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Theoretical Model  (Jmol Viewer)

(-) Description

Title :  COMPARATIVE MODELING OF NODULIN 26 FROM GLYCINE MAX.
 
Authors :  S. Biswas
Date :  28 May 03  (Deposition) - 10 Feb 04  (Release) - 10 Feb 04  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,B,C,D
Keywords :  Membrane Protein, Helix Bundle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Biswas
Functional Properties Of Soybean Nodulin 26 From A Comparative Three-Dimensional Model
Febs Lett. V. 558 39 2004
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NODULIN 26
    Chains: A, B, C, D
    Fragment: RESIDUES 36-250
    Organism Common: SOYBEAN
    Organism Scientific: GLYCINE MAX

 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 1UFD)

(-) Sites  (0, 0)

(no "Site" information available for 1UFD)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (9, 9)

Theoretical Model
No.Residues
1Thr A:107 -Arg A:108
2Cys A:172 -Gly A:173
3Thr B:107 -Arg B:108
4Cys B:172 -Gly B:173
5Thr C:107 -Arg C:108
6Cys C:172 -Gly C:173
7Pro C:216 -Ala C:217
8Thr D:107 -Arg D:108
9Cys D:172 -Gly D:173

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Theoretical Model (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MIPPS00221 MIP family signature.NO26_SOYBN95-103
 
 
 		  4A:95-103
B:95-103
C:95-103
D:95-103

(-) Exons   (0, 0)

(no "Exon" information available for 1UFD)

(-) 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:215
 aligned with NO26_SOYBN | P08995 from UniProtKB/Swiss-Prot  Length:271

    Alignment length:215
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245     
           NO26_SOYBN    36 FLQKLVAEAVGTYFLIFAGCASLVVNENYYNMITFPGIAIVWGLVLTVLVYTVGHISGGHFNPAVTIAFASTRRFPLIQVPAYVVAQLLGSILASGTLRLLFMGNHDQFSGTVPNGTNLQAFVFEFIMTFFLMFVICGVATDNRAVGEFAGIAIGSTLLLNVIIGGPVTGASMNPARSLGPAFVHGEYEGIWIYLLAPVVGAIAGAWVYNIVRYT 250
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh................hhhhhhhhh..hhhhhhhhhh.........hhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh.......hhhhhh...........hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------MIP      --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ufd A  36 FLQKLVAEAVGTYFLIFAGCASLVVNENYYNMITFPGIAIVWGLVLTVLVYTVGHISGGHFNPAVTIAFASTRRFPLIQVPAYVVAQLLGSILASGTLRLLFMGNHDQFSGTVPNGTNLQAFVFEFIMTFFLMFVICGVATDNRAVGEFAGIAIGSTLLLNVIIGGPVTGASMNPARSLGPAFVHGEYEGIWIYLLAPVVGAIAGAWVYNIVRYT 250
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245     


Chain B from PDB  Type:PROTEIN  Length:215
 aligned with NO26_SOYBN | P08995 from UniProtKB/Swiss-Prot  Length:271

    Alignment length:215
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245     
           NO26_SOYBN    36 FLQKLVAEAVGTYFLIFAGCASLVVNENYYNMITFPGIAIVWGLVLTVLVYTVGHISGGHFNPAVTIAFASTRRFPLIQVPAYVVAQLLGSILASGTLRLLFMGNHDQFSGTVPNGTNLQAFVFEFIMTFFLMFVICGVATDNRAVGEFAGIAIGSTLLLNVIIGGPVTGASMNPARSLGPAFVHGEYEGIWIYLLAPVVGAIAGAWVYNIVRYT 250
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh........hhhhhhhhhhhhhhhhh.hhhhhh..................hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh......hhhhhhhhhh.hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------MIP      --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ufd B  36 FLQKLVAEAVGTYFLIFAGCASLVVNENYYNMITFPGIAIVWGLVLTVLVYTVGHISGGHFNPAVTIAFASTRRFPLIQVPAYVVAQLLGSILASGTLRLLFMGNHDQFSGTVPNGTNLQAFVFEFIMTFFLMFVICGVATDNRAVGEFAGIAIGSTLLLNVIIGGPVTGASMNPARSLGPAFVHGEYEGIWIYLLAPVVGAIAGAWVYNIVRYT 250
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245     


