2QM9 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   TROGLITAZONE BOUND TO FATTY ACID BINDING PROTEIN 4

Authors :   R. E. Gillilan, S. D. Ayers, N. Noy

Date :   14 Jul 07 (Deposition) - 09 Oct 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.31

Chains :   Asym./Biol. Unit : A,B

Keywords :   Beta Clamshell, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. E. Gillilan, S. D. Ayers, N. Noy
Structural Basis For Activation Of Fatty Acid-Binding Protein 4
J. Mol. Biol. V. 372 1246 2007
PubMed-ID: 17761196 | Reference-DOI: 10.1016/J.JMB.2007.07.040

Molecule 1 - FATTY ACID-BINDING PROTEIN, ADIPOCYTE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	FABP4, AP2
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	AFABP, ADIPOCYTE LIPID-BINDING PROTEIN, ALBP, A-FABP, P2 ADIPOCYTE PROTEIN, MYELIN P2 PROTEIN HOMOLOG, 3T3-L1 LIPID-BINDING PROTEIN, 422 PROTEIN, P15

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 5)

No.	Name	Count	Type	Full Name
1	SO4	3	Ligand/Ion	SULFATE ION
2	TDZ	2	Ligand/Ion	(5R)-5-(4-{[(2R)-6-HYDROXY-2,5,7,8-TETRAMETHYL-3,4-DIHYDRO-2H-CHROMEN-2-YL]METHOXY}BENZYL)-1,3-THIAZOLIDINE-2,4-DIONE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER B:13 , GLU B:14 , ASN B:15 , PHE B:16 , ASP B:17	BINDING SITE FOR RESIDUE SO4 B 302
2	AC2	SOFTWARE	SER A:13 , GLU A:14 , ASN A:15 , PHE A:16 , ASP A:17 , HOH A:337	BINDING SITE FOR RESIDUE SO4 A 303
3	AC3	SOFTWARE	SER A:-5 , ARG A:108 , ARG A:130 , ARG B:108 , ARG B:130	BINDING SITE FOR RESIDUE SO4 A 301
4	AC4	SOFTWARE	TYR A:19 , VAL A:25 , PHE A:57 , ASP A:76 , ARG A:78 , CYS A:117 , TYR A:128 , HOH A:339	BINDING SITE FOR RESIDUE TDZ A 201
5	AC5	SOFTWARE	TYR B:19 , MET B:20 , VAL B:25 , ASP B:76 , ARG B:78 , ILE B:104 , CYS B:117	BINDING SITE FOR RESIDUE TDZ B 202

(no "SS Bond" information available for 2QM9)

Asymmetric/Biological Unit

No.	Residues
1	Ser A:-7	-	Ser A:-6
2	Ser A:-5	-	Lys A:-4

(no "SAP(SNP)/Variant" information available for 2QM9)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FABP	PS00214	Cytosolic fatty-acid binding proteins signature.	FABP4_MOUSE	7-24	2	A:6-23 B:6-23

(no "Exon" information available for 2QM9)

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:139
 aligned with FABP4_MOUSE | P04117 from UniProtKB/Swiss-Prot  Length:132

    Alignment length:139
                                   1                                                                                                                                   
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123         
          FABP4_MOUSE     - -------MCDAFVGTWKLVSSENFDDYMKEVGVGFATRKVAGMAKPNMIISVNGDLVTIRSESTFKNTEISFKLGVEFDEITADDRKVKSIITLDGGALVQVQKWDGKSTTIKRKRDGDKLVVECVMKGVTSTRVYERA 132
               SCOP domains d2qm9a_ A: Adipocyte lipid-binding protein, ALBP                                                                                            SCOP domains
               CATH domains 2qm9A00 A:-7-131  [code=2.40.128.20, no name defined]                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeeeeehhhhhhhhhh.hhhhhhhhhh...eeeeeee..eeeeeee.....eeeee.....eeee.....eeeeeeeee..eeeeeeee..eeeeeeeeee..eeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------FABP  PDB: A:6-23 ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qm9 A  -7 SSSKVYKMCDAFVGTWKLVSSENFDDYMKEVGVGFATRKVAGMAKPNMIISVNGDLVTIRSESTFKNTEISFKLGVEFDEITADDRKVKSIITLDGGALVQVQKWDGKSTTIKRKRDGDKLVVECVMKGVTSTRVYERA 131
                                     2        12        22        32        42        52        62        72        82        92       102       112       122

