1EK0

GPPNHP-BOUND YPT51 AT 1.48 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

High-resolution crystal structure of S. cerevisiae Ypt51(DeltaC15)-GppNHp, a small GTP-binding protein involved in regulation of endocytosis.

Esters, H.Alexandrov, K.Constantinescu, A.T.Goody, R.S.Scheidig, A.J.

(2000) J Mol Biol 298: 111-121

  • DOI: 10.1006/jmbi.2000.3645
  • Primary Citation of Related Structures:  
    1EK0

  • PubMed Abstract: 
  • Ypt/Rab proteins are membrane-associated small GTP-binding proteins which play a central role in the coordination, activation and regulation of vesicle-mediated transport in eukaryotic cells. We present the 1.5 A high-resolution crystal structure of Ypt51 in its active, GppNHp-bound conformation ...

    Ypt/Rab proteins are membrane-associated small GTP-binding proteins which play a central role in the coordination, activation and regulation of vesicle-mediated transport in eukaryotic cells. We present the 1.5 A high-resolution crystal structure of Ypt51 in its active, GppNHp-bound conformation. Ypt51 is an important regulator involved in the endocytic membrane traffic of Saccharomyces cerevisiae. The structure reveals small but significant structural differences compared with H-Ras p21. The effector loop and the catalytic loop are well defined and stabilized by extensive hydrophobic interactions. The switch I and switch II regions form a well-defined epitope for hypothetical effector protein binding. Sequence comparisons between the different isoforms Ypt51, Ypt52 and Ypt53 provide the first insights into determinants for specific effector binding and for fine-tuning of the intrinsic GTP-hydrolysis rate.


    Organizational Affiliation

    Abteilung für Physikalische Biochemie, Max-Planck Institut für molekulare Physiologie, Otto-Hahn-Strasse 11, Dortmund, 44227, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (GTP-BINDING PROTEIN YPT51)A170Saccharomyces cerevisiaeMutation(s): 2 
UniProt
Find proteins for P36017 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36017 
Go to UniProtKB:  P36017
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36017
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download Ideal Coordinates CCD File 
D [auth A]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
GDP
Query on GDP

Download Ideal Coordinates CCD File 
E [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
C [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MHO
Query on MHO
A L-PEPTIDE LINKINGC5 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.326α = 90
b = 62.326β = 90
c = 91.221γ = 120
Software Package:
Software NamePurpose
AMoREphasing
SHELXL-97refinement
MAR345data collection
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-04-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description