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(-) Description

Title :  THE MOLECULAR BASIS OF VITAMIN E RETENTION: STRUCTURE OF HUMAN ALPHA-TOCOPHEROL TRANSFER PROTEIN
 
Authors :  R. Meier, T. Tomizaki, C. Schulze-Briese, U. Baumann, A. Stocker
Date :  27 Jun 03  (Deposition) - 14 Jan 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transport, Ataxia, Aved, Transfer Protein, Tocopherol, Vitamin E (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Meier, T. Tomizaki, C. Schulze-Briese, U. Baumann, A. Stocker
The Molecular Basis Of Vitamin E Retention: Structure Of Human Alpha-Tocopherol Transfer Protein
J. Mol. Biol. V. 331 725 2003
PubMed-ID: 12899840  |  Reference-DOI: 10.1016/S0022-2836(03)00724-1

(-) Compounds

Molecule 1 - ALPHA-TOCOPHEROL TRANSFER PROTEIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantSTAR
    Expression System VectorPET-28A
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCONTAINS CRAL_TRIO LIPID BINDING DOMAIN, RESIDUES 89-275
    SynonymALPHA-TTP, TTPA, TPP1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1TRT6Ligand/IonFRAGMENT OF TRITON X-100
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1TRT3Ligand/IonFRAGMENT OF TRITON X-100
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1TRT3Ligand/IonFRAGMENT OF TRITON X-100

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:163 , PHE A:165 , ALA A:168 , ILE A:202 , PHE A:203 , VAL A:206 , ILE A:222 , MET A:224 , TRT A:1276 , HOH A:2146 , PHE B:213BINDING SITE FOR RESIDUE TRT A1274
2AC2SOFTWARELEU A:115 , TYR A:117 , SER A:136 , SER A:140 , ILE A:143 , ILE A:154 , VAL A:182 , LEU A:189 , VAL A:191BINDING SITE FOR RESIDUE TRT A1275
3AC3SOFTWARETRP A:163 , ALA A:168 , ILE A:171 , TRT A:1274 , VAL B:206 , MET B:209 , TRT B:1276BINDING SITE FOR RESIDUE TRT A1276
4AC4SOFTWAREPHE B:165 , ILE B:202 , VAL B:206 , ILE B:222 , MET B:224 , TRT B:1276BINDING SITE FOR RESIDUE TRT B1275
5AC5SOFTWAREMET A:209 , ILE A:210 , TRT A:1276 , ILE B:179 , TRT B:1275 , TRT B:1277 , HOH B:2148BINDING SITE FOR RESIDUE TRT B1276
6AC6SOFTWARETYR B:100 , LEU B:115 , TYR B:117 , ILE B:119 , VAL B:132 , PHE B:133 , SER B:136 , SER B:140 , ILE B:154 , ALA B:156 , PHE B:158 , ILE B:171 , ILE B:179 , LEU B:183 , LEU B:189 , VAL B:191 , TRT B:1276 , HOH B:2091BINDING SITE FOR RESIDUE TRT B1277

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (8, 16)

Asymmetric Unit (8, 16)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_022388R59WTTPA_HUMANDisease (AVED)397515522A/BR59W
2UniProtVAR_005668H101QTTPA_HUMANDisease (AVED)121917849A/BH101Q
3UniProtVAR_022389A120TTTPA_HUMANDisease (AVED)143010236A/BA120T
4UniProtVAR_022390E141KTTPA_HUMANDisease (AVED)397515524A/BE141K
5UniProtVAR_037973T172STTPA_HUMANPolymorphism34647756A/BT172S
6UniProtVAR_007858R192HTTPA_HUMANDisease (AVED)28936369A/BR192H
7UniProtVAR_022391R221WTTPA_HUMANDisease (AVED)35916840A/BR221W
8UniProtVAR_022392G246RTTPA_HUMANDisease (AVED)397515526A/BG246R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (8, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_022388R59WTTPA_HUMANDisease (AVED)397515522AR59W
2UniProtVAR_005668H101QTTPA_HUMANDisease (AVED)121917849AH101Q
3UniProtVAR_022389A120TTTPA_HUMANDisease (AVED)143010236AA120T
4UniProtVAR_022390E141KTTPA_HUMANDisease (AVED)397515524AE141K
5UniProtVAR_037973T172STTPA_HUMANPolymorphism34647756AT172S
6UniProtVAR_007858R192HTTPA_HUMANDisease (AVED)28936369AR192H
7UniProtVAR_022391R221WTTPA_HUMANDisease (AVED)35916840AR221W
8UniProtVAR_022392G246RTTPA_HUMANDisease (AVED)397515526AG246R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (8, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_022388R59WTTPA_HUMANDisease (AVED)397515522BR59W
2UniProtVAR_005668H101QTTPA_HUMANDisease (AVED)121917849BH101Q
3UniProtVAR_022389A120TTTPA_HUMANDisease (AVED)143010236BA120T
4UniProtVAR_022390E141KTTPA_HUMANDisease (AVED)397515524BE141K
5UniProtVAR_037973T172STTPA_HUMANPolymorphism34647756BT172S
6UniProtVAR_007858R192HTTPA_HUMANDisease (AVED)28936369BR192H
7UniProtVAR_022391R221WTTPA_HUMANDisease (AVED)35916840BR221W
8UniProtVAR_022392G246RTTPA_HUMANDisease (AVED)397515526BG246R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CRAL_TRIOPS50191 CRAL-TRIO lipid binding domain profile.TTPA_HUMAN88-253
 
