3FIQ - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   ODORANT BINDING PROTEIN OBP1

Authors :   S. A. White

Date :   12 Dec 08 (Deposition) - 19 May 09 (Release) - 19 May 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Lipocalin, Oderant-Binding Protein, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. A. White, L. Briand, D. J. Scott, A. J. Borysik
Structure Of Rat Odorant-Binding Protein Obp1 At 1. 6 A Resolution
Acta Crystallogr. , Sect. D V. 65 403 2009
PubMed-ID: 19390145 | Reference-DOI: 10.1107/S090744490900420X
(for further references see the PDB file header)

Molecule 1 - ODORANT-BINDING PROTEIN 1F
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Common	:	YEAST
	Expression System Plasmid	:	PPIC9
	Expression System Strain	:	GS115
	Expression System Taxid	:	4922
	Expression System Vector Type	:	PLASMID
	Gene	:	OBP1F, OBP-1F, RCG_36470
	Organism Common	:	RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	OBP1, RCG36470

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 5)

No.	Name	Count	Type	Full Name
1	EDO	5	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	EDO	3	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:32 , LEU A:59 , ASP A:60 , HIS A:73 , ASP A:75 , ARG A:77	BINDING SITE FOR RESIDUE EDO A 158
2	AC2	SOFTWARE	SER A:10 , HOH A:248 , TYR B:87 , HOH B:168 , HOH B:429	BINDING SITE FOR RESIDUE EDO A 159
3	AC3	SOFTWARE	THR A:65 , HIS A:66 , THR A:67 , GLU B:50	BINDING SITE FOR RESIDUE EDO A 160
4	AC4	SOFTWARE	GLN A:64 , THR A:65 , HIS A:66 , HOH A:232 , GLY B:45 , ASP B:46 , GLN B:49 , GLU B:50	BINDING SITE FOR RESIDUE EDO B 158
5	AC5	SOFTWARE	ASP A:95 , ASP A:96 , ASP B:75 , ARG B:77 , HOH B:281	BINDING SITE FOR RESIDUE EDO B 159

Asymmetric Unit

No.	Residues
1	A:44	-	A:48
2	A:63	-	A:155
3	B:44	-	B:48
4	B:63	-	B:155

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

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LIPOCALIN	PS00213	Lipocalin signature.	OBP_RAT	22-35	2	A:6-19 B:6-19

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LIPOCALIN	PS00213	Lipocalin signature.	OBP_RAT	22-35	1	A:6-19 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LIPOCALIN	PS00213	Lipocalin signature.	OBP_RAT	22-35	1	- B:6-19

(no "Exon" information available for 3FIQ)

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:154
 aligned with OBP_RAT | P08937 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:154
                                                                                                                                        129                                           
                                                                                                                                      128 |                                           
                                    29        39        49        59        69        79        89        99       109       119        |-|      138       148       158       168    
              OBP_RAT    20 NLDISPSEVNGDWRTLYIVADNVEKVAEGGSLRAYFQHMECGDECQELKIIFNVKLDSECQTHTVVGQKHEDGRYTTDYSGRNYFHVLKKTDDIIFFHNVNVDESGRRQ-CDLVAGKREDLNKAQKQELRKLAEEYNIPNENTQHLVPTDTCNQ 172
               SCOP domains d3fiqa_ A: automated matches                                                                                                                               SCOP domains
               CATH domains 3fiqA00 A:4-157  [code=2.40.128.20, no name defined]                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhee.eeeeeee.hhhhh........eeeeeee.hhh.eeeeeeeeee..eeeeeeeeeee.....eeee...eeeeeeeee...eeeeeeeee.....eeeeeeeee.....hhhhhhhhhhhhhhh..hhhhhee.hhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --LIPOCALIN     ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fiq A   4 NLDISPSEVNGDWRTLYIVADNVEKVAEGGSLRAYFQHMECGDECQELKIIFNVKLDSECQTHTVVGQKHEDGRYTTDYSGRNYFHVLKKTDDIIFFHNVNVDESGKETNVILVAGKREDLNKAQKQELRKLAEEYNIPNENTQHLVPTDTCNQ 157
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153

Chain A from PDB  Type:PROTEIN  Length:154
 aligned with Q9QYU9_RAT | Q9QYU9 from UniProtKB/TrEMBL  Length:173

