2CYD

Crystal structure of Lithium bound rotor ring of the V-ATPase from Enterococcus hirae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.208

Literature

Macromolecules
Sequence Display for 2CYD

Classification: HYDROLASE

Total Structure Weight: 175961.17

Macromolecule Entities
Molecule Chains Length Organism Details
V-type sodium ATP synthase subunit K A, B, C..., D, E, F, G, H, I, JA, B, C, D, E, F, G, H, I, J 156 Enterococcus hirae EC#: 3.6.3.14 IUBMB
Gene Name(s): ntpK ntpN EHR_08240
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: inferred by homology | Group: ALPHA-HELICAL

Subgroup Name: Bacterial V-type ATPase

Protein Name: Rotor of V-type Na+-ATPase


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

A, B, C, D, E, F, G, H, I, J 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UMQ
Query on UMQ

C, F UNDECYL-MALTOSIDE
UNDECYL-BETA-D-MALTOPYRANOSIDE (Synonym)
C23 H44 O11
UYEMNFYVTFDKRG-ZNGNCRBCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LI
Query on LI

A, B, C, D, E, F, G, H, I, J LITHIUM ION
Li
HBBGRARXTFLTSG-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.208
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 119.65 α = 90.00
b = 125.78 β = 90.00
c = 210.20 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-07-06
  • Released Date: 2006-06-27
  • Deposition author(s): Murata, T., Yamato, I., Kakinuma, Y., Shirouzu, M., Walker, J.E., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History

  • Version 1_0: 2006-06-27

    Type: Initial release

  • Version 1_1: 2008-04-30

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Advisory, Version format compliance