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(-) Description

Title :  STRUCTURE OF PLEXIN D1 INTRACELLULAR DOMAIN
 
Authors :  G. Shang, X. Zhang
Date :  17 Mar 17  (Deposition) - 31 May 17  (Release) - 07 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Rap Gap, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Shang, C. A. Brautigam, R. Chen, D. Lu, J. Torres-Vazquez, X. Zhang
Structure Analyses Reveal A Regulated Oligomerization Mechanism Of The Plexind1/Gipc/Myosin Vi Complex.
Elife V. 6 2017
PubMed-ID: 28537552  |  Reference-DOI: 10.7554/ELIFE.27322

(-) Compounds

Molecule 1 - PLEXIN-D1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1339-1925
    Gene: PLXND1
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5V6R)

(-) Sites  (0, 0)

(no "Site" information available for 5V6R)

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:1402 -A:1921
2B:1402 -B:1921

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5V6R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5V6R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5V6R)

(-) Exons   (0, 0)

(no "Exon" information available for 5V6R)

(-) 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:505
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhh.hhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhh........eeeeeeee...eeeeee...hhhhhhhhhhhhhh...hhhhh.hhh.eeeee.......ee.........ee..eee............eeeeeee....ee......hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh....hhhhhhhhhhh.....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5v6r A 1345 GIPFLEYKHFVTRTFFPTHPLLGEWNIPEHCRPSMEEGISLFSSLLNNKHFLIVFVHALEQQKDFAVRDRCSLASLLTIALHGKLEYYTSIMKELLVDLIDASAAKNPKLMLRRTESVVEKMLTNWMSICMYGCLRETVGEPFFLLLCAIKQQINKGSIDAITGKARYTLNEEWLLRENIEAKPRNLNVSFQDSLSVRAMDTDTLTQVKEKILEAFCKNVPYSQWPRAEDVDLEWFASSTQSYVLRDLDDTSVVEDGRKKLNTLAHYKIPEGASLAMSLTTEKYFHLVKVLPEIYLTRLLSTKGTLQKFLDDLFKAILSIREDKPPLAVKYFFDFLEEQAEKRGISDPDTLHIWKTNSLPLRFWVNILKNPQFVFDIEKTDHIDACLSVIAQAFIDACSISNKLLYAKEIPEYRKTVQRYYKQIQDMTPLSEQEMNAHLAEESRKYQNEFNTNVAMAEIYKYAKRYRPQIMAALEANPTARRTQLQHKFEQVVALMENNIYECYS 1923
                                  1354      1391      1401      1411      1421      1431      1441      1451      1461      1471      1481      1491      1501      1511      1521      1531      1541      1551      1561 ||   1575      1585      1595      1605      1615      1625      1635      1645      1655|     1698      1708      1718      1728      1738      1748      1758      1768      1778      1788      1798      1808||    1828      1838      1848      1858      1868      1878      1888      1898      1908      1918     
                                         1361|                                                                                                                                                                          1563|                                                                                   1655|   1677|                                                                                                            1809|                                                                                                       
                                          1389                                                                                                                                                                           1568                                                                                    1670    1697                                                                                                             1820                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:503
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhh.hhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhh.....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..............hhhhh........eeeeeeee..eeeeeee...hhhhhhhhhhhhhh...hhhhh.hhh.eeeeee......eee.............ee............eeeeeee.....ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5v6r B 1345 GIPFLEYKHFVTRTFFPTHPLLGEWNIPEHCRPSMEEGISLFSSLLNNKHFLIVFVHALEQQKDFAVRDRCSLASLLTIALHGKLEYYTSIMKELLVDLIDASAAKNPKLMLRRTESVVEKMLTNWMSICMYGCLRETVGEPFFLLLCAIKQQINKGSIDAITGKARYTLNEEWLLRENIEAKPRNLNVSFQDSLSVRAMDTDTLTQVKEKILEAFCKNVPYSQWPRAEDVDLEWFASSTQSYVLRDLDDTSVVEDGRKKLNTLAHYKIPEGASLAMSLTDTEKYFHLVVLPEIYLTRLLSTKGTLQKFLDDLFKAILSIREDKPPLAVKYFFDFLEEQAEKRGISDPDTLHIWKTNSLPLRFWVNILKNPQFVFDIEKTDHIDACLSVIAQAFIDACSISKLLYAKEIPEYRKTVQRYYKQIQDMTPLSEQEMNAHLAEESRKYQNEFNTNVAMAEIYKYAKRYRPQIMAALEANPTARRTQLQHKFEQVVALMENNIYECY 1922
                                  1354      1391      1401      1411      1421      1431      1441      1451      1461      1471      1481      1491      1501      1511      1521      1531      1541      1551      1561 ||   1575      1585      1595      1605      1615      1625      1635      1645      1655||    1698      1708      1718      1728      1738      1748      1758      1768      1778      1788      1798      1808||    1829      1839      1849      1859      1869      1879      1889      1899      1909      1919   
                                         1361|                                                                                                                                                                          1563|                                                                                    1656|   1677|                                                                                                           1809|                                                                                                     
                                          1389                                                                                                                                                                           1568                                                                                     1670    1698                                                                                                            1821
   Legend:   → Mismatch (orange background)
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  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 5V6R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5V6R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5V6R)

(-) Gene Ontology  (27, 27)

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  5v6r
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 Related Entries

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

UniProtKB/Swiss-Prot
        PLXD1_MOUSE | Q3UH93: 5v6t

(-) Related Entries Specified in the PDB File

5v6b 5v6e 5v6h 5v6t