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(-) Description

Title :  HUMAN CALPAIN PROTEASE CORE INHIBITED BY ZLLYCH2F
 
Authors :  Q. Li, R. P. Hanzlik, R. F. Weaver, E. Schonbrunn
Date :  12 Apr 05  (Deposition) - 31 Jan 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Calcium Binding, Hydrolase, Protease, Thiol Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Q. Li, R. P. Hanzlik, R. F. Weaver, E. Schonbrunn
Molecular Mode Of Action Of A Covalently Inhibiting Peptidomimetic On The Human Calpain Protease Core
Biochemistry V. 45 701 2006
PubMed-ID: 16411745  |  Reference-DOI: 10.1021/BI052077B
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CALPAIN 1, LARGE [CATALYTIC] SUBUNIT
    ChainsA
    EC Number3.4.22.52
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET24D(+)
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRESIDUES 33 TO 353
    GeneCAPN1, CANPL1
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCALCIUM-ACTIVATED NEUTRAL PROTEINASE, CANP, MU- TYPE, MUCANP, MICROMOLAR-CALPAIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1C1N1Ligand/IonN-[(BENZYLOXY)CARBONYL]LEUCYL-N~1~-[3-FLUORO-1-(4-HYDROXYBENZYL)-2-OXOPROPYL]LEUCINAMIDE
2CA2Ligand/IonCALCIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:302 , ASP A:309 , MET A:329 , ASP A:331 , GLU A:333 , HOH A:1184BINDING SITE FOR RESIDUE CA A 1001
2AC2SOFTWAREVAL A:99 , GLY A:101 , ASP A:106 , GLU A:185 , HOH A:1185 , HOH A:1197BINDING SITE FOR RESIDUE CA A 1002
3AC3SOFTWAREGLN A:109 , GLY A:113 , ASP A:114 , CYS A:115 , TRP A:116 , SER A:206 , GLY A:207 , GLY A:208 , THR A:210 , GLU A:261 , GLY A:271 , HIS A:272 , TYR A:284 , ARG A:285 , GLN A:287 , VAL A:288 , HOH A:1319BINDING SITE FOR RESIDUE C1N A 1115

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_021085T103ACAN1_HUMANPolymorphism17885718AT103A
2UniProtVAR_077899R295PCAN1_HUMANDisease (SPG76)  ---AR295P

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CALPAIN_CATPS50203 Cysteine proteinase, calpain-type, catalytic domain profile.CAN1_HUMAN55-354  1A:55-353
2THIOL_PROTEASE_CYSPS00139 Eukaryotic thiol (cysteine) proteases cysteine active site.CAN1_HUMAN109-120  1A:109-120

(-) Exons   (9, 9)

Asymmetric/Biological Unit (9, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.6aENST000002792476aENSE00001535113chr11:64949343-64949484142CAN1_HUMAN-00--
1.7gENST000002792477gENSE00002177234chr11:64950172-64950439268CAN1_HUMAN1-89891A:33-8957
1.8ENST000002792478ENSE00000731735chr11:64950599-6495066870CAN1_HUMAN90-113241A:90-11324
1.9fENST000002792479fENSE00002188401chr11:64950945-64951063119CAN1_HUMAN113-152401A:113-15240
1.10gENST0000027924710gENSE00001273856chr11:64953388-64953521134CAN1_HUMAN153-197451A:153-19745
1.10iENST0000027924710iENSE00001192601chr11:64953641-64953809169CAN1_HUMAN197-253571A:197-25357
1.11aENST0000027924711aENSE00001119935chr11:64954686-6495476984CAN1_HUMAN254-281281A:254-28128
1.12dENST0000027924712dENSE00001119924chr11:64955426-6495551186CAN1_HUMAN282-310291A:282-31029
1.13bENST0000027924713bENSE00001170399chr11:64955885-6495595975CAN1_HUMAN310-335261A:310-33526
1.14bENST0000027924714bENSE00001273808chr11:64956057-64956217161CAN1_HUMAN335-389551A:335-35319
1.17ENST0000027924717ENSE00001273802chr11:64972154-64972329176CAN1_HUMAN389-447590--
1.18aENST0000027924718aENSE00001735163chr11:64973181-6497319212CAN1_HUMAN448-45140--
1.19cENST0000027924719cENSE00001192571chr11:64973934-64974145212CAN1_HUMAN452-522710--
1.20ENST0000027924720ENSE00001119914chr11:64974251-6497429040CAN1_HUMAN522-535140--
1.21ENST0000027924721ENSE00001170362chr11:64975526-6497559166CAN1_HUMAN536-557220--
1.22ENST0000027924722ENSE00001273772chr11:64975676-6497573358CAN1_HUMAN558-577200--
1.23eENST0000027924723eENSE00001273768chr11:64976794-6497685865CAN1_HUMAN577-598220--
1.23fENST0000027924723fENSE00001273762chr11:64977320-6497738869CAN1_HUMAN599-621230--
1.23hENST0000027924723hENSE00001170341chr11:64977489-6497756779CAN1_HUMAN622-648270--
1.24bENST0000027924724bENSE00001119936chr11:64977807-64977923117CAN1_HUMAN648-687400--
1.25aENST0000027924725aENSE00001170334chr11:64978285-6497834359CAN1_HUMAN687-706200--
1.25fENST0000027924725fENSE00001338286chr11:64978731-64979476746CAN1_HUMAN707-71480--

