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(-) Description

Title :  CRYSTAL STRUCTURE OF RAT ODORANT BINDING PROTEIN 3 (OBP3)
 
Authors :  K. L. Portman, J. Long, S. Carr, L. Brand, D. J. Winzor, M. Searle, D. J. Sc
Date :  05 Mar 13  (Deposition) - 12 Mar 14  (Release) - 14 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Odorant Binding Protein, Lipocalin, Enthalpy-Entropy (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. L. Portman, J. Long, S. Carr, L. Briand, D. J. Winzor, M. S. Searle, D. J. Scott
Enthalpy/Entropy Compensation Effects From Cavity Desolvation Underpin Broad Ligand Binding Selectivity For Rat Odorant Binding Protein 3
Biochemistry V. 53 2371 2014
PubMed-ID: 24665925  |  Reference-DOI: 10.1021/BI5002344

(-) Compounds

Molecule 1 - OBP3 PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE31
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: ODORANT BINDING PROTEIN 3, PROTEIN LOC259244, RCG31933, ISOFORM CRA_A, RAT SALIVARY GLAND (ALPHA)2(MU) GLOBULIN, TYPE 1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3ZQ3)

(-) Sites  (0, 0)

(no "Site" information available for 3ZQ3)

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:83 -A:176
2B:83 -B:176
3C:83 -C:176
4D:83 -D:176

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ZQ3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZQ3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ZQ3)

(-) Exons   (0, 0)

(no "Exon" information available for 3ZQ3)

(-) 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:159
 aligned with Q63213_RAT | Q63213 from UniProtKB/TrEMBL  Length:181

    Alignment length:159
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169         
           Q63213_RAT    20 EEASFERGNLDVDKLNGDWFSIVVASDKREKIEENGSMRVFVQHIDVLENSLGFTFRIKENGVCTEFSLVADKTAKDGEYFVEYDGENTFTILKTDYDNYVMFHLVNVNNGETFQLMELYGRTKDLSSDIKEKFAKLCVAHGITRDNIIDLTKTDRCLQ 178
               SCOP domains d3zq3a_ A: automated matches                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhee.eeeeeee.hhhhhh......eeeeeeeee..eeeeeeeeee..eeeeeeeeeee......eeee...eeeeeeeee....eeeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhhhhh..hhh.eee.hhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zq3 A  20 EEASFERGNLDVDKLNGDWFSIVVASDKREKIEENGSMRVFVQHIDVLENSLGFTFRIKENGVCTEFSLVADKTAKDGEYFVEYDGENTFTILKTDYDNYVMFHLVNVNNGETFQLMELYGRTKDLSSDIKEKFAKLCVAHGITRDNIIDLTKTDRCLQ 178
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169         


Chain A from PDB  Type:PROTEIN  Length:159
 aligned with Q78E14_RAT | Q78E14 from UniProtKB/TrEMBL  Length:179

    Alignment length:159
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169         
           Q78E14_RAT    20 EEASFERGNLDVDKLNGDWFSIVVASDKREKIEENGSMRVFVQHIDVLENSLGFTFRIKENGVCTEFSLVADKTAKDGEYFVEYDGENTFTILKTDYDNYVMFHLVNVNNGETFQLMELYGRTKDLSSDIKEKFAKLCVAHGITRDNIIDLTKTDRCLQ 178
               SCOP domains d3zq3a_ A: automated matches                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhee.eeeeeee.hhhhhh......eeeeeeeee..eeeeeeeeee..eeeeeeeeeee......eeee...eeeeeeeee....eeeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhhhhh..hhh.eee.hhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zq3 A  20 EEASFERGNLDVDKLNGDWFSIVVASDKREKIEENGSMRVFVQHIDVLENSLGFTFRIKENGVCTEFSLVADKTAKDGEYFVEYDGENTFTILKTDYDNYVMFHLVNVNNGETFQLMELYGRTKDLSSDIKEKFAKLCVAHGITRDNIIDLTKTDRCLQ 178
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169         


Chain B from PDB  Type:PROTEIN  Length:159
 aligned with Q63213_RAT | Q63213 from UniProtKB/TrEMBL  Length:181

