5D80 Hydrolase date Aug 14, 2015
title Crystal Structure Of Yeast V1-Atpase In The Autoinhibited Fo
authors R.A.Oot, P.M.Kane, E.A.Berry, S.Wilkens
compound source
Molecule: V-Type Proton Atpase Catalytic Subunit A
Chain: A, B, C, a, b, c
Synonym: V-Atpase Subunit A,Vacuolar Proton Pump Subunit A
Ec: 3.6.3.14,3.1.-.-
 Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Variant: Vma5 Delete

Molecule: V-Type Proton Atpase Subunit B
Chain: D, E, F, d, e, f
Synonym: V-Atpase Subunit B,V-Atpase 57 Kda Subunit,Vacuola Pump Subunit B;
Ec: 3.6.3.14
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Variant: Vma5 Delete

Molecule: V-Type Proton Atpase Subunit H
Chain: H, h
Synonym: V-Atpase Subunit H,V-Atpase 54 Kda Subunit,Vacuola Pump Subunit H;
Ec: 3.6.3.14
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Variant: Vma5 Delete

Molecule: V-Type Proton Atpase Subunit G
Chain: J, L, N, j, l, n
Synonym: V-Atpase Subunit G,V-Atpase 13 Kda Subunit,Vacuola Pump Subunit G;
Ec: 3.6.3.14
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Variant: Vma5 Delete

Molecule: V-Type Proton Atpase Subunit E
Chain: I, K, M, I, k, m
Synonym: V-Atpase Subunit E,V-Atpase 27 Kda Subunit,Vacuola Pump Subunit E;
Ec: 3.6.3.14
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Variant: Vma5 Delete

Molecule: V-Type Proton Atpase Subunit D
Chain: G, g
Synonym: V-Atpase Subunit D,Vacuolar Proton Pump Subunit D
Ec: 3.6.3.14
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Variant: Vma5 Delete

Molecule: V-Type Proton Atpase Subunit F
Chain: o, O
Synonym: V-Atpase Subunit F,V-Atpase 14 Kda Subunit,Vacuola Pump Subunit F;
Ec: 3.6.3.14
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Variant: Vma5 Delete
symmetry Space Group: C 1 2 1
R_factor 0.255 R_Free 0.302
crystal
cell
length a length b length c angle alpha angle beta angle gamma
468.020 159.650 248.270 90.00 113.75 90.00
method X-Ray Diffractionresolution 6.20 Å
ligand
enzyme Hydrolase E.C.3.6.3.14 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, d, E, f, e, D


K, k, M, i, m, I


N, j, L, n, J, l


O, o


a, C, A, B, c, b


g, G
  • ATPase activity, coupled to ...
  • proton-transporting ATPase a...


    • h, H


    Primary referenceCrystal structure of yeast V1-ATPase in the autoinhibited state., Oot RA, Kane PM, Berry EA, Wilkens S, EMBO J. 2016 Jun 13. pii: e201593447. PMID:27295975
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1016 Kb) [Save to disk]
  • Biological Unit Coordinates (5d80.pdb1.gz) 494 Kb
  • Biological Unit Coordinates (5d80.pdb2.gz) 490 Kb
  • CSU: Contacts of Structural Units for 5D80
  • Structure Factors (351 Kb)
  • Retrieve 5D80 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5D80 from S2C, [Save to disk]
  • Re-refined 5d80 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5D80 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 5D80
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5d80_C] [5d80_o] [5d80] [5d80_h] [5d80_D] [5d80_n] [5d80_c] [5d80_b] [5d80_F] [5d80_B] [5d80_l] [5d80_H] [5d80_J] [5d80_a] [5d80_f] [5d80_K] [5d80_j] [5d80_A] [5d80_M] [5d80_I] [5d80_d] [5d80_O] [5d80_L] [5d80_g] [5d80_G] [5d80_N] [5d80_m] [5d80_k] [5d80_i] [5d80_E] [5d80_e]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5D80: [AAA ] by SMART
    • Other resources with information on 5D80
  • Community annotation for 5D80 at PDBWiki (http://pdbwiki.org)

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