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Asym./Biol. Unit (Jmol Viewer)

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

Title :   LIVER FATTY ACID BINDING PROTEIN-OLEATE COMPLEX

Authors :   J. Thompson, N. Winter, D. Terwey, J. Bratt, L. Banaszak

Date :   09 Dec 96 (Deposition) - 16 Jun 97 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A

Keywords :   Intracellular Lipid Transport Protein, Fatty Acid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Thompson, N. Winter, D. Terwey, J. Bratt, L. Banaszak
The Crystal Structure Of The Liver Fatty Acid-Binding Protein. A Complex With Two Bound Oleates.
J. Biol. Chem. V. 272 7140 1997
PubMed-ID: 9054409 | Reference-DOI: 10.1074/JBC.272.11.7140
(for further references see the PDB file header)

Molecule 1 - LIVER FATTY ACID BINDING PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PJBL2
	Expression System Strain	:	K12 H1
	Expression System Taxid	:	562
	Organ	:	LIVER
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Other Details	:	AMINO-TERMINAL INITIATOR METHIONINE AND MODIFIED CYSTEINE 69 PRESENT
	Synonym	:	LFABP

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 6)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP
2	BEO	1	Ligand/Ion	BUTENOIC ACID
3	OLA	2	Ligand/Ion	OLEIC ACID
4	SMC	1	Mod. Amino Acid	S-METHYLCYSTEINE
5	UNX	1	Ligand/Ion	UNKNOWN ATOM OR ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:31 , GLY A:32 , TYR A:54 , GLY A:55 , SER A:56 , LYS A:57 , ASP A:88 , ARG A:122 , OLA A:129	BINDING SITE FOR RESIDUE OLA A 128
2	AC2	SOFTWARE	SER A:39 , PHE A:63 , GLU A:72 , MET A:74 , THR A:102 , ARG A:122 , OLA A:128 , UNX A:131 , HOH A:179 , HOH A:181	BINDING SITE FOR RESIDUE OLA A 129
3	AC3	SOFTWARE	ASN A:14 , PHE A:15 , GLU A:16 , PRO A:17	BINDING SITE FOR RESIDUE BEO A 130
4	AC4	SOFTWARE	ILE A:59 , OLA A:129	BINDING SITE FOR RESIDUE UNX A 131

(no "SS Bond" information available for 1LFO)

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

(no "SAP(SNP)/Variant" information available for 1LFO)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FABP	PS00214	Cytosolic fatty-acid binding proteins signature.	FABPL_RAT	5-22	1	A:5-22

Asymmetric/Biological Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSRNOT00000008840	1	ENSRNOE00000061099	chr4:104412205-104412306	102	FABPL_RAT	1-23	23	1	A:1-23	23
1.2	ENSRNOT00000008840	2	ENSRNOE00000061517	chr4:104413761-104413933	173	FABPL_RAT	23-80	58	1	A:23-80	58
1.3	ENSRNOT00000008840	3	ENSRNOE00000061670	chr4:104415158-104415250	93	FABPL_RAT	81-111	31	1	A:81-111	31
1.4	ENSRNOT00000008840	4	ENSRNOE00000061878	chr4:104415861-104415981	121	FABPL_RAT	112-127	16	1	A:112-127	16

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
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Chain A from PDB  Type:PROTEIN  Length:128
 aligned with FABPL_RAT | P02692 from UniProtKB/Swiss-Prot  Length:127

