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(-) Description

Title :  CRYSTAL STRUCTURE OF ZEBRAFISH ILEAL BILE ACID-BINDIN PROTEIN COMPLEXED WITH CHOLIC ACID (CRYSTAL FORM B).
 
Authors :  S. Capaldi, G. Saccomani, D. Fessas, M. Signorelli, M. Perduca, H. L. Mo
Date :  23 Sep 08  (Deposition) - 13 Jan 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ileal Bile Acid-Binding Protein, Zebrafish (Danio Rerio), Cholic Acid, Lipid-Binding, Transport, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Capaldi, G. Saccomani, D. Fessas, M. Signorelli, M. Perduca, H. L. Monaco
The X-Ray Structure Of Zebrafish (Danio Rerio) Ileal Bile Acid-Binding Protein Reveals The Presence Of Binding Sites On The Surface Of The Protein Molecule.
J. Mol. Biol. V. 385 99 2009
PubMed-ID: 18952094  |  Reference-DOI: 10.1016/J.JMB.2008.10.007

(-) Compounds

Molecule 1 - ILEAL BILE ACID-BINDING PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE50
    Expression System Strain: SG13009
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: LEOPARD DANIO,ZEBRA DANIO,ZEBRA FISH
    Organism Scientific: DANIO RERIO
    Organism Taxid: 7955
    Synonym: FATTY ACID BINDING PROTEIN 6, ILEAL (GASTROTROPIN)

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 9)

Asymmetric Unit (1, 9)
No.NameCountTypeFull Name
1CHD9Ligand/IonCHOLIC ACID
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1CHD4Ligand/IonCHOLIC ACID
Biological Unit 2 (1, 5)
No.NameCountTypeFull Name
1CHD5Ligand/IonCHOLIC ACID

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:49 , GLN A:51 , ASN A:61 , PHE A:63 , MET A:71 , THR A:73 , VAL A:74 , PHE A:79 , TYR A:97 , GLN A:99 , THR A:101 , CHD A:151 , CHD A:153BINDING SITE FOR RESIDUE CHD A 150
2AC2SOFTWARETYR A:14 , ILE A:21 , VAL A:27 , GLY A:31 , TYR A:53 , VAL A:74 , LEU A:123 , CHD A:150 , CHD A:152 , GLY B:66BINDING SITE FOR RESIDUE CHD A 151
3AC3SOFTWAREPRO A:54 , HIS A:57 , VAL A:74 , CHD A:151 , LYS B:19 , LEU B:20 , SER B:93BINDING SITE FOR RESIDUE CHD A 152
4AC4SOFTWARETHR A:73 , PHE A:79 , LYS A:80 , PHE A:94 , TYR A:97 , CHD A:150BINDING SITE FOR RESIDUE CHD A 153
5AC5SOFTWAREPHE B:17 , ILE B:21 , TRP B:49 , PHE B:63 , VAL B:83 , LEU B:90 , ILE B:92 , TYR B:97 , GLN B:99 , THR B:101 , CHD B:151 , CHD B:153 , HOH B:547BINDING SITE FOR RESIDUE CHD B 150
6AC6SOFTWARETYR B:14 , ILE B:21 , GLY B:31 , LEU B:36 , GLN B:51 , TYR B:53 , ARG B:125 , CHD B:150 , CHD B:152 , HOH B:522 , HOH B:547BINDING SITE FOR RESIDUE CHD B 151
7AC7SOFTWAREILE B:21 , GLY B:22 , PRO B:24 , ASN B:55 , HIS B:57 , VAL B:74 , CHD B:151BINDING SITE FOR RESIDUE CHD B 152
8AC8SOFTWARELEU B:20 , ILE B:21 , LYS B:77 , PHE B:94 , LYS B:96 , TYR B:97 , CHD B:150BINDING SITE FOR RESIDUE CHD B 153
9AC9SOFTWAREGLU B:12 , PRO B:16 , LYS B:89 , THR B:100 , GLU B:102 , SER B:104 , VAL B:109 , THR B:111 , ALA B:121 , VAL B:122BINDING SITE FOR RESIDUE CHD B 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3EM0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3EM0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3EM0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3EM0)

