3ELZ - JenaLib

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Title :   CRYSTAL STRUCTURE OF ZEBRAFISH ILEAL BILE ACID-BINDIN PROTEIN COMPLEXED WITH CHOLIC ACID (CRYSTAL FORM A).

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,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (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

Molecule 1 - ILEAL BILE ACID-BINDING PROTEIN
	Chains	:	A, B, C
	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)

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 13)

No.	Name	Count	Type	Full Name
1	CHD	13	Ligand/Ion	CHOLIC ACID

Biological Unit 1 (1, 5)

No.	Name	Count	Type	Full Name
1	CHD	5	Ligand/Ion	CHOLIC ACID

Biological Unit 2 (1, 5)

No.	Name	Count	Type	Full Name
1	CHD	5	Ligand/Ion	CHOLIC ACID

Biological Unit 3 (1, 3)

No.	Name	Count	Type	Full Name
1	CHD	3	Ligand/Ion	CHOLIC ACID

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TRP A:49 , PHE A:63 , GLU A:72 , THR A:73 , VAL A:74 , VAL A:83 , LEU A:90 , ILE A:92 , TYR A:97 , GLN A:99 , THR A:101 , CHD A:151 , CHD A:200 , HOH A:201 , HOH A:202 , HOH A:203	BINDING SITE FOR RESIDUE CHD A 150
02	AC2	SOFTWARE	TYR A:14 , GLY A:31 , TYR A:53 , VAL A:74 , LEU A:123 , ARG A:125 , CHD A:150 , HOH A:204	BINDING SITE FOR RESIDUE CHD A 151
03	AC3	SOFTWARE	HIS A:57 , CHD B:152 , CHD B:200	BINDING SITE FOR RESIDUE CHD A 152
04	AC4	SOFTWARE	THR A:73 , LYS A:78 , CHD A:200 , HOH A:237	BINDING SITE FOR RESIDUE CHD A 153
05	AC5	SOFTWARE	THR A:73 , VAL A:74 , GLY A:75 , CHD A:150 , CHD A:153 , PRO B:24 , ASP B:26	BINDING SITE FOR RESIDUE CHD A 200
06	AC6	SOFTWARE	TRP B:49 , GLN B:51 , GLU B:72 , THR B:73 , VAL B:74 , LEU B:90 , ILE B:92 , TYR B:97 , GLN B:99 , THR B:101 , CHD B:153 , CHD B:200 , HOH B:245	BINDING SITE FOR RESIDUE CHD B 150
07	AC7	SOFTWARE	TYR B:14 , ILE B:23 , GLY B:31 , TYR B:53 , VAL B:74 , LEU B:123 , CHD B:200 , HOH B:231 , HOH B:234 , HOH B:246 , HOH B:264	BINDING SITE FOR RESIDUE CHD B 151
08	AC8	SOFTWARE	CHD A:152 , PRO B:54 , ASN B:55	BINDING SITE FOR RESIDUE CHD B 152
09	AC9	SOFTWARE	THR B:73 , LYS B:77 , LYS B:78 , PHE B:79 , SER B:115 , CHD B:150 , PRO C:95	BINDING SITE FOR RESIDUE CHD B 153
10	BC1	SOFTWARE	PRO A:24 , CHD A:152 , PRO B:24 , THR B:73 , VAL B:74 , GLY B:75 , LYS B:77 , CHD B:150 , CHD B:151	BINDING SITE FOR RESIDUE CHD B 200
11	BC2	SOFTWARE	TRP C:49 , GLN C:51 , GLU C:72 , THR C:73 , VAL C:74 , LEU C:90 , ILE C:92 , TYR C:97 , GLN C:99 , THR C:101 , CHD C:153 , HOH C:253	BINDING SITE FOR RESIDUE CHD C 150
12	BC3	SOFTWARE	TYR C:14 , VAL C:27 , LYS C:30 , TYR C:53 , LEU C:123	BINDING SITE FOR RESIDUE CHD C 151
13	BC4	SOFTWARE	PRO B:95 , ILE C:21 , THR C:73 , LYS C:77 , LYS C:78 , LYS C:96 , SER C:115 , CHD C:150	BINDING SITE FOR RESIDUE CHD C 153

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

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

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

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

(no "Exon" information available for 3ELZ)

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:132
 aligned with Q6IMW5_DANRE | Q6IMW5 from UniProtKB/TrEMBL  Length:131

