5DN6 Hydrolase date Sep 09, 2015
title Atp Synthase From Paracoccus Denitrificans
authors E.Morales-Rios, M.G.Montgomery, A.G.W.Leslie, J.E.Walker
compound source
Molecule: Chain A
Chain: 1
 Organism_scientific: Paracoccus Denitrificans
Organism_taxid: 266

Molecule: Chain B
Chain: 2
Organism_scientific: Paracoccus Denitrificans
Organism_taxid: 266

Molecule: Chain C
Chain: 3
Organism_scientific: Paracoccus Denitrificans
Organism_taxid: 266

Molecule: Atp Synthase Subunit Alpha
Chain: A, B, C
Synonym: Atp Synthase F1 Sector Subunit Alpha,F-Atpase Subu
Ec: 7.1.2.2
Organism_scientific: Paracoccus Denitrificans
Organism_taxid: 266

Molecule: Atp Synthase Subunit Beta
Chain: D, E, F
Synonym: Atp Synthase F1 Sector Subunit Beta,F-Atpase Subun
Ec: 7.1.2.2
Organism_scientific: Paracoccus Denitrificans
Organism_taxid: 266

Molecule: Atp Synthase Gamma Chain
Chain: G
Synonym: Atp Synthase F1 Sector Gamma Subunit,F-Atpase Gamm
Organism_scientific: Paracoccus Denitrificans
Organism_taxid: 266

Molecule: Atp Synthase Subunit Delta
Chain: H
Synonym: Atp Synthase F(1) Sector Subunit Delta,F-Type Atpa Delta,F-Atpase Subunit Delta;
Organism_scientific: Paracoccus Denitrificans
Organism_taxid: 266

Molecule: Atp Synthase Epsilon Chain
Chain: I
Synonym: Atp Synthase F1 Sector Epsilon Subunit,F-Atpase Ep Subunit;
Organism_scientific: Paracoccus Denitrificans
Organism_taxid: 266

Molecule: Atp Synthase F0 Subcomplex C Subunit
Chain: J, K, L, M, N, O, P, Q, R, S, T, U
Organism_scientific: Paracoccus Denitrificans
Organism_taxid: 266

Molecule: Chain V
Chain: V
Organism_scientific: Paracoccus Denitrificans
Organism_taxid: 266

Molecule: Chain W
Chain: W
Organism_scientific: Paracoccus Denitrificans
Organism_taxid: 266

Molecule: Atp Synthase Subunit A,Atp Synthase Subunit A,Atp Subunit A,Atp Synthase Subunit A;
Chain: X
Synonym: Atp Synthase F0 Sector Subunit A,F-Atpase Subunit
Other_details: The Unk Residues Actually Appear Earlier Tha Proper Residues Listed. We Used Higher Numbers So People Wo Mis-Assign Them.,The Unk Residues Actually Appear Earlier T Proper Residues Listed. We Used Higher Numbers So People Wo Mis-Assign Them.,The Unk Residues Actually Appear Earlier T Proper Residues Listed. We Used Higher Numbers So People Wo Mis-Assign Them.,The Unk Residues Actually Appear Earlier T Proper Residues Listed. We Used Higher Numbers So People Wo Mis-Assign Them.;
Organism_scientific: Paracoccus Denitrificans
Organism_taxid: 266

Molecule: Chain Y
Chain: Y
Organism_scientific: Paracoccus Denitrificans
Organism_taxid: 266

Molecule: Zeta Inhibitor Protein
Chain: Z
Organism_scientific: Paracoccus Denitrificans
Organism_taxid: 266
symmetry Space Group: P 1 21 1
R_factor 0.295 R_Free 0.324
crystal
cell
length a length b length c angle alpha angle beta angle gamma
112.001 187.943 164.724 90.00 97.44 90.00
method X-Ray Diffractionresolution 3.98 Å
ligand ADP, ATP, MG enzyme E.C.7.1.2.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
C, A, B


F, E, D


G


H


I


S, T, N, K, Q, M, L, J, O, P, R, U


X


Primary referenceStructure of ATP synthase from Paracoccus denitrificans determined by X-ray crystallography at 4.0 A resolution., Morales-Rios E, Montgomery MG, Leslie AG, Walker JE, Proc Natl Acad Sci U S A. 2015 Oct 27;112(43):13231-6. doi:, 10.1073/pnas.1517542112. Epub 2015 Oct 12. PMID:26460036
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (657 Kb) [Save to disk]
  • Biological Unit Coordinates (5dn6.pdb1.gz) 642 Kb
  • LPC: Ligand-Protein Contacts for 5DN6
  • CSU: Contacts of Structural Units for 5DN6
  • Structure Factors (1110 Kb)
  • Retrieve 5DN6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5DN6 from S2C, [Save to disk]
  • Re-refined 5dn6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5DN6 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 5DN6
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5dn6_Q] [5dn6_Y] [5dn6_A] [5dn6_W] [5dn6_F] [5dn6_X] [5dn6_R] [5dn6_C] [5dn6_H] [5dn6_3] [5dn6_P] [5dn6_T] [5dn6_O] [5dn6_B] [5dn6_Z] [5dn6_K] [5dn6_L] [5dn6_V] [5dn6_M] [5dn6_J] [5dn6_1] [5dn6_D] [5dn6_I] [5dn6_U] [5dn6] [5dn6_E] [5dn6_2] [5dn6_N] [5dn6_S] [5dn6_G]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5DN6: [AAA ] by SMART
    • Other resources with information on 5DN6
  • Community annotation for 5DN6 at PDBWiki (http://pdbwiki.org)

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