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(-) Description

Title :  CALPAIN DOMAIN VI
 
Authors :  B. Todd, D. Moore, C. C. S. Deivanayagam, G. -D. Lin, D. Chattopadhyay, M K. K. W. Wang, S. V. L. Narayana
Date :  07 Feb 03  (Deposition) - 19 Aug 03  (Release) - 02 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hydrolase, Calcium Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Todd, D. Moore, C. C. S. Deivanayagam, G. -D. Lin, D. Chattopadhyay, M. Maki, K. K. W. Wang, S. V. L. Narayana
A Structural Model For The Inhibition Of Calpain By Calpastatin: Crystal Structures Of The Native Domain Vi Of Calpain And Its Complexes With Calpastatin Peptide And A Small Molecule Inhibitor.
J. Mol. Biol. V. 328 131 2003
PubMed-ID: 12684003  |  Reference-DOI: 10.1016/S0022-2836(03)00274-2

(-) Compounds

Molecule 1 - CALCIUM-DEPENDENT PROTEASE, SMALL SUBUNIT
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: DOMAIN VI
    Gene: CAPNS1 OR CAPN4
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823
    Synonym: CALPAIN REGULATORY SUBUNIT, CALCIUM-ACTIVATED NEUTRAL PROTEINASE, CANP

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:135 , ASP A:223 , ASP A:225 , ASN A:226BINDING SITE FOR RESIDUE CA A 1
2AC2SOFTWAREASP A:150 , ASP A:152 , THR A:154 , LYS A:156 , GLU A:161 , HOH A:273BINDING SITE FOR RESIDUE CA A 2
3AC3SOFTWAREALA A:107 , ASP A:110 , GLU A:112 , GLU A:117 , HOH A:267BINDING SITE FOR RESIDUE CA A 3
4AC4SOFTWAREASP A:180 , ASP A:182 , SER A:184 , THR A:186 , GLU A:191BINDING SITE FOR RESIDUE CA A 4

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NX2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1NX2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NX2)

(-) PROSITE Motifs  (2, 5)

Asymmetric Unit (2, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_1PS00018 EF-hand calcium-binding domain.CPNS1_PIG150-162
180-192		  2A:150-162
A:180-192
2EF_HAND_2PS50222 EF-hand calcium-binding domain profile.CPNS1_PIG167-202
137-165
232-266		  3A:167-202
A:137-165
A:232-266
Biological Unit 1 (2, 10)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_1PS00018 EF-hand calcium-binding domain.CPNS1_PIG150-162
180-192		  4A:150-162
A:180-192
2EF_HAND_2PS50222 EF-hand calcium-binding domain profile.CPNS1_PIG167-202
137-165
232-266		  6A:167-202
A:137-165
A:232-266

(-) Exons   (0, 0)

(no "Exon" information available for 1NX2)

(-) Sequences/Alignments

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:173
 aligned with CPNS1_PIG | P04574 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:173
                                   103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263   
            CPNS1_PIG    94 EEVRQFRRLFAQLAGDDMEVSATELMNILNKVVTRHPDLKTDGFGIDTCRSMVAVMDSDTTGKLGFEEFKYLWNNIKKWQAIYKQFDVDRSGTIGSSELPGAFEAAGFHLNEHLYSMIIRRYSDEGGNMDFDNFISCLVRLDAMFRAFKSLDKDGTGQIQVNIQEWLQLTMYS 266
               SCOP domains d1nx2a_ A: Calpain small (regulatory) subunit (domain VI)                                                                                                                     SCOP domains
               CATH domains 1nx2A00 A:94-266 EF-hand                                                                                                                                                      CATH domains
               Pfam domains ---------------EF_hand_6-1nx2A02 A:109-168                                 --EF_hand_4-1nx2A01 A:171-201    ----------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..........hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh......ee..hhhhhhhhh....hhhhhhhhhhhhh....eehhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------------------------EF_HAND_1    -----------------EF_HAND_1    ---------------------------------------EF_HAND_2  PDB: A:232-266           PROSITE (1)
                PROSITE (2) -------------------------------------------EF_HAND_2  PDB: A:137-165    -EF_HAND_2  PDB: A:167-202           ---------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nx2 A  94 EEVRQFRRLFAQLAGDDMEVSATELMNILNKVVTRHPDLKTDGFGIDTCRSMVAVMDSDTTGKLGFEEFKYLWNNIKKWQAIYKQFDVDRSGTIGSSELPGAFEAAGFHLNEHLYSMIIRRYSDEGGNMDFDNFISCLVRLDAMFRAFKSLDKDGTGQIQVNIQEWLQLTMYS 266
                                   103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: EF_hand (270)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (CPNS1_PIG | P04574)
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.
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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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.

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  1nx2
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  CPNS1_PIG | P04574
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CPNS1_PIG | P04574: 1alv 1alw 1nx0 1nx1 1nx3 4phn

(-) Related Entries Specified in the PDB File

1nx0 1nx1 1nx3