Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  PKCI-1-ZINC
 
Authors :  C. D. Lima, M. G. Klein, I. B. Weinstein, W. A. Hendrickson
Date :  06 Jan 96  (Deposition) - 11 Jul 96  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pkci-1, Pkc, Signal Transduction, Zinc Binding Protein, Protein Kinase C Interacting Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. D. Lima, M. G. Klein, I. B. Weinstein, W. A. Hendrickson
Three-Dimensional Structure Of Human Protein Kinase C Interacting Protein 1, A Member Of The Hit Family Of Proteins.
Proc. Natl. Acad. Sci. Usa V. 93 5357 1996
PubMed-ID: 8643579  |  Reference-DOI: 10.1073/PNAS.93.11.5357
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HUMAN PROTEIN KINASE C INTERACTING PROTEIN 1 (ZINC PROTEIN)
    ChainsA, B
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System GeneHPKCI-1
    Expression System PlasmidPHIL-D5
    Expression System Taxid4922
    GeneHPKCI-1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsEXPRESSED AS AN ACETYLATED PROTEIN ON AMINO ACID 2. THIS IS SIMILAR TO THE NATIVE PROTEIN PURIFIED DIRECTLY FROM BOVINE BRAIN.
    SynonymPKCI-1, PROTEIN KINASE C INHIBITOR 1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1KPA)

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1ZNAUNKNOWNHIS A:51 , HIS A:112 , HIS A:114TRIAD OF HISTIDINES POTENTIALLY INVOLVED IN ZINC COORDINATION.
2ZNBUNKNOWNHIS B:51 , HIS B:112 , HIS B:114TRIAD OF HISTIDINES POTENTIALLY INVOLVED IN ZINC COORDINATION.

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Trp A:123 -Pro A:124
2Trp B:123 -Pro B:124

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (6, 12)

Asymmetric/Biological Unit (6, 12)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_069212R37PHINT1_HUMANDisease (NMAN)149782619A/BR37P
2UniProtVAR_069213H51RHINT1_HUMANDisease (NMAN)397514491A/BH51R
3UniProtVAR_069214C84RHINT1_HUMANDisease (NMAN)397514489A/BC84R
4UniProtVAR_069215G89VHINT1_HUMANDisease (NMAN)397514490A/BG89V
5UniProtVAR_069216G93DHINT1_HUMANDisease (NMAN)397514493A/BG93D
6UniProtVAR_069217H112NHINT1_HUMANDisease (NMAN)373849532A/BH112N

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HIT_2PS51084 HIT domain profile.HINT1_HUMAN18-126
 
  2A:18-126
B:18-126
2HIT_1PS00892 HIT domain signature.HINT1_HUMAN99-117
 
  2A:99-117
B:99-117

(-) Exons   (3, 6)

Asymmetric/Biological Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000003040432aENSE00001130420chr5:130501178-130500788391HINT1_HUMAN1-37372A:14-37
B:14-37
24
24
1.3aENST000003040433aENSE00001131914chr5:130498369-130498265105HINT1_HUMAN38-72352A:38-72
B:38-72
35
35
1.5fENST000003040435fENSE00001130414chr5:130495304-130494720585HINT1_HUMAN73-126542A:73-126
B:73-126
54
54

(-) 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:113
 aligned with HINT1_HUMAN | P49773 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:113
                                    23        33        43        53        63        73        83        93       103       113       123   
          HINT1_HUMAN    14 GGDTIFGKIIRKEIPAKIIFEDDRCLAFHDISPQAPTHFLVIPKKHISQISVAEDDDESLLGHLMIVGKKCAADLGLNKGYRMVVNEGSDGGQSVYHVHLHVLGGRQMHWPPG 126
               SCOP domains d1kpaa_ A: Protein kinase C inhibitor-1, PKCI-1                                                                   SCOP domains
               CATH domains 1kpaA00 A:14-126 HIT family, subunit A                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh.......eeee...eeeee.......eeeeeee......hhh..hhhhhhhhhhhhhhhhhhhhh.....eeeeeeehhhh.......eeeeee......... Sec.struct. author
                 SAPs(SNPs) -----------------------P-------------R--------------------------------R----V---D------------------N-------------- SAPs(SNPs)
                PROSITE (1) ----HIT_2  PDB: A:18-126 UniProt: 18-126                                                                          PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------HIT_1  PDB: A:99-11--------- PROSITE (2)
               Transcript 1 Exon 1.2a  PDB: A:14-37 Exon 1.3a  PDB: A:38-72            Exon 1.5f  PDB: A:73-126 UniProt: 73-126               Transcript 1
                 1kpa A  14 GGDTIFGKIIRKEIPAKIIFEDDRCLAFHDISPQAPTHFLVIPKKHISQISVAEDDDESLLGHLMIVGKKCAADLGLNKGYRMVVNEGSDGGQSVYHVHLHVLGGRQMHWPPG 126
                                    23        33        43        53        63        73        83        93       103       113       123   

