5ZEA

Crystal structure of the nucleotide-free mutant A3B3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.384 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Metastable asymmetrical structure of a shaftless V1motor.

Maruyama, S.Suzuki, K.Imamura, M.Sasaki, H.Matsunami, H.Mizutani, K.Saito, Y.Imai, F.L.Ishizuka-Katsura, Y.Kimura-Someya, T.Shirouzu, M.Uchihashi, T.Ando, T.Yamato, I.Murata, T.

(2019) Sci Adv 5: eaau8149-eaau8149


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
V-type sodium ATPase catalytic subunit A
A, B, C, G, H, I
594Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258)Mutation(s): 0 
Gene Names: ntpA
EC: 7.2.2.1
Find proteins for Q08636 (Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258))
Go to UniProtKB:  Q08636
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
V-type sodium ATPase subunit B
D, E, F, J, K, L
462Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258)Mutation(s): 1 
Gene Names: ntpB
Find proteins for Q08637 (Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258))
Go to UniProtKB:  Q08637
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, C, D, G, H, K
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.384 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.215 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 180.840α = 90.00
b = 107.770β = 99.39
c = 193.370γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
XSCALEdata scaling
PHENIXrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-02-06
    Type: Initial release
  • Version 1.1: 2019-02-20
    Type: Data collection, Database references