    Alignment length:159
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169         
           Q63213_RAT    20 EEASFERGNLDVDKLNGDWFSIVVASDKREKIEENGSMRVFVQHIDVLENSLGFTFRIKENGVCTEFSLVADKTAKDGEYFVEYDGENTFTILKTDYDNYVMFHLVNVNNGETFQLMELYGRTKDLSSDIKEKFAKLCVAHGITRDNIIDLTKTDRCLQ 178
               SCOP domains d3zq3b_ B: automated matches                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhee.eeeeeee.hhhhhh......eeeeeeeee..eeeeeeeeee..eeeeeeeeeee......eeee...eeeeeeeee....eeeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhhhhh..hhh.eee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zq3 B  20 EEASFERGNLDVDKLNGDWFSIVVASDKREKIEENGSMRVFVQHIDVLENSLGFTFRIKENGVCTEFSLVADKTAKDGEYFVEYDGENTFTILKTDYDNYVMFHLVNVNNGETFQLMELYGRTKDLSSDIKEKFAKLCVAHGITRDNIIDLTKTDRCLQ 178
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169         


Chain B from PDB  Type:PROTEIN  Length:159
 aligned with Q78E14_RAT | Q78E14 from UniProtKB/TrEMBL  Length:179

    Alignment length:159
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169         
           Q78E14_RAT    20 EEASFERGNLDVDKLNGDWFSIVVASDKREKIEENGSMRVFVQHIDVLENSLGFTFRIKENGVCTEFSLVADKTAKDGEYFVEYDGENTFTILKTDYDNYVMFHLVNVNNGETFQLMELYGRTKDLSSDIKEKFAKLCVAHGITRDNIIDLTKTDRCLQ 178
               SCOP domains d3zq3b_ B: automated matches                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhee.eeeeeee.hhhhhh......eeeeeeeee..eeeeeeeeee..eeeeeeeeeee......eeee...eeeeeeeee....eeeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhhhhh..hhh.eee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zq3 B  20 EEASFERGNLDVDKLNGDWFSIVVASDKREKIEENGSMRVFVQHIDVLENSLGFTFRIKENGVCTEFSLVADKTAKDGEYFVEYDGENTFTILKTDYDNYVMFHLVNVNNGETFQLMELYGRTKDLSSDIKEKFAKLCVAHGITRDNIIDLTKTDRCLQ 178
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169         


Chain C from PDB  Type:PROTEIN  Length:159
 aligned with Q63213_RAT | Q63213 from UniProtKB/TrEMBL  Length:181

    Alignment length:159
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169         
           Q63213_RAT    20 EEASFERGNLDVDKLNGDWFSIVVASDKREKIEENGSMRVFVQHIDVLENSLGFTFRIKENGVCTEFSLVADKTAKDGEYFVEYDGENTFTILKTDYDNYVMFHLVNVNNGETFQLMELYGRTKDLSSDIKEKFAKLCVAHGITRDNIIDLTKTDRCLQ 178
               SCOP domains d3zq3c_ C: automated matches                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhee.eeeeeee.hhhhhh......eeeeeeeee..eeeeeeeeee..eeeeeeeeeee......eeee...eeeeeeeee....eeeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhhhhh..hhh.eee.hhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zq3 C  20 EEASFERGNLDVDKLNGDWFSIVVASDKREKIEENGSMRVFVQHIDVLENSLGFTFRIKENGVCTEFSLVADKTAKDGEYFVEYDGENTFTILKTDYDNYVMFHLVNVNNGETFQLMELYGRTKDLSSDIKEKFAKLCVAHGITRDNIIDLTKTDRCLQ 178
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169         


Chain C from PDB  Type:PROTEIN  Length:159
 aligned with Q78E14_RAT | Q78E14 from UniProtKB/TrEMBL  Length:179

    Alignment length:159
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169         
           Q78E14_RAT    20 EEASFERGNLDVDKLNGDWFSIVVASDKREKIEENGSMRVFVQHIDVLENSLGFTFRIKENGVCTEFSLVADKTAKDGEYFVEYDGENTFTILKTDYDNYVMFHLVNVNNGETFQLMELYGRTKDLSSDIKEKFAKLCVAHGITRDNIIDLTKTDRCLQ 178
               SCOP domains d3zq3c_ C: automated matches                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhee.eeeeeee.hhhhhh......eeeeeeeee..eeeeeeeeee..eeeeeeeeeee......eeee...eeeeeeeee....eeeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhhhhh..hhh.eee.hhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zq3 C  20 EEASFERGNLDVDKLNGDWFSIVVASDKREKIEENGSMRVFVQHIDVLENSLGFTFRIKENGVCTEFSLVADKTAKDGEYFVEYDGENTFTILKTDYDNYVMFHLVNVNNGETFQLMELYGRTKDLSSDIKEKFAKLCVAHGITRDNIIDLTKTDRCLQ 178
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169         


