTRHPDLKTDGFGIDTCRSMVAVMDSDTTGKLGFEEFKYLWNNIKKWQGIYKRFDTDRSGTIGSNELPGAFEAAGFHLNQHIYSMIIRRYSDETGNMDFDNFISCLVRLDAMFRAF 245
               SCOP domains d1np8a_ A: Calpain small (regulatory) subunit (domain VI)                                                                                             SCOP domains
               CATH domains 1np8A00 A:11-159 EF-hand                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh........hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhh....hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------------EF_HAND_1    -----------------EF_HAND_1    ---------------------------------------EF_HAND_2  PROSITE (1)
                PROSITE (2) --------------------------------------------EF_HAND_2  PDB: A:55-83      -EF_HAND_2  PDB: A:85-120            --------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1np8 A  11 SEEERQFRKLFVQLAGDDMEVSATELMNILNKVVTRHPDLKTDGFGIDTCRSMVAVMDSDTTGKLGFEEFKYLWNNIKKWQGIYKRFDTDRSGTIGSNELPGAFEAAGFHLNQHIYSMIIRRYSDETGNMDFDNFISCLVRLDAMFRAF 159
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain B from PDB  Type:PROTEIN  Length:149
 aligned with CPNS1_RAT | Q64537 from UniProtKB/Swiss-Prot  Length:270

    Alignment length:149
                                   106       116       126       136       146       156       166       176       186       196       206       216       226       236         
            CPNS1_RAT    97 SEEERQFRKLFVQLAGDDMEVSATELMNILNKVVTRHPDLKTDGFGIDTCRSMVAVMDSDTTGKLGFEEFKYLWNNIKKWQGIYKRFDTDRSGTIGSNELPGAFEAAGFHLNQHIYSMIIRRYSDETGNMDFDNFISCLVRLDAMFRAF 245
               SCOP domains d1np8b_ B: Calpain small (regulatory) subunit (domain VI)                                                                                             SCOP domains
               CATH domains 1np8B00 B:511-659 EF-hand                                                                                                                             CATH domains
           Pfam domains (1) ----------------EF_hand_6-1np8B03 B:527-586                                 ---------------------------------------------------------------------EF_h Pfam domains (1)
           Pfam domains (2) ----------------EF_hand_6-1np8B04 B:527-586                                 ---------------------------------------------------------------------EF_h Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh........hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhh....hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------------EF_HAND_1    -----------------EF_HAND_1    ---------------------------------------EF_HAND_2  PROSITE (1)
                PROSITE (2) --------------------------------------------EF_HAND_2  PDB: B:555-583    -EF_HAND_2  PDB: B:585-620           --------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1np8 B 511 SEEERQFRKLFVQLAGDDMEVSATELMNILNKVVTRHPDLKTDGFGIDTCRSMVAVMDSDTTGKLGFEEFKYLWNNIKKWQGIYKRFDTDRSGTIGSNELPGAFEAAGFHLNQHIYSMIIRRYSDETGNMDFDNFISCLVRLDAMFRAF 659
                                   520       530       540       550       560       570       580       590       600       610       620       630       640       650

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: All alpha proteins (14657)

Fold: EF Hand-like (739)

Superfamily: EF-hand (657)

Family: Penta-EF-hand proteins (30)

Protein domain: Calpain small (regulatory) subunit (domain VI) (16)

Norway rat (Rattus norvegicus) [TaxId: 10116] (8)

1a	d1np8a_	A:
1b	d1np8b_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Recoverin; domain 1 (474)

Homologous Superfamily: EF-hand (412)

Norway rat (Rattus norvegicus) (37)

1a	1np8A00	A:11-159
1b	1np8B00	B:511-659

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: EF_hand (270)

Family: EF_hand_3 (27)

Rattus norvegicus (Rat) (3)

1a	EF_hand_3-1np8B01	B:656-659
1b	EF_hand_3-1np8B02	B:656-659

Family: EF_hand_6 (75)

Rattus norvegicus (Rat) (9)

2a	EF_hand_6-1np8B03	B:527-586
2b	EF_hand_6-1np8B04	B:527-586

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (CPNS1_RAT | Q64537)

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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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).
	GO:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
	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: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
		CD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1np8)

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
	1np8
		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
	CPNS1_RAT \| Q64537
		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)
	(no 'Enzyme Classificator' available)
		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
	CPNS1_RAT \| Q64537
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	CPNS1_RAT \| Q64537	:	1aj5 1df0 1dvi 1u5i 3bow 3df0

(no "Related Entries Specified in the PDB File" available for 1NP8)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 13)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 10)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (2, 4)

Gene Ontology (9, 9)

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