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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PANCREATIC SECRETORY PROTEIN ZG16P WITH METHYL ALPHA-D-MANNOPYRANOSIDE
 
Authors :  M. Kanagawa, Y. Yamaguchi
Date :  11 Oct 12  (Deposition) - 16 Oct 13  (Release) - 03 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-Prism Fold, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Kanagawa, Y. Liu, S. Hanashima, A. Ikeda, W. Chai, Y. Nakano, K. Kojima-Aikawa, T. Feizi, Y. Yamaguchi
Structural Basis For Multiple Sugar Recognition Of Jacalin-Related Human Zg16P Lectin
J. Biol. Chem. V. 289 16954 2014
PubMed-ID: 24790092  |  Reference-DOI: 10.1074/JBC.M113.539114

(-) Compounds

Molecule 1 - ZYMOGEN GRANULE MEMBRANE PROTEIN 16
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPCOLD-1( MBP FUSION)
    Expression System StrainE. COLI BL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 21-159
    GeneZG16
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymZYMOGEN GRANULE PROTEIN 16, HZG16, SECRETORY LECTIN ZG16

 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
1CL2Ligand/IonCHLORIDE ION
2MMA1Ligand/IonO1-METHYL-MANNOSE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:35 , TYR A:104 , GLY A:147 , SER A:148 , LEU A:149 , ASP A:151 , HOH A:325 , HOH A:326BINDING SITE FOR RESIDUE MMA A 201
2AC2SOFTWARETYR A:117BINDING SITE FOR RESIDUE CL A 202
3AC3SOFTWARELYS A:70 , TRP A:72 , SER A:127 , PHE A:128BINDING SITE FOR RESIDUE CL A 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VZF)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:28 -Glu A:29

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_034587G32SZG16_HUMANPolymorphism235636AS32S
2UniProtVAR_070695L109VZG16_HUMANPolymorphism  ---AV109V

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1JACALIN_LECTINPS51752 Jacalin-type lectin domain profile.ZG16_HUMAN24-159  1A:24-159

(-) Exons   (0, 0)

(no "Exon" information available for 3VZF)

(-) 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:138
 aligned with ZG16_HUMAN | O60844 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:138
                                    31        41        51        61        71        81        91       101       111       121       131       141       151        
           ZG16_HUMAN    22 RSSSYSGEYGGGGGKRFSHSGNQLDGPITALRVRVNTYYIVGLQVRYGKVWSDYVGGRNGDLEEIFLHPGESVIQVSGKYKWYLKKLLFVTDKGRYLSFGKDSGTSFNAVPLHPNTVLRFISGRSGSLIDAIGLHWDV 159
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee....eeee.hhhhhhh.eeeeeeee....eeeeeeee..ee...ee....eeeeee......eeeeeeee...eeeeeeee....eeeee....eeeee.......eeeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------S----------------------------------------------------------------------------V-------------------------------------------------- SAPs(SNPs)
                    PROSITE --JACALIN_LECTIN  PDB: A:24-159 UniProt: 24-159                                                                                            PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vzf A  22 RSSSYSGEYGSGGGKRFSHSGNQLDGPITALRVRVNTYYIVGLQVRYGKVWSDYVGGRNGDLEEIFLHPGESVIQVSGKYKWYLKKLVFVTDKGRYLSFGKDSGTSFNAVPLHPNTVLRFISGRSGSLIDAIGLHWDV 159
                                    31        41        51        61        71        81        91       101       111       121       131       141       151        

   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  (0, 0)

(no "SCOP Domain" information available for 3VZF)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VZF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VZF)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ZG16_HUMAN | O60844)
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: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:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005796    Golgi lumen    The volume enclosed by the membranes of any cisterna or subcompartment of the Golgi apparatus, including the cis- and trans-Golgi networks.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0060205    cytoplasmic vesicle lumen    The volume enclosed by a cytoplasmic vesicle.
    GO:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    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.
    GO:0005578    proteinaceous extracellular matrix    A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.
    GO:0042589    zymogen granule membrane    The lipid bilayer surrounding a zymogen granule.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ZG16_HUMAN | O608443apa 3vy6 3vy7 3vze 3vzg

(-) Related Entries Specified in the PDB File

3vze 3vzg