  2A:88-253
B:88-253
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CRAL_TRIOPS50191 CRAL-TRIO lipid binding domain profile.TTPA_HUMAN88-253
 
  1A:88-253
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CRAL_TRIOPS50191 CRAL-TRIO lipid binding domain profile.TTPA_HUMAN88-253
 
  1-
B:88-253

(-) Exons   (5, 10)

Asymmetric Unit (5, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002601161aENSE00002100795chr8:63998612-63998377236TTPA_HUMAN1-68682A:9-68
B:11-68
60
58
1.2ENST000002601162ENSE00001201488chr8:63985647-63985494154TTPA_HUMAN69-120522A:69-120
B:69-120
52
52
1.3ENST000002601163ENSE00001201483chr8:63978656-63978463194TTPA_HUMAN120-184652A:120-184
B:120-184
65
65
1.4ENST000002601164ENSE00000819496chr8:63976875-63976765111TTPA_HUMAN185-221372A:185-221
B:185-221
37
37
1.5ENST000002601165ENSE00001201491chr8:63973984-639723421643TTPA_HUMAN222-278572A:222-274
B:222-275
53
54

(-) 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:266
 aligned with TTPA_HUMAN | P49638 from UniProtKB/Swiss-Prot  Length:278

    Alignment length:266
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268      
           TTPA_HUMAN     9 SAGPQLNALPDHSPLLQPGLAALRRRAREAGVPLAPLPLTDSFLLRFLRARDFDLDLAWRLLKNYYKWRAECPEISADLHPRSIIGLLKAGYHGVLRSRDPTGSKVLIYRIAHWDPKVFTAYDVFRVSLITSELIVQEVETQRNGIKAIFDLEGWQFSHAFQITPSVAKKIAAVLTDSFPLKVRGIHLINEPVIFHAVFSMIKPFLTEKIKERIHMHGNNYKQSLLQHFPDILPLEYGGEEFSMEDICQEWTNFIMKSEDYLSSIS 274
               SCOP domains d1oiza1 A:9-90 Alpha-tocopherol transfer protein                                  d1oiza2 A:91-274 Alpha-tocopherol transfer protein                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh....hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh..eee.........eeeeee.hhh.....hhhhhhhhhhhhhhhhh.hhhhhhhheeeeee....hhhhhh..hhhhhhhhhhhhhh.....eeeeeee..hhhhhhhhhhhh......hhh.eee....hhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------W-----------------------------------------Q------------------T--------------------K------------------------------S-------------------H----------------------------W------------------------R---------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------CRAL_TRIO  PDB: A:88-253 UniProt: 88-253                                                                                                                              --------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:9-68 UniProt: 1-68 [INCOMPLETE]           Exon 1.2  PDB: A:69-120 UniProt: 69-120             ----------------------------------------------------------------Exon 1.4  PDB: A:185-221             Exon 1.5  PDB: A:222-274 UniProt: 222-278             Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------Exon 1.3  PDB: A:120-184 UniProt: 120-184                        ------------------------------------------------------------------------------------------ Transcript 1 (2)
                 1oiz A   9 SAGPQLNALPDHSPLLQPGLAALRRRAREAGVPLAPLPLTDSFLLRFLRARDFDLDLAWRLLKNYYKWRAECPEISADLHPRSIIGLLKAGYHGVLRSRDPTGSKVLIYRIAHWDPKVFTAYDVFRVSLITSELIVQEVETQRNGIKAIFDLEGWQFSHAFQITPSVAKKIAAVLTDSFPLKVRGIHLINEPVIFHAVFSMIKPFLTEKIKERIHMHGNNYKQSLLQHFPDILPLEYGGEEFSMEDICQEWTNFIMKSEDYLSSIS 274
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268      

Chain B from PDB  Type:PROTEIN  Length:265
 aligned with TTPA_HUMAN | P49638 from UniProtKB/Swiss-Prot  Length:278

