1TY8

Crystal structure of yeast ymx7, an ADP-ribose-1''-monophosphatase, complexed with ADP

Structural Biology Knowledgebase: 1TY8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.244
  • R-Value Work: 0.190

Literature

Macromolecules
Sequence Display for 1TY8

Classification: structural genomics unknown function

Total Structure Weight: 32615.10

Macromolecule Entities
Molecule Chains Length Organism Details
Hypothetical 32.1 kDa protein in ADH3-RCA1 intergenic region A 284 Saccharomyces cerevisiae EC#: 3.1.3.84 IUBMB
Gene Name(s): YMR087W YM9582.12
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.244
  • R-Value Work: 0.190
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 107.95 α = 90.00
b = 38.05 β = 111.75
c = 63.14 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-07-07
  • Released Date: 2004-11-30
  • Deposition author(s): Kumaran, D., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values