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(-) Description

Title :  CRYSTAL STRUCTURE OF FULL-LENGTH HUMAN ROGDI
 
Authors :  H. Lee, C. Lee
Date :  07 Jun 17  (Deposition) - 12 Jul 17  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (3x)
Keywords :  Rogdi, Kohlschutter-Tonz Syndrome, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Lee, H. Jeong, J. Choe, Y. Jun, C. Lim, C. Lee
The Crystal Structure Of Human Rogdi Provides Insight Into The Causes Of Kohlschutter-Tonz Syndrome
Sci Rep V. 7 3972 2017
PubMed-ID: 28638151  |  Reference-DOI: 10.1038/S41598-017-04120-X

(-) Compounds

Molecule 1 - PROTEIN ROGDI HOMOLOG
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: ROGDI
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (3x): ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5XQI)

(-) Sites  (0, 0)

(no "Site" information available for 5XQI)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5XQI)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Met A:91 -Pro A:92
2Ala A:181 -Pro A:182
3Met B:91 -Pro B:92
4Ala B:181 -Pro B:182
5Ala C:181 -Pro C:182

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5XQI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5XQI)

(-) Exons   (0, 0)

(no "Exon" information available for 5XQI)

(-) 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:275
                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeee.......eeeeeeee..eeeeeeeee........eeeee.....eehhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhee......eeeeeee...eeeeeeeeeee............ee.......eee...eeeeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5xqi A   1 MATVMAATAAERAVLEEEFRWLLHDEVHAVLKQLQDILKEASLRFTLAKQENFILGSCGTDQVKGVLTLQGDALSQADVNLKMPRNNQLLHFAFREDKQWKLQQIQDARNHVSQAIYLLTSRDQSYQFKTGAEVLKLMDAVMLQLTRARNRLTTPATLTLPEIAASGLTRMFAPALPSDLLVNVYINLNKLCLTVYQLHALQNSTKNFRPAGGAVLHSPGAMFEWSQRLEVSHVHKVECVIPWLNDALVYFTVSLQLCQQLKDKISVFSSYWSYR 285
                                    10        20        30        40      ||58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208 ||    219       229    || 240       250       260       270       280     
                                                                         47|                                                                                                                                                       210|                   234|                                                 
                                                                          56                                                                                                                                                        212                    236                                                 


Chain B from PDB  Type:PROTEIN  Length:276
                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeee.......eeeeeeee..eeeeeeeee........eeeee.....eehhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhh..hhh.ee......eeeeeeee..eeeeeeeeeee.....................eeee..eeeeeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5xqi B   1 MATVMAATAAERAVLEEEFRWLLHDEVHAVLKQLQDILKEASLRFTLAKQENFILGSCGTDQVKGVLTLQGDALSQADVNLKMPRNNQLLHFAFREDKQWKLQQIQDARNHVSQAIYLLTSRDQSYQFKTGAEVLKLMDAVMLQLTRARNRLTTPATLTLPEIAASGLTRMFAPALPSDLLVNVYINLNKLCLTVYQLHALQNSTKNFRPAGGAVLHSPGAMFEWGSQRLEVSHVHKVECVIPWLNDALVYFTVSLQLCQQLKDKISVFSSYWSYR 285
                                    10        20        30        40      ||58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208 ||    219       229       239       249       259       269       279      
                                                                         47|                                                                                                                                                       210|                                                                         
                                                                          56                                                                                                                                                        212                                                                         


Chain C from PDB  Type:PROTEIN  Length:254
                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee..eeeeeeee..eeeeeeeee...eeeee.....eehhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhee......eeeeeeee..eeeeeeeeeee............eeee..eeeeeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5xqi C   1 MATVMAATAAERAVLEEEFRWLLHDEVHAVLKQLQDILKEASLRFTLKQENFILDQVKGVLTLQGDALSQADVNLKMLLHFAFREDKQWKLQQIQDARNHVSQAIYLLTSRDQSYQFKTGAEVLKLMDAVMLQLTRARNRLTTPATLTLPEIAASGLTRMFAPALPSDLLVNVYINLNKLCLTVYQLHALQPGAVLHSPGAMFEWGSQRLEVSHVHKVECVIPWLNDALVYFTVSLQLCQQLKDKISVFSSYWS 283
                                    10        20        30        40      ||59   ||   74        84      ||99       109       119       129       139       149       159       169       179       189       199       209 ||    229       239       249       259       269       279    
                                                                         47|    63|                    91|                                                                                                               211|                                                             
                                                                          57     69                     97                                                                                                                222                                                             


Chain D from PDB  Type:PROTEIN  Length:255
                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee..eeeeeeee..eeeeeeeee.....eee.......eehhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.......eeeeeee...eeeeeeeeeee............eeee..eeeeeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5xqi D   1 MATVMAATAAERAVLEEEFRWLLHDEVHAVLKQLQDILKEASLRFTLKQENFILDQVKGVLTLQGDALSQADVNLKMPRLLHFAFREDKQWKLQQIQDARNHVSQAIYLLTSRDQSYQFKTGAEVLKLMDAVMLQLTRARNRLTTPATLTLPEIAASGLTRMFPALPSDLLVNVYINLNKLCLTVYQLHALQPGAVLHSPGAMFEWGSQRLEVSHVHKVECVIPWLNDALVYFTVSLQLCQQLKDKISVFSSYWS 283
                                    10        20        30        40      ||59   ||   74        84        97       107       117       127       137       147       157       167       177  ||   188       198       208  ||   228       238       248       258       268       278     
                                                                         47|    63|                      93|                                                                                180|                          211|                                                             
                                                                          57     69                       97                                                                                 182                           222
   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 5XQI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5XQI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5XQI)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5XQI)

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  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 5xqi)
 
  Sites
(no "Sites" information available for 5xqi)
 
  Cis Peptide Bonds
    Ala A:181 - Pro A:182   [ RasMol ]  
    Ala B:181 - Pro B:182   [ RasMol ]  
    Ala C:181 - Pro C:182   [ RasMol ]  
    Met A:91 - Pro A:92   [ RasMol ]  
    Met B:91 - Pro B:92   [ RasMol ]  
 
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 Databases and Analysis Tools

(-) Databases

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  5xqi
    Family and Domain Information: ProDom | SYSTERS
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  ROGDI_HUMAN | Q9GZN7
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  ROGDI_HUMAN | Q9GZN7
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 Related Entries

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

UniProtKB/Swiss-Prot
        ROGDI_HUMAN | Q9GZN7: 5xqh

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5XQI)