(-) Exons   (0, 0)

(no "Exon" information available for 3EM0)

(-) Sequences/Alignments

Asymmetric 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 Q6IMW5_DANRE | Q6IMW5 from UniProtKB/TrEMBL  Length:131

    Alignment length:131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 
         Q6IMW5_DANRE     1 MAFNGKWETESQEGYEPFCKLIGIPDDVIAKGRDFKLVTEIVQNGDDFTWTQYYPNNHVVTNKFIVGKESDMETVGGKKFKGIVSMEGGKLTISFPKYQQTTEISGGKLVETSTASGAQGTAVLVRTSKKV 131
               SCOP domains d3em0a_ A: automated matches                                                                                                        SCOP domains
               CATH domains 3em0A00 A:0-130  [code=2.40.128.20, no name defined]                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeehhhhhhhhh..hhhhhhhhh....eeeeeee..eeeeeeee...eeeeeeee....eeee.....eeee..eee..eeeee...eeeeeeee..eeeeeeeee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3em0 A   0 SAFNGKWETESQEGYEPFCKLIGIPDDVIAKGRDFKLVTEIVQNGDDFTWTQYYPNNHVVTNKFIVGKESDMETVGGKKFKGIVSMEGGKLTISFPKYQQTTEISGGKLVETSTASGAQGTAVLVRTSKKV 130
                                     9        19        29        39        49        59        69        79        89        99       109       119       129 


Chain B from PDB  Type:PROTEIN  Length:135
 aligned with Q6IMW5_DANRE | Q6IMW5 from UniProtKB/TrEMBL  Length:131

    Alignment length:135
                                                                                                                                                            131    
                                    10        20        30        40        50        60        70        80        90       100       110       120       130|    
         Q6IMW5_DANRE     1 MAFNGKWETESQEGYEPFCKLIGIPDDVIAKGRDFKLVTEIVQNGDDFTWTQYYPNNHVVTNKFIVGKESDMETVGGKKFKGIVSMEGGKLTISFPKYQQTTEISGGKLVETSTASGAQGTAVLVRTSKKV----   -
               SCOP domains d3em0b_ B: automated matches                                                                                                            SCOP domains
               CATH domains 3em0B00 B:0-134  [code=2.40.128.20, no name defined]                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeehhhhhhhhhh.hhhhhhhhh....eeeeeee..eeeeeeeehhheeeeeeee....eeee.....eeee..eee..eeeeee..eeeeeeee..eeeeeeeee....eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3em0 B   0 SAFNGKWETESQEGYEPFCKLIGIPDDVIAKGRDFKLVTEIVQNGDDFTWTQYYPNNHVVTNKFIVGKESDMETVGGKKFKGIVSMEGGKLTISFPKYQQTTEISGGKLVETSTASGAQGTAVLVRTSKKVLVPR 134
                                     9        19        29        39        49        59        69        79        89        99       109       119       129
   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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EM0)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q6IMW5_DANRE | Q6IMW5)
molecular function
    GO:0032052    bile acid binding    Interacting selectively and non-covalently with bile acids, any of a group of steroid carboxylic acids occurring in bile.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    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:0008206    bile acid metabolic process    The chemical reactions and pathways involving bile acids, any of a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

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        Q6IMW5_DANRE | Q6IMW5: 3elx 3elz

(-) Related Entries Specified in the PDB File

3elx CRYSTAL STRUCTURE OF APO ZEBRAFISH ILEAL BILE ACID-BINDIN PROTEIN.
3elz CRYSTAL STRUCTURE OF ZEBRAFISH ILEAL BILE ACID-BINDIN PROTEIN COMPLEXED WITH CHOLIC ACID (CRYSTAL FORM A).