Chain B from PDB  Type:PROTEIN  Length:132
 aligned with FABP4_MOUSE | P04117 from UniProtKB/Swiss-Prot  Length:132

    Alignment length:132
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  
          FABP4_MOUSE     1 MCDAFVGTWKLVSSENFDDYMKEVGVGFATRKVAGMAKPNMIISVNGDLVTIRSESTFKNTEISFKLGVEFDEITADDRKVKSIITLDGGALVQVQKWDGKSTTIKRKRDGDKLVVECVMKGVTSTRVYERA 132
               SCOP domains d2qm9b_ B: Adipocyte lipid-binding protein, ALBP                                                                                     SCOP domains
               CATH domains 2qm9B00 B:0-131  [code=2.40.128.20, no name defined]                                                                                 CATH domains
           Pfam domains (1) -----Lipocalin-2qm9B01 B:5-131                                                                                                       Pfam domains (1)
           Pfam domains (2) -----Lipocalin-2qm9B02 B:5-131                                                                                                       Pfam domains (2)
         Sec.struct. author hhhhh.eeeeeeeeehhhhhhhhhh.hhhhhhhhhh...eeeeeee..eeeeeee.....eeeee.....eeee.....eeeeeeeee..eeeeeeee..eeeeeeeeee..eeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------FABP  PDB: B:6-23 ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qm9 B   0 MCDAFVGTWKLVSSENFDDYMKEVGVGFATRKVAGMAKPNMIISVNGDLVTIRSESTFKNTEISFKLGVEFDEITADDRKVKSIITLDGGALVQVQKWDGKSTTIKRKRDGDKLVVECVMKGVTSTRVYERA 131
                                     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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Lipocalins (514)

Superfamily: Lipocalins (514)

Family: Fatty acid binding protein-like (183)

Protein domain: Adipocyte lipid-binding protein, ALBP (34)

Mouse (Mus musculus) [TaxId: 10090] (19)

1a	d2qm9a_	A:
1b	d2qm9b_	B:

Asymmetric/Biological 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)

House mouse (Mus musculus) (39)

1a	2qm9A00	A:-7-131
1b	2qm9B00	B:0-131

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Calycin (163)

Family: Lipocalin (123)

Mus musculus (Mouse) (25)

1a	Lipocalin-2qm9B01	B:5-131
1b	Lipocalin-2qm9B02	B:5-131

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (FABP4_MOUSE | P04117)

molecular function
	GO:0005504	fatty acid binding	Interacting selectively and non-covalently with fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
	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:0050873	brown fat cell differentiation	The process in which a relatively unspecialized cell acquires specialized features of a brown adipocyte, an animal connective tissue cell involved in adaptive thermogenesis. Brown adipocytes contain multiple small droplets of triglycerides and a high number of mitochondria.
	GO:0071285	cellular response to lithium ion	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lithium (Li+) ion stimulus.
	GO:0042632	cholesterol homeostasis	Any process involved in the maintenance of an internal steady state of cholesterol within an organism or cell.
	GO:0001816	cytokine production	The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
	GO:0006469	negative regulation of protein kinase activity	Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity.
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0050729	positive regulation of inflammatory response	Any process that activates or increases the frequency, rate or extent of the inflammatory response.
	GO:0050727	regulation of inflammatory response	Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents.
	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.
	GO:0050872	white fat cell differentiation	The process in which a relatively unspecialized cell acquires specialized features of a white adipocyte, an animal connective tissue cell involved in energy storage. White adipocytes have cytoplasmic lipids arranged in a unique vacuole.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric/Biological Unit
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		Ser A:-7 - Ser A:-6	[ RasMol ]

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Description

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SS Bonds (0, 0)

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