    Alignment length:132
                             1                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129  
         Q6IMW5_DANRE     - -MAFNGKWETESQEGYEPFCKLIGIPDDVIAKGRDFKLVTEIVQNGDDFTWTQYYPNNHVVTNKFIVGKESDMETVGGKKFKGIVSMEGGKLTISFPKYQQTTEISGGKLVETSTASGAQGTAVLVRTSKKV 131
               SCOP domains d3elza_ A: automated matches                                                                                                         SCOP domains
               CATH domains 3elzA00 A:-1-130  [code=2.40.128.20, no name defined]                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeeeeehhhhhhhhh..hhhhhhhhh....eeeeeee..eeeeeeeehhheeeeeeee....eeee.....eeee.eeee..eeeeee..eeeeeeee..eeeeeeeee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3elz A  -1 GSAFNGKWETESQEGYEPFCKLIGIPDDVIAKGRDFKLVTEIVQNGDDFTWTQYYPNNHVVTNKFIVGKESDMETVGGKKFKGIVSMEGGKLTISFPKYQQTTEISGGKLVETSTASGAQGTAVLVRTSKKV 130
                                     8        18        28        38        48        58        68        78        88        98       108       118       128

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

    Alignment length:135
                               1                                                                                                                               131 
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127   | 
         Q6IMW5_DANRE     - ---MAFNGKWETESQEGYEPFCKLIGIPDDVIAKGRDFKLVTEIVQNGDDFTWTQYYPNNHVVTNKFIVGKESDMETVGGKKFKGIVSMEGGKLTISFPKYQQTTEISGGKLVETSTASGAQGTAVLVRTSKKV-   -
               SCOP domains d3elzb_ B: automated matches                                                                                                            SCOP domains
               CATH domains 3elzB00 B:-3-131  [code=2.40.128.20, no name defined]                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeehhhhhhhhhh.hhhhhhhhh....eeeeeee..eeeeeeee...eeeeeeee....eeee.....eeee..eee..eeeeee..eeeeeeee..eeeeeeeeee..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3elz B  -3 MRGSAFNGKWETESQEGYEPFCKLIGIPDDVIAKGRDFKLVTEIVQNGDDFTWTQYYPNNHVVTNKFIVGKESDMETVGGKKFKGIVSMEGGKLTISFPKYQQTTEISGGKLVETSTASGAQGTAVLVRTSKKVL 131
                                     6        16        26        36        46        56        66        76        86        96       106       116       126

Chain C from PDB  Type:PROTEIN  Length:134
 aligned with Q6IMW5_DANRE | Q6IMW5 from UniProtKB/TrEMBL  Length:131

    Alignment length:134
                                                                                                                                                            131   
                                    10        20        30        40        50        60        70        80        90       100       110       120       130|   
         Q6IMW5_DANRE     1 MAFNGKWETESQEGYEPFCKLIGIPDDVIAKGRDFKLVTEIVQNGDDFTWTQYYPNNHVVTNKFIVGKESDMETVGGKKFKGIVSMEGGKLTISFPKYQQTTEISGGKLVETSTASGAQGTAVLVRTSKKV---   -
               SCOP domains d3elzc_ C: automated matches                                                                                                           SCOP domains
               CATH domains 3elzC00 C:0-133  [code=2.40.128.20, no name defined]                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeehhhhhhhhh..hhhhhh.......eeeeeee..eeeeeeee...eeeeeeee....eeee.....eeee..eee..eeeeee..eeeeeeee..eeeeeeeeee..eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3elz C   0 SAFNGKWETESQEGYEPFCKLIGIPDDVIAKGRDFKLVTEIVQNGDDFTWTQYYPNNHVVTNKFIVGKESDMETVGGKKFKGIVSMEGGKLTISFPKYQQTTEISGGKLVETSTASGAQGTAVLVRTSKKVLVP 133
                                     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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Lipocalins (514)

Superfamily: Lipocalins (514)

Family: automated matches (40)

Protein domain: automated matches (40)

Zebrafish (Danio rerio) [TaxId: 7955] (3)

1a	d3elza_	A:
1b	d3elzb_	B:
1c	d3elzc_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Lipocalin (526)

Homologous Superfamily: [code=2.40.128.20, no name defined] (352)

Leopard danio,zebra danio,zebra fish (Danio rerio) (3)

1a	3elzB00	B:-3-131
1b	3elzC00	C:0-133
1c	3elzA00	A:-1-130

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (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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	Q6IMW5_DANRE \| Q6IMW5	:	3elx 3em0

3elx	CRYSTAL STRUCTURE OF APO ZEBRAFISH ILEAL BILE ACID-BINDIN PROTEIN.
3em0	CRYSTAL STRUCTURE OF ZEBRAFISH ILEAL BILE ACID-BINDIN PROTEIN COMPLEXED WITH CHOLIC ACID (CRYSTAL FORM B).

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Ligands, Modified Residues, Ions (1, 13)

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