Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  RAT TRANSTHYRETIN (ALSO CALLED PREALBUMIN) COMPLEX WITH 3', 5'-DIBROMOFLAVONE (EMD21388)
 
Authors :  A. Wojtczak, P. Neumann, T. Muziol, V. Cody, J. R. Luft, W. Pangborn
Date :  27 Nov 01  (Deposition) - 27 Nov 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Prealbumin, Transport, Dibromoflavone, Aurone, Thyroid Hormone, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Muziol, V. Cody, A. Wojtczak
Comparison Of Binding Interactions Of Dibromoflavonoids With Transthyretin.
Acta Biochim. Pol. V. 48 885 2001
PubMed-ID: 11995999
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSTHYRETIN
    Chains: A, B, C, D
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: PREALBUMIN, TBPA
    Tissue: PLASMA

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1FL82Ligand/Ion6,4'-DIHYDROXY-3-METHYL-3',5'-DIBROMOFLAVONE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:15 , LEU A:17 , ALA A:108 , LEU A:110 , SER A:117 , THR A:119 , LYS C:415 , LEU C:417 , THR C:506 , ALA C:508 , LEU C:510 , SER C:517 , THR C:518 , THR C:519 , HOH C:761 , HOH C:872 , HOH C:913BINDING SITE FOR RESIDUE FL8 C 128
2AC2SOFTWARELYS B:215 , LEU B:217 , ALA B:308 , SER B:317 , THR B:319 , LEU D:617 , ALA D:708 , LEU D:710 , SER D:717BINDING SITE FOR RESIDUE FL8 B 328

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 8)

Asymmetric/Biological Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRANSTHYRETIN_1PS00768 Transthyretin signature 1.TTHY_RAT35-50
 
 
 		  4A:15-30
B:215-230
C:415-430
D:615-630
2TRANSTHYRETIN_2PS00769 Transthyretin signature 2.TTHY_RAT125-137
 
 
 		  4A:105-117
B:305-317
C:505-517
D:705-717

(-) Exons   (3, 12)

Asymmetric/Biological Unit (3, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000221131ENSRNOE00000155027chr18:12406551-1240664898TTHY_RAT1-23230--
1.2ENSRNOT000000221132ENSRNOE00000155619chr18:12407695-12407825131TTHY_RAT24-67444A:5-47
B:207-247
C:407-447
D:608-647		43
41
41
40
1.3ENSRNOT000000221133ENSRNOE00000156091chr18:12410367-12410502136TTHY_RAT67-112464A:47-92
B:247-292
C:447-492
D:647-692		46
46
46
46
1.4ENSRNOT000000221134ENSRNOE00000156567chr18:12413430-12413680251TTHY_RAT113-147354A:93-127
B:293-327
C:493-527
D:693-727		35
35
35
35

(-) Sequences/Alignments

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:123
 aligned with TTHY_RAT | P02767 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:123
                                    34        44        54        64        74        84        94       104       114       124       134       144   
             TTHY_RAT    25 AGESKCPLMVKVLDAVRGSPAVDVAVKVFKKTADGSWEPFASGKTAESGELHGLTTDEKFTEGVYRVELDTKSYWKALGISPFHEYAEVVFTANDSGHRHYTIAALLSPYSYSTTAVVSNPQN 147
               SCOP domains d1kgja_ A: Transthyretin (synonym: prealbumin)                                                                              SCOP domains
               CATH domains 1kgjA00 A:5-127  [code=2.60.40.180, no name defined]                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeee....ee....eeeeeee.....eeeeeeee.....ee...........eeeeeeehhhhhhhhhh....eeeeeeeeee.......eeeeeeee..eeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------TRANSTHYRETIN_1 --------------------------------------------------------------------------TRANSTHYRETIN---------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:5-47 UniProt: 24-67       ---------------------------------------------Exon 1.4  PDB: A:93-127             Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------Exon 1.3  PDB: A:47-92 UniProt: 67-112        ----------------------------------- Transcript 1 (2)
                 1kgj A   5 AGESKCPLMVKVLDAVRGSPAVDVAVKVFKKTADGSWEPFASGKTAESGELHGLTTDEKFTEGVYRVELDTKSYWKALGISPFHEYAEVVFTANDSGHRHYTIAALLSPYSYSTTAVVSNPQN 127
                                    14        24        34        44        54        64        74        84        94       104       114       124   


