2DB4

Crystal structure of rotor ring with DCCD of the V- ATPase from Enterococcus hirae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.225

Literature

Macromolecules
Sequence Display for 2DB4

Classification: HYDROLASE

Total Structure Weight: 182339.22

Macromolecule Entities
Molecule Chains Length Organism Details
V-Type Sodium ATPase 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 4 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

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

A, B, C, D, E, F, G, H, I, J DICYCLOHEXYLUREA
C13 H24 N2 O
ADFXKUOMJKEIND-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, B, C, D, E, F, G, H, I, J 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: 2.4 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.225
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 120.21 α = 90.00
b = 125.23 β = 90.00
c = 211.58 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-12-15
  • Released Date: 2006-12-05
  • Deposition author(s): Murata, T., Yamato, I., Kakinuma, Y., Shirouzu, M., Walker, J.E., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History

  • 2012-05-23
    Type: Non-polymer description | Details: --
  • 2011-09-28
    Type: Citation | Details: Citation update
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4