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(-) Description

Title :  CRYSTAL STRUCTURE OF YPT7 COVALENTLY MODIFIED WITH GTP
 
Authors :  D. Koch, D. Wiegandt, S. Vieweg, F. Hofmann, 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 :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Ypt7, Acryl-Nucleotides, Agtp, Covalent, 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, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
12UJ1Ligand/IonN-[3-(PROPANOYLAMINO)PROPYL]GUANOSINE 5'-(TETRAHYDROGENTRIPHOSPHATE)
2MG1Ligand/IonMAGNESIUM ION
3YT33Ligand/IonYTTRIUM (III) ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:22 , THR A:40 , 2UJ A:202 , HOH A:324 , HOH A:325binding site for residue MG A 201
2AC2SOFTWARESER A:17 , GLY A:18 , VAL A:19 , GLY A:20 , LYS A:21 , THR A:22 , SER A:23 , TYR A:33 , SER A:34 , CYS A:35 , GLN A:36 , TYR A:37 , THR A:40 , GLY A:67 , ASN A:126 , LYS A:127 , ASP A:129 , SER A:158 , ALA A:159 , LYS A:160 , MG A:201 , HOH A:324 , HOH A:325 , HOH A:333 , HOH A:341binding site for residue 2UJ A 202
3AC3SOFTWAREASP A:31 , ASN A:99 , HOH A:305 , HOH A:306 , HOH A:317binding site for residue YT3 A 203
4AC4SOFTWAREGLU A:49 , GLU A:69 , GLU A:106 , HOH A:301 , HOH A:308 , HOH A:310 , HOH A:318binding site for residue YT3 A 204
5AC5SOFTWAREGLU A:117 , GLU A:131 , HOH A:304binding site for residue YT3 A 205

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PHG)

(-) 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    
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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:176
                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee....hhhhhhhhhhhh...........eeeeeeeeee...eeeeeeeeee..hhhhh.hhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhh.........eeeeee...........hhhhhhhhhhhh....eeee......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4phg A   6 KNILKVIILGDSGVGKTSLMHRYVNDKYSCQYIATIGADFLTKEVTVDGDKVATMQVWDTAGLERFQSLGVAFYRGADCCVLVYDVTNASSFENIKSWRDEFLVHANVNSPETFPFVILGNKIDAEESKKIVSEKSAQELAKSLGDIPLFLTSAKNAINVDTAFEEIARSALQQNQ 181
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175
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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 4PHG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)

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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 4phf 4phh

(-) Related Entries Specified in the PDB File

4phf 4phh