Chain B from PDB  Type:PROTEIN  Length:121
 aligned with TTHY_RAT | P02767 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:121
                                    36        46        56        66        76        86        96       106       116       126       136       146 
             TTHY_RAT    27 ESKCPLMVKVLDAVRGSPAVDVAVKVFKKTADGSWEPFASGKTAESGELHGLTTDEKFTEGVYRVELDTKSYWKALGISPFHEYAEVVFTANDSGHRHYTIAALLSPYSYSTTAVVSNPQN 147
               SCOP domains d1kgjb_ B: Transthyretin (synonym: prealbumin)                                                                            SCOP domains
               CATH domains 1kgjB00 B:207-327  [code=2.60.40.180, no name defined]                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee....ee....eeeeeee.....eeeeeeee.....ee...........eeeeeeeehhhhhhh......eeeeeeeeee......eeeeeeeee..eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------TRANSTHYRETIN_1 --------------------------------------------------------------------------TRANSTHYRETIN---------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: B:207-247 UniProt: 24-67  ---------------------------------------------Exon 1.4  PDB: B:293-327            Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------Exon 1.3  PDB: B:247-292 UniProt: 67-112      ----------------------------------- Transcript 1 (2)
                 1kgj B 207 ESKCPLMVKVLDAVRGSPAVDVAVKVFKKTADGSWEPFASGKTAESGELHGLTTDEKFTEGVYRVELDTKSYWKALGISPFHEYAEVVFTANDSGHRHYTIAALLSPYSYSTTAVVSNPQN 327
                                   216       226       236       246       256       266       276       286       296       306       316       326 


Chain C from PDB  Type:PROTEIN  Length:121
 aligned with TTHY_RAT | P02767 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:121
                                    36        46        56        66        76        86        96       106       116       126       136       146 
             TTHY_RAT    27 ESKCPLMVKVLDAVRGSPAVDVAVKVFKKTADGSWEPFASGKTAESGELHGLTTDEKFTEGVYRVELDTKSYWKALGISPFHEYAEVVFTANDSGHRHYTIAALLSPYSYSTTAVVSNPQN 147
               SCOP domains d1kgjc_ C: Transthyretin (synonym: prealbumin)                                                                            SCOP domains
               CATH domains 1kgjC00 C:407-527  [code=2.60.40.180, no name defined]                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee....ee....eeeeeee.....eeeeeeee.....ee...........eeeeeeehhhhhhhhh........eeeeeee.......eeeeeeee..eeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------TRANSTHYRETIN_1 --------------------------------------------------------------------------TRANSTHYRETIN---------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: C:407-447 UniProt: 24-67  ---------------------------------------------Exon 1.4  PDB: C:493-527            Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------Exon 1.3  PDB: C:447-492 UniProt: 67-112      ----------------------------------- Transcript 1 (2)
                 1kgj C 407 ESKCPLMVKVLDAVRGSPAVDVAVKVFKKTADGSWEPFASGKTAESGELHGLTTDEKFTEGVYRVELDTKSYWKALGISPFHEYAEVVFTANDSGHRHYTIAALLSPYSYSTTAVVSNPQN 527
                                   416       426       436       446       456       466       476       486       496       506       516       526 