(-) Sequences/Alignments

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_HUMAN | P07384 from UniProtKB/Swiss-Prot  Length:714

    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_HUMAN    33 NAIKYLGQDYEQLRVRCLQSGTLFRDEAFPPVPQSLGYKDLGPNSSKTYGIKWKRPTELLSNPQFIVDGATRTDICQGALGDCWLLAAIASLTLNDTLLHRVVPHGQSFQNGYAGIFHFQLWQFGEWVDVVVDDLLPIKDGKLVFVHSAEGNEFWSALLEKAYAKVNGSYEALSGGSTSEGFEDFTGGVTEWYELRKAPSDLYQIILKALERGSLLGCSIDISSVLDMEAITFKKLVKGHAYSVTGAKQVNYRGQVVSLIRMRNPWGEVEWTGAWSDSSSEWNNVDPYERDQLRVKMEDGEFWMSFRDFMREFTRLEICNL 353
               SCOP domains d1zcma1 A:33-353 Calpain large subunit, catalytic domain (domain II)                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------Peptidase_C2-1zcmA01 A:55-353                                                                                                                                                                                                                                                                               Pfam domains
         Sec.struct. author ..ee.hhhhhhhhhhhhhhh...........hhhhhh.......hhhhh..eeehhhhhh..........hhhhh......hhhhhhhhhhhh.hhhhhhhhh............eeeeeeee..eeeeeeee..eeee..ee..........hhhhhhhhhhhhhh..hhhhh..hhhhhhhhh...eeeeee.hhh..hhhhhhhhhhhhh.eeeee......................eeeeeeeeeee..eeeeeeeee...............hhhhhhhhhhhhhhhh......eeeeehhhhhhhh.eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------A-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P---------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------CALPAIN_CAT  PDB: A:55-353 UniProt: 55-354                                                                                                                                                                                                                                                                  PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------THIOL_PROTEA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.7g  PDB: A:33-89 UniProt: 1-89 [INCOMPLETE]       Exon 1.8  PDB: A:90-113 ---------------------------------------Exon 1.10g  PDB: A:153-197 UniProt: 153-197  --------------------------------------------------------Exon 1.11a  PDB: A:254-281  Exon 1.12d  PDB: A:282-310   ------------------------Exon 1.14b          Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------Exon 1.9f  PDB: A:113-152               --------------------------------------------Exon 1.10i  PDB: A:197-253 UniProt: 197-253              --------------------------------------------------------Exon 1.13b  PDB: A:310-335------------------ Transcript 1 (2)
                 1zcm A  33 NAIKYLGQDYEQLRVRCLQSGTLFRDEAFPPVPQSLGYKDLGPNSSKTYGIKWKRPTELLSNPQFIVDGATRTDICQGALGDCWLLAAIASLTLNDTLLHRVVPHGQSFQNGYAGIFHFQLWQFGEWVDVVVDDLLPIKDGKLVFVHSAEGNEFWSALLEKAYAKVNGSYEALSGGSTSEAFEDFTGGVTEWYELRKAPSDLYQIILKALERGSLLGCSIDISSVLDMEAITFKKLVKGHAYSVTGAKQVNYRGQVVSLIRMRNPWGEVEWTGAWSDSSSEWNNVDPYERDQLRVKMEDGEFWMSFRDFMREFTRLEICNL 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 

   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/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CAN1_HUMAN | P07384)
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:0022617    extracellular matrix disassembly    A process that results in the breakdown of the extracellular matrix.
    GO:0060056    mammary gland involution    The tissue remodeling that removes differentiated mammary epithelia during weaning.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    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.
    GO:0032801    receptor catabolic process    The chemical reactions and pathways resulting in the breakdown of a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0016241    regulation of macroautophagy    Any process that modulates the frequency, rate or extent of macroautophagy.
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:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    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:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        CAN1_HUMAN | P073842ary

(-) Related Entries Specified in the PDB File

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