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(-) Description

Title :  CRYSTAL STRUCTURE OF A SECONDARY VITAMIN D3 BINDING SITE OF MILK BETA-LACTOGLOBULIN
 
Authors :  M. C. Yang, H. H. Guan, M. Y. Liu, J. M. Yang, W. L. Chen, C. J. Chen, S. J. Mao
Date :  30 Mar 06  (Deposition) - 02 Oct 07  (Release) - 20 Oct 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-Lactoglobulin, Vitamin D3, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Yang, H. H. Guan, M. Y. Liu, Y. H. Lin, J. M. Yang, W. L. Chen, C. J. Chen, S. J. Mao
Crystal Structure Of A Secondary Vitamin D3 Binding Site Of Milk Beta-Lactoglobulin.
Proteins V. 71 1197 2008
PubMed-ID: 18004750  |  Reference-DOI: 10.1002/PROT.21811
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-LACTOGLOBULIN
    Chains: A
    Organism Common: CATTLE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Synonym: BETA-LG, ALLERGEN BOS D 5

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1VD32Ligand/Ion(1S,3Z)-3-[(2E)-2-[(1R,3AR,7AS)-7A-METHYL-1-[(2R)-6-METHYLHEPTAN-2-YL]-2,3,3A,5,6,7-HEXAHYDRO-1H-INDEN-4-YLIDENE]ETHYLIDENE]-4-METHYLIDENE-CYCLOHEXAN-1-OL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:38 , LEU A:39 , VAL A:43 , ILE A:56 , LYS A:60 , GLU A:62 , ILE A:71 , ILE A:84 , ALA A:86 , LEU A:87 , PHE A:105 , MET A:107BINDING SITE FOR RESIDUE VD3 A 163
2AC2SOFTWAREGLU A:134 , ASP A:137 , LYS A:138 , LEU A:140 , LYS A:141 , LEU A:143 , MET A:145 , HIS A:146 , ILE A:147 , ARG A:148 , LEU A:149 , SER A:150 , HOH A:194BINDING SITE FOR RESIDUE VD3 A 164

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:66 -A:160
2A:106 -A:119

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:112 -Pro A:113

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 5)

Asymmetric/Biological Unit (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_LACB_BOVIN_001 *E61QLACB_BOVIN  ---  ---AE45Q
2UniProtVAR_LACB_BOVIN_002 *I72LLACB_BOVIN  ---  ---AI56L
3UniProtVAR_LACB_BOVIN_003 *Q75HLACB_BOVIN  ---  ---AQ59H
4UniProtVAR_LACB_BOVIN_004 *G80DLACB_BOVIN  ---  ---AG64D
5UniProtVAR_LACB_BOVIN_005 *A134VLACB_BOVIN  ---  ---AA118V
   * 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.LACB_BOVIN25-38  1A:9-22

(-) Exons   (0, 0)

(no "Exon" information available for 2GJ5)

(-) 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:161
 aligned with LACB_BOVIN | P02754 from UniProtKB/Swiss-Prot  Length:178

    Alignment length:161
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177 
           LACB_BOVIN    18 IVTQTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQKWENGECAQKKIIAEKTKIPAVFKIDALNENKVLVLDTDYKKYLLFCMENSAEPEQSLACQCLVRTPEVDDEALEKFDKALKALPMHIRLSFNPTQLEEQCHI 178
               SCOP domains d2gj5a_ A: beta-Lactoglobulin                                                                                                                                     SCOP domains
               CATH domains 2gj5A00 A:2-162  [code=2.40.128.20, no name defined]                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhee.eeeeeee.hhhhhh.......eeeeeeee.....eeeeeeeee..eeeeeeeeeee.....eeeee...eeeeeeeee....eeeeeeee.......eeeeeee.....hhhhhhhhhhhhhh....eeee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------Q----------L--H----D-----------------------------------------------------V-------------------------------------------- SAPs(SNPs)
                    PROSITE -------LIPOCALIN     -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gj5 A   2 IVTQTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQKWENGECAQKKIIAEKTKIPAVFKIDALNENKVLVLDTDYKKYLLFCMENSAEPEQSLACQCLVRTPEVDDEALEKFDKALKALPMHIRLSFNPTQLEEQCHI 162
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161
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 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 2GJ5)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LACB_BOVIN | P02754)
molecular function
    GO:0019841    retinol binding    Interacting selectively and non-covalently with retinol, vitamin A1, 2,6,6-trimethyl-1-(9'-hydroxy-3',7'-dimethylnona-1',3',5',7'-tetraenyl)cyclohex-1-ene, one of the three components that makes up vitamin A. Retinol is an intermediate in the vision cycle and it also plays a role in growth and differentiation.
    GO:0036094    small molecule binding    Interacting selectively and non-covalently with a small molecule, any low molecular weight, monomeric, non-encoded molecule.
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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 Related Entries

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

UniProtKB/Swiss-Prot
        LACB_BOVIN | P02754: 1b0o 1b8e 1beb 1bso 1bsq 1bsy 1cj5 1dv9 1gx8 1gx9 1gxa 1qg5 1uz2 1yup 2akq 2blg 2q2m 2q2p 2q39 2r56 3blg 3kza 3npo 3nq3 3nq9 3ph5 3ph6 3ueu 3uev 3uew 3uex 4dq3 4dq4 4gny 4ib6 4ib7 4ib8 4ib9 4iba 4kii 4lzu 4lzv 4y0p 4y0q 4y0r 5eee 5htd 5hte 5io5 5io7 5k06 5lke 5lkf

(-) Related Entries Specified in the PDB File

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