    Alignment length:128
                             1                                                                                                                              
                             |       9        19        29        39        49        59        69        79        89        99       109       119        
            FABPL_RAT     - -MNFSGKYQVQSQENFEPFMKAMGLPEDLIQKGKDIKGVSEIVHEGKKVKLTITYGSKVIHNEFTLGEECELETMTGEKVKAVVKMEGDNKMVTTFKGIKSVTEFNGDTITNTMTLGDIVYKRVSKRI 127
               SCOP domains d1lfoa_ A: Liver fatty acid binding protein                                                                                      SCOP domains
               CATH domains -1lfoA00 A:1-127  [code=2.40.128.20, no name defined]                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee.hhhhhhhh...hhhhhhhhh...eeeeeee..eeeeeeee..eeeeeeee...................eee...eeeeee..eeeeeeee..eeeeeeee..eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----FABP  PDB: A:5-22 --------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) -Exon 1.1  PDB: A:1-23  ---------------------------------------------------------Exon 1.3  PDB: A:81-111        Exon 1.4         Transcript 1 (1)
           Transcript 1 (2) -----------------------Exon 1.2  PDB: A:23-80 UniProt: 23-80                     ----------------------------------------------- Transcript 1 (2)
                 1lfo A   0 xMNFSGKYQVQSQENFEPFMKAMGLPEDLIQKGKDIKGVSEIVHEGKKVKLTITYGSKVIHNEFTLGEEcELETMTGEKVKAVVKMEGDNKMVTTFKGIKSVTEFNGDTITNTMTLGDIVYKRVSKRI 127
                            |        9        19        29        39        49        59        69        79        89        99       109       119        
                            |                                                                   69-SMC                                                      
                            0-ACE

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	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: Liver fatty acid binding protein (26)

Norway rat (Rattus norvegicus) [TaxId: 10116] (4)

d1lfoa_

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)

Norway rat (Rattus norvegicus) (24)

1lfoA00

A:1-127

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (FABPL_RAT | P02692)

molecular function
	GO:0016209	antioxidant activity	Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
	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:0003682	chromatin binding	Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	GO:0008144	drug binding	Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
	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:0005324	long-chain fatty acid transporter activity	Enables the directed movement of long-chain fatty acids into, out of or within a cell, or between cells. A long-chain fatty acid is a fatty acid with a chain length between C13 and C22.
	GO:0051978	lysophospholipid transporter activity	Enables the directed movement of lysophospholipids into, out of or within a cell, or between cells. A lysophospholipid is a phospholipid that lacks one of its fatty acyl chains; it is an intermediate formed during digestion of dietary and biliary phospholipids.
	GO:0005543	phospholipid binding	Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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:0098869	cellular oxidant detoxification	Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
	GO:0070301	cellular response to hydrogen peroxide	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 hydrogen peroxide (H2O2) stimulus.
	GO:0071456	cellular response to hypoxia	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 stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
	GO:0050892	intestinal absorption	Any process in which nutrients are taken up from the contents of the intestine.
	GO:0015909	long-chain fatty acid transport	The directed movement of long-chain fatty acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A long-chain fatty acid is a fatty acid with a chain length between C13 and C22.
	GO:0051977	lysophospholipid transport	The directed movement of phospholipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A lysophospholipid is a phospholipid that lacks one of its fatty acyl chains; it is an intermediate formed during digestion of dietary and biliary phospholipids.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0043154	negative regulation of cysteine-type endopeptidase activity involved in apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of a cysteine-type endopeptidase activity involved in the apoptotic process.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:0002230	positive regulation of defense response to virus by host	Any host process that results in the promotion of antiviral immune response mechanisms, thereby limiting viral replication.
	GO:0032000	positive regulation of fatty acid beta-oxidation	Any process that activates or increases the frequency, rate or extent of fatty acid beta-oxidation.
	GO:0051345	positive regulation of hydrolase activity	Any process that activates or increases the frequency, rate or extent of hydrolase activity, the catalysis of the hydrolysis of various bonds.
	GO:0098779	positive regulation of macromitophagy in response to mitochondrial depolarization	The macromitophagy process that is triggered by a detection of the loss of mitochondrial membrane potential.
	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:0098792	xenophagy	The macroautophagy process in which a region of cytoplasm containing an intracellular pathogen or some part of an intracellular pathogen (e.g. viral capsid) is enclosed in a double membrane bound autophagosome, which then fuses with the lysosome leading to degradation of the contents.
cellular component
	GO:0045179	apical cortex	The region that lies just beneath the plasma membrane on the apical edge of a cell.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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.
	GO:0005782	peroxisomal matrix	The volume contained within the membranes of a peroxisome; in many cells the matrix contains a crystalloid core largely composed of urate oxidase.
	GO:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

Asymmetric/Biological Unit
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(no "Related Entries Specified in the PDB File" available for 1LFO)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 6)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (4, 4)

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