    Alignment length:154
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169    
           Q9QYU9_RAT    20 NLDISPSEVNGDWRTLYIVADNVEKVAEGGSLRAYFQHMECGDECQELKIIFNVKLDSECQTHTVVGQKHEDGRYTTDYSGRNYFHVLKKTDDIIFFHNVNVDESGKETNVILVAGKREDLNKAQKQELRKLAEEYNIPNENTQHLVPTDTCNQ 173
               SCOP domains d3fiqa_ A: automated matches                                                                                                                               SCOP domains
               CATH domains 3fiqA00 A:4-157  [code=2.40.128.20, no name defined]                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhee.eeeeeee.hhhhh........eeeeeee.hhh.eeeeeeeeee..eeeeeeeeeee.....eeee...eeeeeeeee...eeeeeeeee.....eeeeeeeee.....hhhhhhhhhhhhhhh..hhhhhee.hhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fiq A   4 NLDISPSEVNGDWRTLYIVADNVEKVAEGGSLRAYFQHMECGDECQELKIIFNVKLDSECQTHTVVGQKHEDGRYTTDYSGRNYFHVLKKTDDIIFFHNVNVDESGKETNVILVAGKREDLNKAQKQELRKLAEEYNIPNENTQHLVPTDTCNQ 157
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153

Chain B from PDB  Type:PROTEIN  Length:157
 aligned with OBP_RAT | P08937 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:157
                                                                                                                                           129                                           
                                                                                                                                         128 |                                           
                                    26        36        46        56        66        76        86        96       106       116       126 | |   135       145       155       165       
              OBP_RAT    17 HHENLDISPSEVNGDWRTLYIVADNVEKVAEGGSLRAYFQHMECGDECQELKIIFNVKLDSECQTHTVVGQKHEDGRYTTDYSGRNYFHVLKKTDDIIFFHNVNVDESGRRQ-CDLVAGKREDLNKAQKQELRKLAEEYNIPNENTQHLVPTDTCNQ 172
               SCOP domains d3fiqb_ B: automated matches                                                                                                                                  SCOP domains
               CATH domains 3fiqB00 B:1-157  [code=2.40.128.20, no name defined]                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhee.eeeeeee.hhhhh........eeeeeee.hhh.eeeeeeeeee..eeeeeeeeeee.....eeee...eeeeeeeeee..eeeeeeeee.....eeeeeeeee.....hhhhhhhhhhhhhhh..hhhhhee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----LIPOCALIN     ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fiq B   1 HHENLDISPSEVNGDWRTLYIVADNVEKVAEGGSLRAYFQHMECGDECQELKIIFNVKLDSECQTHTVVGQKHEDGRYTTDYSGRNYFHVLKKTDDIIFFHNVNVDESGKETNVILVAGKREDLNKAQKQELRKLAEEYNIPNENTQHLVPTDTCNQ 157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain B from PDB  Type:PROTEIN  Length:157
 aligned with Q9QYU9_RAT | Q9QYU9 from UniProtKB/TrEMBL  Length:173

    Alignment length:157
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       
           Q9QYU9_RAT    17 HHENLDISPSEVNGDWRTLYIVADNVEKVAEGGSLRAYFQHMECGDECQELKIIFNVKLDSECQTHTVVGQKHEDGRYTTDYSGRNYFHVLKKTDDIIFFHNVNVDESGKETNVILVAGKREDLNKAQKQELRKLAEEYNIPNENTQHLVPTDTCNQ 173
               SCOP domains d3fiqb_ B: automated matches                                                                                                                                  SCOP domains
               CATH domains 3fiqB00 B:1-157  [code=2.40.128.20, no name defined]                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhee.eeeeeee.hhhhh........eeeeeee.hhh.eeeeeeeeee..eeeeeeeeeee.....eeee...eeeeeeeeee..eeeeeeeee.....eeeeeeeee.....hhhhhhhhhhhhhhh..hhhhhee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fiq B   1 HHENLDISPSEVNGDWRTLYIVADNVEKVAEGGSLRAYFQHMECGDECQELKIIFNVKLDSECQTHTVVGQKHEDGRYTTDYSGRNYFHVLKKTDDIIFFHNVNVDESGKETNVILVAGKREDLNKAQKQELRKLAEEYNIPNENTQHLVPTDTCNQ 157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

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)

Norway rat (Rattus norvegicus) [TaxId: 10116] (2)

1a	d3fiqa_	A:
1b	d3fiqb_	B:

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)

Rat (Rattus norvegicus) (2)

1a	3fiqA00	A:4-157
1b	3fiqB00	B:1-157

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (OBP_RAT | P08937)

molecular function
	GO:0005549	odorant binding	Interacting selectively and non-covalently with an odorant, any substance capable of stimulating the sense of smell.
	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:0050896	response to stimulus	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
	GO:0007608	sensory perception of smell	The series of events required for an organism to receive an olfactory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Olfaction involves the detection of chemical composition of an organism's ambient medium by chemoreceptors. This is a neurological 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.

Chain A,B (Q9QYU9_RAT | Q9QYU9)

molecular function
	GO:0005549	odorant binding	Interacting selectively and non-covalently with an odorant, any substance capable of stimulating the sense of smell.
	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: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.

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Description

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