1OCU

CRYSTAL STRUCTURE OF THE YEAST PX-DOMAIN PROTEIN GRD19P (SORTING NEXIN 3) COMPLEXED TO PHOSPHATIDYLINOSYTOL-3-PHOSPAHTE.

Structural Biology Knowledgebase: 1OCU SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.221

Literature

Macromolecules
Sequence Display for 1OCU

Classification: SORTING PROTEIN

Total Structure Weight: 38862.65

Macromolecule Entities
Molecule Chains Length Organism Details
SORTING NEXIN A, B 162 Saccharomyces cerevisiae Fragment: PX-DOMAIN
Details: CHEMICALLY MODIFIED CYSTEINE. D-MYO-PHOSPHATIDYLINOSITOL 3-PHOSPHATE
Gene Name(s): SNX3 Gene View GRD19 YOR357C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PIB
Query on PIB

A, B 2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY- 5-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]METHYL}ETHYL BUTANOATE
3-O-PHOSPHO,,2-DI-O-BUTANOYLGLYCERYL (Synonym)
C17 H32 O16 P2
NKJZZWLREOAJGO-HODIZBBFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CME
Query on CME
A, B L-PEPTIDE LINKING C5 H11 N O3 S2 CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.221
  • Space Group: P 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 31.43 α = 110.75
b = 55.76 β = 97.35
c = 64.75 γ = 99.49

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-02-10
  • Released Date: 2003-12-12
  • Deposition author(s): Zhou, C.Z., Li De La Sierra-Gallay, I., Cheruel, S., Collinet, B., Minard, P., Blondeau, K., Henkes, G., Aufrere, R., Leulliot, N., Graille, M., Sorel, I., Savarin, P., De La Torre, F., Poupon, A., Janin, J., Van Tilbeurgh, H.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4