3A5D Hydrolase date Aug 06, 2009
title Inter-Subunit Interaction And Quaternary Rearrangement Defin Central Stalk Of Prokaryotic V1-Atpase
authors N.Numoto, Y.Hasegawa, K.Takeda, K.Miki
compound source
Molecule: V-Type Atp Synthase Alpha Chain
Chain: A, B, C, I, J, K
Synonym: V-Type Atpase Subunit A
Ec: 3.6.3.14
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: V-Type Atp Synthase Beta Chain
Chain: D, E, F, L, M, N
Synonym: V-Type Atpase Subunit B
Ec: 3.6.3.14

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: V-Type Atp Synthase Subunit D
Chain: G, O
Synonym: V-Type Atpase Subunit D
Ec: 3.6.3.14

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: V-Type Atp Synthase Subunit F
Chain: H, P
Synonym: V-Type Atpase Subunit F
Ec: 3.6.3.14

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
symmetry Space Group: P 3 2 1
R_factor 0.441 R_Free 0.454
crystal
cell
length a length b length c angle alpha angle beta angle gamma
380.701 380.701 147.971 90.00 90.00 120.00
method X-Ray Diffractionresolution 4.80 Å
ligand
enzyme Hydrolase E.C.3.6.3.14 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, N, E, M, L, D


K, C, A, J, B, I


O, G


P, H


Primary referenceInter-subunit interaction and quaternary rearrangement defined by the central stalk of prokaryotic V(1)-ATPase., Numoto N, Hasegawa Y, Takeda K, Miki K, EMBO Rep. 2009 Sep 25. PMID:19779483
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (578 Kb) [Save to disk]
  • Biological Unit Coordinates (3a5d.pdb1.gz) 278 Kb
  • Biological Unit Coordinates (3a5d.pdb2.gz) 279 Kb
  • CSU: Contacts of Structural Units for 3A5D
  • Structure Factors (541 Kb)
  • Retrieve 3A5D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3A5D from S2C, [Save to disk]
  • Re-refined 3a5d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3A5D in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3A5D
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3A5D, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3a5d_L] [3a5d_M] [3a5d_O] [3a5d_I] [3a5d_P] [3a5d_K] [3a5d_A] [3a5d_J] [3a5d_E] [3a5d_G] [3a5d_F] [3a5d_B] [3a5d_N] [3a5d_C] [3a5d_D] [3a5d] [3a5d_H]
  • SWISS-PROT database: [Q56403] [Q56404] [O87880] [P74903]
  • Belongs to the h(+)- or na(+)-translocating f-type, v-type and a-type atpase (f-atpase) superfamily according to TCDB.
  • Domain organization of [VATA_THET8] [VATB_THET8] [VATD_THET8] [VATF_THET8] by SWISSPFAM
  • Other resources with information on 3A5D
  • Community annotation for 3A5D at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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