3VR4

Crystal structure of Enterococcus hirae V1-ATPase [eV1]

Structural Biology Knowledgebase: 3VR4 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.211
  • R-Value Work: 0.167

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3VR4

Classification: HYDROLASE

Total Structure Weight: 399405.38

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
V-type sodium ATPase subunit B D, E, F 465 Enterococcus hirae EC#: 3.6.3.15 IUBMB
Gene Name(s): ntpB EHR_08265
V-type sodium ATPase subunit D G 217 Enterococcus hirae EC#: 1.1.1.112 IUBMB
Gene Name(s): ntpD EHR_08270
V-type sodium ATPase subunit G H 115 Enterococcus hirae EC#: 3.6.3.15 IUBMB
Gene Name(s): ntpG ntpQ EHR_08255

Membrane Protein

Source: mpstruc | 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
B3P
Query on B3P

F 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)- PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3- DIOL
C11 H26 N2 O6
HHKZCCWKTZRCCL-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B, D, F, G GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
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, G, H L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.211
  • R-Value Work: 0.167
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 127.98 α = 90.00
b = 128.48 β = 90.00
c = 225.93 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): Saijo, S., Arai, 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