Chain D from PDB  Type:PROTEIN  Length:159
 aligned with Q63213_RAT | Q63213 from UniProtKB/TrEMBL  Length:181

    Alignment length:159
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169         
           Q63213_RAT    20 EEASFERGNLDVDKLNGDWFSIVVASDKREKIEENGSMRVFVQHIDVLENSLGFTFRIKENGVCTEFSLVADKTAKDGEYFVEYDGENTFTILKTDYDNYVMFHLVNVNNGETFQLMELYGRTKDLSSDIKEKFAKLCVAHGITRDNIIDLTKTDRCLQ 178
               SCOP domains d3zq3d_ D: automated matches                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhee.eeeeeee.hhhhhh......eeeeeeeee..eeeeeeeeee..eeeeeeeeeee......eeee...eeeeeeeee....eeeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhhhhh..hhh.eee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zq3 D  20 EEASFERGNLDVDKLNGDWFSIVVASDKREKIEENGSMRVFVQHIDVLENSLGFTFRIKENGVCTEFSLVADKTAKDGEYFVEYDGENTFTILKTDYDNYVMFHLVNVNNGETFQLMELYGRTKDLSSDIKEKFAKLCVAHGITRDNIIDLTKTDRCLQ 178
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169         


Chain D from PDB  Type:PROTEIN  Length:159
 aligned with Q78E14_RAT | Q78E14 from UniProtKB/TrEMBL  Length:179

    Alignment length:159
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169         
           Q78E14_RAT    20 EEASFERGNLDVDKLNGDWFSIVVASDKREKIEENGSMRVFVQHIDVLENSLGFTFRIKENGVCTEFSLVADKTAKDGEYFVEYDGENTFTILKTDYDNYVMFHLVNVNNGETFQLMELYGRTKDLSSDIKEKFAKLCVAHGITRDNIIDLTKTDRCLQ 178
               SCOP domains d3zq3d_ D: automated matches                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhee.eeeeeee.hhhhhh......eeeeeeeee..eeeeeeeeee..eeeeeeeeeee......eeee...eeeeeeeee....eeeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhhhhh..hhh.eee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zq3 D  20 EEASFERGNLDVDKLNGDWFSIVVASDKREKIEENGSMRVFVQHIDVLENSLGFTFRIKENGVCTEFSLVADKTAKDGEYFVEYDGENTFTILKTDYDNYVMFHLVNVNNGETFQLMELYGRTKDLSSDIKEKFAKLCVAHGITRDNIIDLTKTDRCLQ 178
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169
   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, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZQ3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZQ3)

(-) Gene Ontology  (6, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q63213_RAT | Q63213)
molecular function
    GO:0005550    pheromone binding    Interacting selectively and non-covalently with a pheromone, a substance, or characteristic mixture of substances, that is secreted and released by an organism and detected by a second organism of the same or a closely related species, in which it causes a specific reaction, such as a definite behavioral reaction or a developmental process.
    GO:0036094    small molecule binding    Interacting selectively and non-covalently with a small molecule, any low molecular weight, monomeric, non-encoded molecule.
    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.
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,C,D   (Q78E14_RAT | Q78E14)
molecular function
    GO:0005549    odorant binding    Interacting selectively and non-covalently with an odorant, any substance capable of stimulating the sense of smell.
    GO:0005550    pheromone binding    Interacting selectively and non-covalently with a pheromone, a substance, or characteristic mixture of substances, that is secreted and released by an organism and detected by a second organism of the same or a closely related species, in which it causes a specific reaction, such as a definite behavioral reaction or a developmental process.
    GO:0036094    small molecule binding    Interacting selectively and non-covalently with a small molecule, any low molecular weight, monomeric, non-encoded molecule.
    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.
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.

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  3zq3
    Family and Domain Information: ProDom | SYSTERS
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  Q63213_RAT | Q63213
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  Q78E14_RAT | Q78E14
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  Q63213_RAT | Q63213
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 Related Entries

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

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