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(-) Description

Title :  3-D STRUCTURE OF A SALIVARY LIPOCALIN FROM BOAR
 
Authors :  S. Spinelli, F. Vincent, P. Pelosi, M. Tegoni, C. Cambillau
Date :  11 Sep 01  (Deposition) - 30 May 02  (Release) - 07 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.13
Chains :  Asym./Biol. Unit :  A
Keywords :  Odorant-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Spinelli, F. Vincent, P. Pelosi, M. Tegoni, C. Cambillau
Boar Salivary Lipocalin. Three-Dimensional X-Ray Structure And Androsterol/Androstenone Docking Simulations.
Eur. J. Biochem. V. 269 2449 2002
PubMed-ID: 12027882  |  Reference-DOI: 10.1046/J.1432-1033.2002.02901.X

(-) Compounds

Molecule 1 - SALIVARY LIPOCALIN
    Chains: A
    Organ: SUBMAXILLARY GLANDS
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823
    Other Details: N-ACETYL-GLUCOSAMINE SITE, CADMIUM ION, GLYCEROL IN THE CAVITY
    Other Details - Source: FROM MATURE MALE PIG
    Synonym: SAL
    Tissue: GLAND

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1CD1Ligand/IonCADMIUM ION
2GOL1Ligand/IonGLYCEROL
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:21 , GLU A:46 , HIS A:47BINDING SITE FOR RESIDUE CD A1166
2AC2SOFTWAREPHE A:58 , LEU A:108 , LEU A:119 , GLU A:121BINDING SITE FOR RESIDUE GOL A1167
3AC3SOFTWAREASN A:53 , SER A:55 , ASP A:76 , ASP A:128 , THR A:155 , ARG A:159 , HOH A:2109 , HOH A:2110 , HOH A:2111BINDING SITE FOR CHAIN A OF MONO-SACCHARIDE NAG A1168 BOUND TO ASN A 53

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:68 -A:160

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1GM6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric/Biological Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_SAL_PIG_001 *V61ASAL_PIG  ---  ---AV45A
2UniProtVAR_SAL_PIG_002 *I64VSAL_PIG  ---  ---AI48V
3UniProtVAR_SAL_PIG_003 *A89VSAL_PIG  ---  ---AA73V
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIPOCALINPS00213 Lipocalin signature.SAL_PIG28-41  1A:12-25

(-) Exons   (0, 0)

(no "Exon" information available for 1GM6)

(-) 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:159
 aligned with SAL_PIG | P81608 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:159
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173         
              SAL_PIG    24 VVTSNFDASKIAGEWYSILLASDAKENIEENGSMRVFVEHIRVLDNSSLAFKFQRKVNGECTDFYAVCDKVGDGVYTVAYYGENKFRLLEVNYSDYVILHLVNVNGDKTFQLMEFYGRKPDVEPKLKDKFVEICQQYGIIKENIIDLTKIDRCFQLRGS 182
               SCOP domains d1gm6a_ A: Salivary lipocalin                                                                                                                                   SCOP domains
               CATH domains 1gm6A00 A:8-165  [code=2.40.128.20, no name defined]                                                                                                          - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............ee.eeeeeee.hhhhhh.......eeeeeee.....eeeeeeeee..eeeeeeeeeeeee..eeeee...eeeeeeeeee...eeeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhhhh...hhh.eee.hhh..hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------A--V------------------------V--------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----LIPOCALIN     --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gm6 A   8 VVTSNFDASKIAGEWYSILLASDAKENIEENGSMRVFVEHIRVLDNSSLAFKFQRKVNGECTDFYAVCDKVGDGVYTVAYYGENKFRLLEVNYSDYVILHLVDVNGDKTFQLMEFYGRKPDVEPKLKDKFVEICQQYGIIKENIIDLTKIDRCFQLRGS 166
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157
   Legend:   → Mismatch (orange background)
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  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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GM6)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SAL_PIG | P81608)
molecular function
    GO:0005550    pheromone binding    Interacting selectively and non-covalently with a pheromone, a substance, or characteristic mixture of substances, that is secreted and released by an organism and detected by a second organism of the same or a closely related species, in which it causes a specific reaction, such as a definite behavioral reaction or a developmental process.
    GO:0036094    small molecule binding    Interacting selectively and non-covalently with a small molecule, any low molecular weight, monomeric, non-encoded molecule.
    GO:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
    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: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.

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  1gm6
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 Related Entries

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