Chain B from PDB  Type:PROTEIN  Length:113
 aligned with HINT1_HUMAN | P49773 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:113
                                    23        33        43        53        63        73        83        93       103       113       123   
          HINT1_HUMAN    14 GGDTIFGKIIRKEIPAKIIFEDDRCLAFHDISPQAPTHFLVIPKKHISQISVAEDDDESLLGHLMIVGKKCAADLGLNKGYRMVVNEGSDGGQSVYHVHLHVLGGRQMHWPPG 126
               SCOP domains d1kpab_ B: Protein kinase C inhibitor-1, PKCI-1                                                                   SCOP domains
               CATH domains 1kpaB00 B:14-126 HIT family, subunit A                                                                            CATH domains
           Pfam domains (1) ----------HIT-1kpaB01 B:24-121                                                                              ----- Pfam domains (1)
           Pfam domains (2) ----------HIT-1kpaB02 B:24-121                                                                              ----- Pfam domains (2)
         Sec.struct. author ....hhhhhh.......eeee...eeeee.......eeeeeee......hhh..hhhhhhhhhhhhhhhhhhhh......eeeeeeehhhh.......eeeeee......... Sec.struct. author
                 SAPs(SNPs) -----------------------P-------------R--------------------------------R----V---D------------------N-------------- SAPs(SNPs)
                PROSITE (1) ----HIT_2  PDB: B:18-126 UniProt: 18-126                                                                          PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------HIT_1  PDB: B:99-11--------- PROSITE (2)
               Transcript 1 Exon 1.2a  PDB: B:14-37 Exon 1.3a  PDB: B:38-72            Exon 1.5f  PDB: B:73-126 UniProt: 73-126               Transcript 1
                 1kpa B  14 GGDTIFGKIIRKEIPAKIIFEDDRCLAFHDISPQAPTHFLVIPKKHISQISVAEDDDESLLGHLMIVGKKCAADLGLNKGYRMVVNEGSDGGQSVYHVHLHVLGGRQMHWPPG 126
                                    23        33        43        53        63        73        83        93       103       113       123   

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: HIT (23)
(-)
Family: HIT (19)
1aHIT-1kpaB01B:24-121
1bHIT-1kpaB02B:24-121

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (HINT1_HUMAN | P49773)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005080    protein kinase C binding    Interacting selectively and non-covalently with protein kinase C.
biological process
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0072332    intrinsic apoptotic signaling pathway by p53 class mediator    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, and ends when the execution phase of apoptosis is triggered.
    GO:0050850    positive regulation of calcium-mediated signaling    Any process that activates or increases the frequency, rate or extent of calcium-mediated signaling.
    GO:0009154    purine ribonucleotide catabolic process    The chemical reactions and pathways resulting in the breakdown of a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    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:0000118    histone deacetylase complex    A protein complex that possesses histone deacetylase activity.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    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.

 Visualization

(-) Interactive Views

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
(no "Ligands, Modified Residues, Ions" information available for 1kpa)
 
  Sites
    ZNA  [ RasMol ]  +environment [ RasMol ]
    ZNB  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Trp A:123 - Pro A:124   [ RasMol ]  
    Trp B:123 - Pro B:124   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1kpa
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  HINT1_HUMAN | P49773
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  137200
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  HINT1_HUMAN | P49773
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        HINT1_HUMAN | P497731av5 1kpb 1kpc 1kpe 1kpf 3tw2 4eqe 4eqg 4eqh 4zkl 4zkv 5ed3 5ed6 5emt 5i2e 5i2f 5ipb 5ipc 5ipd 5ipe 5kly 5klz 5km0 5km1 5km2 5km3 5km4 5km6 5km7 5kma 5kmb 5kmc 5o8g 5o8i

(-) Related Entries Specified in the PDB File

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