    Alignment length:265
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270     
           TTPA_HUMAN    11 GPQLNALPDHSPLLQPGLAALRRRAREAGVPLAPLPLTDSFLLRFLRARDFDLDLAWRLLKNYYKWRAECPEISADLHPRSIIGLLKAGYHGVLRSRDPTGSKVLIYRIAHWDPKVFTAYDVFRVSLITSELIVQEVETQRNGIKAIFDLEGWQFSHAFQITPSVAKKIAAVLTDSFPLKVRGIHLINEPVIFHAVFSMIKPFLTEKIKERIHMHGNNYKQSLLQHFPDILPLEYGGEEFSMEDICQEWTNFIMKSEDYLSSISE 275
               SCOP domains d1oizb1 B:11-90 Alpha-tocopherol transfer protein                               d1oizb2 B:91-275 Alpha-tocopherol transfer protein                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh....hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.eee.........eeeeee.hhh.....hhhhhhhhhhhhhhhhh.hhhhhhhheeeeee....hhhhhhh.hhhhhhhhhhhhhh.....eeeeeee..hhhhhhhhhhhh......hhh.eee....hhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------W-----------------------------------------Q------------------T--------------------K------------------------------S-------------------H----------------------------W------------------------R----------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------CRAL_TRIO  PDB: B:88-253 UniProt: 88-253                                                                                                                              ---------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: B:11-68 UniProt: 1-68 [INCOMPLETE]        Exon 1.2  PDB: B:69-120 UniProt: 69-120             ----------------------------------------------------------------Exon 1.4  PDB: B:185-221             Exon 1.5  PDB: B:222-275 UniProt: 222-278 [INCOMPLETE] Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------Exon 1.3  PDB: B:120-184 UniProt: 120-184                        ------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1oiz B  11 GPQLNALPDHSPLLQPGLAALRRRAREAGVPLAPLPLTDSFLLRFLRARDFDLDLAWRLLKNYYKWRAECPEISADLHPRSIIGLLKAGYHGVLRSRDPTGSKVLIYRIAHWDPKVFTAYDVFRVSLITSELIVQEVETQRNGIKAIFDLEGWQFSHAFQITPSVAKKIAAVLTDSFPLKVRGIHLINEPVIFHAVFSMIKPFLTEKIKERIHMHGNNYKQSLLQHFPDILPLEYGGEEFSMEDICQEWTNFIMKSEDYLSSISE 275
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270     

   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  (2, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1OIZ)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (25, 25)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (TTPA_HUMAN | P49638)
molecular function
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0043325    phosphatidylinositol-3,4-bisphosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-3,4-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' and 4' positions.
    GO:0005546    phosphatidylinositol-4,5-bisphosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-4,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' and 5' positions.
    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.
    GO:0008431    vitamin E binding    Interacting selectively and non-covalently with vitamin E, tocopherol, which includes a series of eight structurally similar compounds. Alpha-tocopherol is the most active form in humans and is a powerful biological antioxidant.
    GO:0019842    vitamin binding    Interacting selectively and non-covalently with a vitamin, one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body.
biological process
    GO:0032502    developmental process    A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.
    GO:0001892    embryonic placenta development    The embryonically driven process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin.
    GO:0051452    intracellular pH reduction    Any process that reduces the internal pH of a cell, measured by the concentration of the hydrogen ion.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0060548    negative regulation of cell death    Any process that decreases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
    GO:0090212    negative regulation of establishment of blood-brain barrier    Any process that decreases the rate, frequency or extent of the establishment of the blood-brain barrier, a selectively permeable structural and functional barrier that exists between the capillaries and the brain.
    GO:0046909    obsolete intermembrane transport    OBSOLETE. The directed movement of substances between any membrane of a cell, including the plasma membrane and its regions.
    GO:0001890    placenta development    The process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin.
    GO:0007584    response to nutrient    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 nutrient stimulus.
    GO:0009268    response to pH    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 pH stimulus. pH is a measure of the acidity or basicity of an aqueous solution.
    GO:0009636    response to toxic substance    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 toxic stimulus.
    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:0042360    vitamin E metabolic process    The chemical reactions and pathways involving vitamin E, tocopherol, which includes a series of eight structurally similar compounds. Alpha-tocopherol is the most active form in humans and is a powerful biological antioxidant.
    GO:0051180    vitamin transport    The directed movement of vitamins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A vitamin is one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body.
cellular component
    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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0005770    late endosome    A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TTPA_HUMAN | P496381oip 1r5l

(-) Related Entries Specified in the PDB File

1oip THE MOLECULAR BASIS OF VITAMIN E RETENTION: STRUCTURE OF HUMAN ALPHA-TOCOPHEROL TRANSFER PROTEIN
1r5l CRYSTAL STRUCTURE OF HUMAN ALPHA-TOCOPHEROL TRANSFERPROTEIN BOUND TO ITS LIGAND