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

Literature

Macromolecules
Sequence Display for 1EK0

Classification: ENDOCYTOSIS / EXOCYTOSIS

Total Structure Weight: 20012.06

Macromolecule Entities
Molecule Chains Length Organism Details
PROTEIN (GTP-BINDING PROTEIN YPT51) A 170 Saccharomyces cerevisiae Fragment: GTPASE DOMAIN
Mutation: M75X, M124X
Gene Name(s): VPS21 VPS12 VPT12 YPT21 YPT51 YOR089C YOR3154C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GNP
Query on GNP

A PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GDP
Query on GDP

A GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NI
Query on NI

A NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MHO
Query on MHO
A L-PEPTIDE LINKING C5 H11 N O3 S MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.178
  • Space Group: P 61

Unit Cell:

Length (Å) Angle (°)
a = 62.33 α = 90.00
b = 62.33 β = 90.00
c = 91.22 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-03-06
  • Released Date: 2000-04-17
  • Deposition author(s): Esters, H., Scheidig, A.J.

Revision History

  • 2008-04-27
    Type: Version format compliance
  • 2011-07-13
    Type: Version format compliance