Chain C from PDB  Type:PROTEIN  Length:215
 aligned with NO26_SOYBN | P08995 from UniProtKB/Swiss-Prot  Length:271

    Alignment length:215
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245     
           NO26_SOYBN    36 FLQKLVAEAVGTYFLIFAGCASLVVNENYYNMITFPGIAIVWGLVLTVLVYTVGHISGGHFNPAVTIAFASTRRFPLIQVPAYVVAQLLGSILASGTLRLLFMGNHDQFSGTVPNGTNLQAFVFEFIMTFFLMFVICGVATDNRAVGEFAGIAIGSTLLLNVIIGGPVTGASMNPARSLGPAFVHGEYEGIWIYLLAPVVGAIAGAWVYNIVRYT 250
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhh........hhhhhhhhh............hhhhhhhhhhhhhh........................hhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhh........hhhhhh...........hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------MIP      --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ufd C  36 FLQKLVAEAVGTYFLIFAGCASLVVNENYYNMITFPGIAIVWGLVLTVLVYTVGHISGGHFNPAVTIAFASTRRFPLIQVPAYVVAQLLGSILASGTLRLLFMGNHDQFSGTVPNGTNLQAFVFEFIMTFFLMFVICGVATDNRAVGEFAGIAIGSTLLLNVIIGGPVTGASMNPARSLGPAFVHGEYEGIWIYLLAPVVGAIAGAWVYNIVRYT 250
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245     


Chain D from PDB  Type:PROTEIN  Length:215
 aligned with NO26_SOYBN | P08995 from UniProtKB/Swiss-Prot  Length:271

    Alignment length:215
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245     
           NO26_SOYBN    36 FLQKLVAEAVGTYFLIFAGCASLVVNENYYNMITFPGIAIVWGLVLTVLVYTVGHISGGHFNPAVTIAFASTRRFPLIQVPAYVVAQLLGSILASGTLRLLFMGNHDQFSGTVPNGTNLQAFVFEFIMTFFLMFVICGVATDNRAVGEFAGIAIGSTLLLNVIIGGPVTGASMNPARSLGPAFVHGEYEGIWIYLLAPVVGAIAGAWVYNIVRYT 250
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh...............hhhhhhhhhhhh..hhhhhhh.......hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhh.............hhhhhhhhhhhhhh.........hhhhhhh............hhhhh...hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------MIP      --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ufd D  36 FLQKLVAEAVGTYFLIFAGCASLVVNENYYNMITFPGIAIVWGLVLTVLVYTVGHISGGHFNPAVTIAFASTRRFPLIQVPAYVVAQLLGSILASGTLRLLFMGNHDQFSGTVPNGTNLQAFVFEFIMTFFLMFVICGVATDNRAVGEFAGIAIGSTLLLNVIIGGPVTGASMNPARSLGPAFVHGEYEGIWIYLLAPVVGAIAGAWVYNIVRYT 250
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245
   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 1UFD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Theoretical Model(hide GO term definitions)
Chain A,B,C,D   (NO26_SOYBN | P08995)
molecular function
    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:0009877    nodulation    The formation of nitrogen-fixing root nodules on plant roots.
    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: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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043661    peribacteroid membrane    A membrane that surrounds one or more bacteroids (such as nitrogen-fixing bacteroids within legume root nodule cells).

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  Cis Peptide Bonds
    Cys A:172 - Gly A:173   [ RasMol ]  
    Cys B:172 - Gly B:173   [ RasMol ]  
    Cys C:172 - Gly C:173   [ RasMol ]  
    Cys D:172 - Gly D:173   [ RasMol ]  
    Pro C:216 - Ala C:217   [ RasMol ]  
    Thr A:107 - Arg A:108   [ RasMol ]  
    Thr B:107 - Arg B:108   [ RasMol ]  
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