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
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  HUMAN LITHOSTATHINE
 
Authors :  J. A. Bertrand, D. Pignol, J. -P. Bernard, J. -M. Verdier, J. -C. Dagorn, J. C. Fontacilla-Camps
Date :  17 Jan 96  (Deposition) - 11 Jan 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A
Keywords :  Pancreatic Stone Inhibitor, Lectin (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. A. Bertrand, D. Pignol, J. P. Bernard, J. M. Verdier, J. C. Dagorn, J. C. Fontecilla-Camps
Crystal Structure Of Human Lithostathine, The Pancreatic Inhibitor Of Stone Formation.
Embo J. V. 15 2678 1996
PubMed-ID: 8654365
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LITHOSTATHINE
    ChainsA
    OrganPANCREAS
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1LIT)

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:14 -A:25
2A:42 -A:140
3A:115 -A:132

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:106 -Pro A:107

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.REG1A_HUMAN43-163  1A:21-141
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.REG1A_HUMAN137-162  1A:115-140

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002337351bENSE00001332291chr2:79347584-7934764057REG1A_HUMAN-00--
1.1dENST000002337351dENSE00002157874chr2:79347942-79348051110REG1A_HUMAN1-22220--
1.2aENST000002337352aENSE00001724795chr2:79348688-79348806119REG1A_HUMAN22-61401A:14-3926
1.2dENST000002337352dENSE00001674317chr2:79349114-79349251138REG1A_HUMAN62-107461A:40-8546
1.3aENST000002337353aENSE00001645129chr2:79349967-79350078112REG1A_HUMAN108-145381A:86-12338
1.4ENST000002337354ENSE00000846820chr2:79350274-79350545272REG1A_HUMAN145-166221A:123-14422

(-) 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:131
 aligned with REG1A_HUMAN | P05451 from UniProtKB/Swiss-Prot  Length:166

    Alignment length:131
                                    45        55        65        75        85        95       105       115       125       135       145       155       165 
          REG1A_HUMAN    36 CPEGTNAYRSYCYYFNEDRETWVDADLYCQNMNSGNLVSVLTQAEGAFVASLIKESGTDDFNVWIGLHDPKKNRRWHWSSGSLVSYKSWGIGAPSSVNPGYCVSLTSSTGFQKWKDVPCEDKFSFVCKFKN 166
               SCOP domains d1lita_ A: Lithostathine, inhibitor of stone formation                                                                              SCOP domains
               CATH domains 1litA00 A:14-144 Mannose-Binding Protein A, subunit A                                                                               CATH domains
               Pfam domains -----------------Lectin_C-1litA01 A:31-142                                                                                       -- Pfam domains
         Sec.struct. author .....eee..eeeeee.....hhhhhhhhhhhh.........hhhhhhhhhhhhhh.....eee.....................................eeeeehhh....eeee.......eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------C_TYPE_LECTIN_2  PDB: A:21-141 UniProt: 43-163                                                                           --- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1           ---- PROSITE (2)
           Transcript 1 (1) Exon 1.2a  PDB: A:14-39   Exon 1.2d  PDB: A:40-85 UniProt: 62-107       Exon 1.3a  PDB: A:86-123              --------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------Exon 1.4               Transcript 1 (2)
                 1lit A  14 CPEGTNAYRSYCYYFNEDRETWVDADLYCQNMNSGNLVSVLTQAEGAFVASLIKESGTDDFNVWIGLHDPKKNRRWHWSSGSLVSYKSWGIGAPSSVNPGYCVSLTSSTGFQKWKDVPCEDKFSFVCKFKN 144
                                    23        33        43        53        63        73        83        93       103       113       123       133       143 

   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  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: C_Lectin (98)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (REG1A_HUMAN | P05451)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0008083    growth factor activity    The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
biological process
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
cellular component
    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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

 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 1lit)
 
  Sites
(no "Sites" information available for 1lit)
 
  Cis Peptide Bonds
    Ala A:106 - Pro A:107   [ 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
  1lit
    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
  REG1A_HUMAN | P05451
    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)
  (no 'MIM ID' available)
    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
  REG1A_HUMAN | P05451
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        REG1A_HUMAN | P054511qdd

(-) Related Entries Specified in the PDB File

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