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(-) Description

Title :  CRYSTAL STRUCTURE OF YPT7 COVALENTLY MODIFIED WITH GDP
 
Authors :  S. Vieweg, D. Wiegandt, F. Hofmann, D. Koch, Y. Wu, A. Itzen, M. P. Muelle R. S. Goody
Date :  06 May 14  (Deposition) - 28 May 14  (Release) - 31 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Ypt7, Acryl-Nucleotides, Agdp, Covalent, Gdp, Endocytosis, Exocytosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Wiegandt, S. Vieweg, F. Hofmann, D. Koch, F. Li, Y. W. Wu, A. Itzen, M. P. Muller, R. S. Goody
Locking Gtpases Covalently In Their Functional States.
Nat Commun V. 6 7773 2015
PubMed-ID: 26178622  |  Reference-DOI: 10.1038/NCOMMS8773

(-) Compounds

Molecule 1 - GTP-BINDING PROTEIN YPT7
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-182
    Gene: YPT7, VAM4, YML001W, YM8270.02
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: S288C

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
12UH1Ligand/IonN-[3-(PROPANOYLAMINO)PROPYL]GUANOSINE 5'-(TRIHYDROGENDIPHOSPHATE)
2MG1Ligand/IonMAGNESIUM ION
3NO31Ligand/IonNITRATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:18 , VAL A:19 , GLY A:20 , LYS A:21 , THR A:22 , SER A:23 , TYR A:33 , CYS A:35 , ASN A:126 , LYS A:127 , ASP A:129 , SER A:158 , ALA A:159 , LYS A:160 , MG A:202 , HOH A:327 , HOH A:328 , HOH A:343binding site for residue 2UH A 201
2AC2SOFTWARETHR A:22 , 2UH A:201 , HOH A:325 , HOH A:326 , HOH A:327 , HOH A:328binding site for residue MG A 202
3AC3SOFTWAREARG A:27 , LYS A:101 , ALA A:162 , ILE A:163 , ASN A:164 , VAL A:165 , ASP A:166 , HOH A:314binding site for residue NO3 A 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PHF)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4PHF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PHF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PHF)

(-) Exons   (0, 0)

(no "Exon" information available for 4PHF)

(-) Sequences/Alignments

Asymmetric/Biological 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:163
                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhh.........eeeeeeee..eeeeeeeee...hhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhhh........eeeeee....hhhhh..hhhhhhhhhhhh....eeee......hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4phf A   7 NILKVIILGDSGVGKTSLMHRYVNDKYSCTIGADFLTKEVTVDGDKVATMQVWDTGVAFYRGADCCVLVYDVTNASSFENIKSWRDEFLVHANVNSPETFPFVILGNKIDAEESKKIVSEKSAQELAKSLGDIPLFLTSAKNAINVDTAFEEIARSALQQNQA 182
                                    16        26        40        50        60    ||  79        89        99       109       119       129       139       149       159       169       179   
                                                       35|                       65|                                                                                                           
                                                        40                        75
   Legend:   → Mismatch (orange background)
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  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 4PHF)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PHF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PHF)

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)

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  4phf
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  YPT7_YEAST | P32939
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 Related Entries

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

UniProtKB/Swiss-Prot
        YPT7_YEAST | P32939: 1ky2 1ky3 4phg 4phh

(-) Related Entries Specified in the PDB File

4phg 4phh