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Theoretical Model  (Jmol Viewer)

(-) Description

Title :  THEORETICALY MODELED STRUCTURE FOR HUMAN PORIN 6 PROTEIN
 
Authors :  S. Arun Kumar
Date :  23 Jan 04  (Deposition) - 17 Feb 04  (Release) - 17 Feb 04  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A
Keywords :  Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Arun Kumar
Modelling Human Porin
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AQUAPORIN 6
    Chains: A
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Synonym: AQUAPORIN-2 LIKE, HKID
    Tissue: KIDNEY

 Structural Features

(-) Chains, Units

  
Theoretical Model : 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1S6E)

(-) Sites  (0, 0)

(no "Site" information available for 1S6E)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1S6E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1S6E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Theoretical Model (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_047233V234IAQP6_HUMANPolymorphism17124220AV234I
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Theoretical Model (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MIPPS00221 MIP family signature.AQP6_HUMAN80-88  1A:80-88

(-) Exons   (4, 4)

Theoretical Model (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.4bENST000003155204bENSE00001215551chr12:50366620-50367358739AQP6_HUMAN1-1341341A:14-134121
1.5cENST000003155205cENSE00001162930chr12:50368107-50368265159AQP6_HUMAN135-187531A:135-18753
1.6ENST000003155206ENSE00001215493chr12:50368529-5036860981AQP6_HUMAN188-214271A:188-21427
1.7cENST000003155207cENSE00001821447chr12:50369248-50369620373AQP6_HUMAN215-282681A:215-23723

(-) Sequences/Alignments

Theoretical Model
   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:224
 aligned with AQP6_HUMAN | Q13520 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:224
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233    
           AQP6_HUMAN    14 MLACRLWKAISRALFAEFLATGLYVFFGVGSVMRWPTALPSVLQIAITFNLVTAMAVQVTWKASGAHANPAVTLAFLVGSHISLPRAVAYVAAQLVGATVGAALLYGVMPGDIRETLGINVVRNSVSTGQAVAVELLLTLQLVLCVFASTDSRQTSGSPATMIGISVALGHLIGIHFTGCSMNPARSFGPAIIIGKFTVHWVFWVGPLMGALLASLIYNFVLFP 237
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh........hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------I--- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------MIP      ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.4b  PDB: A:14-134 UniProt: 1-134 [INCOMPLETE]                                                                     Exon 1.5c  PDB: A:135-187 UniProt: 135-187           Exon 1.6  PDB: A:188-214   Exon 1.7c [INCOMPLETE]  Transcript 1
                 1s6e A  14 MLACRLWKAISRALFAEFLATGLYVFFGVGSVMRWPTALPSVLQIAITFNLVTAMAVQVTWKTSGAHANPAVTLAFLVGSHISLPRAVAYVAAQLVGATVGAALLYGVMPGDIRETLGINVVRNSVSTGQAVAVELLLTLQLVLCVFASTDSRQTSGSPATMIGISWALGHLIGILFTGCSMNPARSFGPAIIIGKFTVHWVFWVGPLMGALLASLIYNFVLFP 237
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233
   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  (0, 0)

(no "SCOP Domain" information available for 1S6E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1S6E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1S6E)

(-) Gene Ontology  (20, 20)

Theoretical Model(hide GO term definitions)
Chain A   (AQP6_HUMAN | Q13520)
molecular function
    GO:0005253    anion channel activity    Enables the energy-independent passage of anions across a lipid bilayer down a concentration gradient.
    GO:0015254    glycerol channel activity    Enables the facilitated diffusion of glycerol (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
    GO:0015112    nitrate transmembrane transporter activity    Enables the transfer of nitrate ions (NO3-) from one side of a membrane to the other.
    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:0015250    water channel activity    Transport systems of this type enable facilitated diffusion of water (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
biological process
    GO:0098656    anion transmembrane transport    A process in which an anion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0009992    cellular water homeostasis    Any process involved in the maintenance of an internal steady state of water within a cell.
    GO:0007588    excretion    The elimination by an organism of the waste products that arise as a result of metabolic activity. These products include water, carbon dioxide (CO2), and nitrogenous compounds.
    GO:0015793    glycerol transport    The directed movement of glycerol into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Glycerol is 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
    GO:0015706    nitrate transport    The directed movement of nitrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0042476    odontogenesis    The process whose specific outcome is the progression of a tooth or teeth over time, from formation to the mature structure(s). A tooth is any hard bony, calcareous, or chitinous organ found in the mouth or pharynx of an animal and used in procuring or masticating food.
    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:0006833    water transport    The directed movement of water (H2O) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
cellular component
    GO:0016324    apical plasma membrane    The region of the plasma membrane located at the apical end of the cell.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0030659    cytoplasmic vesicle membrane    The lipid bilayer surrounding a cytoplasmic vesicle.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0030658    transport vesicle membrane    The lipid bilayer surrounding a transport vesicle.

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