3VR3

Crystal structure of AMP-PNP bound A3B3 complex from Enterococcus hirae V-ATPase [bA3B3]

Structural Biology Knowledgebase: 3VR3 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.198

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3VR3

Classification: HYDROLASE

Total Structure Weight: 360757.75

Macromolecule Entities
Molecule Chains Length Organism Details
V-type sodium ATPase catalytic subunit A A, B, C 600 Enterococcus hirae EC#: 3.6.3.15 IUBMB
Gene Name(s): ntpA EHR_08260
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
V-type sodium ATPase subunit B D, E, F 465 Enterococcus hirae EC#: 3.6.3.15 IUBMB
Gene Name(s): ntpB EHR_08265
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Bacterial V-type ATPase

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


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

B, C PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

B, C MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B, C, D, E, F L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.198
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 122.11 α = 90.00
b = 124.13 β = 90.00
c = 245.33 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-04-03
  • Released Date: 2013-01-16
  • Deposition author(s): Arai, S., Saijo, S., Suzuki, K., Mizutani, K., Kakinuma, Y., Ishizuka-Katsura, Y., Ohsawa, N., Terada, T., Shirouzu, M., Yokoyama, S., Iwata, S., Yamato, I., Murata, T.

Revision History

  • 2013-02-06
    Type: Citation | Details: Citation update