Chain D from PDB  Type:PROTEIN  Length:120
 aligned with TTHY_RAT | P02767 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:120
                                    37        47        57        67        77        87        97       107       117       127       137       147
             TTHY_RAT    28 SKCPLMVKVLDAVRGSPAVDVAVKVFKKTADGSWEPFASGKTAESGELHGLTTDEKFTEGVYRVELDTKSYWKALGISPFHEYAEVVFTANDSGHRHYTIAALLSPYSYSTTAVVSNPQN 147
               SCOP domains d1kgjd_ D: Transthyretin (synonym: prealbumin)                                                                           SCOP domains
               CATH domains 1kgjD00 D:608-727  [code=2.60.40.180, no name defined]                                                                   CATH domains
           Pfam domains (1) --Transthyretin-1kgjD01 D:610-721                                                                                 ------ Pfam domains (1)
           Pfam domains (2) --Transthyretin-1kgjD02 D:610-721                                                                                 ------ Pfam domains (2)
           Pfam domains (3) --Transthyretin-1kgjD03 D:610-721                                                                                 ------ Pfam domains (3)
           Pfam domains (4) --Transthyretin-1kgjD04 D:610-721                                                                                 ------ Pfam domains (4)
         Sec.struct. author ....eeeeeee....ee....eeeeeee.....eeeeeeee.....ee...........eeeeeeehhhhhhhhh.....eeeeeeeeee.......eeeeeee...eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------TRANSTHYRETIN_1 --------------------------------------------------------------------------TRANSTHYRETIN---------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: D:608-647 UniProt: 24-67 ---------------------------------------------Exon 1.4  PDB: D:693-727            Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------Exon 1.3  PDB: D:647-692 UniProt: 67-112      ----------------------------------- Transcript 1 (2)
                 1kgj D 608 SKCPLMVKVLDAVRGSPAVDVAVKVFKKTADGSWEPFASGKTAESGELHGLTTDEKFTEGVYRVELDTKSYWKALGISPFHEYAEVVFTANDSGHRHYTIAALLSPYSYSTTAVVSNPQN 727
                                   617       627       637       647       657       667       677       687       697       707       717       727
   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/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: Transthyretin (88)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (TTHY_RAT | P02767)
molecular function
    GO:0005179    hormone activity    The action characteristic of a hormone, any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells in the same organism, upon which it has a specific regulatory action. The term was originally applied to agents with a stimulatory physiological action in vertebrate animals (as opposed to a chalone, which has a depressant action). Usage is now extended to regulatory compounds in lower animals and plants, and to synthetic substances having comparable effects; all bind receptors and trigger some biological process.
    GO:0042562    hormone binding    Interacting selectively and non-covalently with any hormone, naturally occurring substances secreted by specialized cells that affect the metabolism or behavior of other cells possessing functional receptors for the hormone.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0070324    thyroid hormone binding    Interacting selectively and non-covalently with thyroxine (T4) or triiodothyronine (T3), tyrosine-based hormones produced by the thyroid gland.
biological process
    GO:0042572    retinol metabolic process    The chemical reactions and pathways involving retinol, one of the three compounds that makes up vitamin A.
    GO:0042403    thyroid hormone metabolic process    The chemical reactions and pathways involving any of the compounds secreted by the thyroid gland, largely thyroxine and triiodothyronine.
    GO:0070327    thyroid hormone transport    The directed movement of thyroid hormone into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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: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: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.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    FL8  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1kgj)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1kgj
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  TTHY_RAT | P02767
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  TTHY_RAT | P02767
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TTHY_RAT | P02767: 1gke 1ie4 1kgi 1rvs 2m5k 2m5m 3zpk

(-) Related Entries Specified in the PDB File

1gke RAT TRANSTHYRETIN
1ked HUMAN TRANSTHYRETIN (ALSO CALLED PREALBUMIN) COMPLEX WITH 3,3',5,5'-TETRAIODOTHYROACETIC ACID (T4AC)
1kgi HUMAN TRANSTHYRETIN (ALSO CALLED PREALBUMIN) COMPLEX WITH 3,3',5,5'-TETRAIODOTHYROACETIC ACID (T4AC)
2rox TRANSTHYRETIN (ALSO CALLED PREALBUMIN) COMPLEX WITH THYROXINE (T4)