6Y11 Membrane Protein date Feb 10, 2020
title Respiratory Complex I From Thermus Thermophilus
authors J.Gutierrez-Fernandez, G.S.Minhas, L.A.Sazanov
compound source
Molecule: Nadh-Quinone Oxidoreductase Subunit 1
Chain: 1, B
Synonym: Nadh Dehydrogenase I Chain 1,Ndh-1 Subunit 1
Ec: 7.1.1.-
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Nadh-Quinone Oxidoreductase Subunit 2
Chain: 2, C
Synonym: Nadh Dehydrogenase I Chain 2,Ndh-1 Subunit 2
Ec: 7.1.1.-

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Nadh-Quinone Oxidoreductase Subunit 3
Chain: 3, D
Synonym: Nadh Dehydrogenase I Chain 3,Ndh-1 Subunit 3
Ec: 7.1.1.-

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Nadh-Quinone Oxidoreductase Subunit 4
Chain: 4, E
Synonym: Nadh Dehydrogenase I Chain 4,Ndh-1 Subunit 4
Ec: 7.1.1.-

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Nadh-Quinone Oxidoreductase Subunit 5
Chain: 5, F
Synonym: Nadh Dehydrogenase I Chain 5,Ndh-1 Subunit 5
Ec: 7.1.1.-

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Nadh-Quinone Oxidoreductase Subunit 6
Chain: 6, G
Synonym: Nadh Dehydrogenase I Subunit 6,Ndh-1 Subunit 6
Ec: 7.1.1.-

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Nadh-Quinone Oxidoreductase Subunit 9
Chain: 9, O
Synonym: Nadh Dehydrogenase I Subunit 9,Ndh-1 Subunit 9
Ec: 7.1.1.-

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Nadh-Quinone Oxidoreductase Subunit 15
Chain: 7, I
Synonym: Nadh Dehydrogenase I Chain 15,Ndh-1 Subunit 15
Ec: 7.1.1.-

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Duf3197 Domain-Containing Protein
Chain: W, X

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Nadh-Quinone Oxidoreductase Subunit 7
Chain: A, P
Synonym: Nadh Dehydrogenase I Chain 7,Ndh-1 Subunit 7
Ec: 7.1.1.-

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Nadh-Quinone Oxidoreductase Subunit 10
Chain: J, R
Synonym: Nadh Dehydrogenase I Chain 10,Ndh-1 Subunit 10
Ec: 7.1.1.-

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Nadh-Quinone Oxidoreductase Subunit 11
Chain: K, S
Synonym: Nadh Dehydrogenase I Chain 11,Ndh-1 Subunit 11
Ec: 7.1.1.-

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Nadh-Quinone Oxidoreductase Subunit 12
Chain: L, T
Synonym: Nadh Dehydrogenase I Chain 12,Ndh-1 Subunit 12
Ec: 7.1.1.-

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Nadh-Quinone Oxidoreductase Subunit 13
Chain: M, U
Synonym: Nadh Dehydrogenase I Chain 13,Ndh-1 Subunit 13
Ec: 7.1.1.-

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Nadh-Quinone Oxidoreductase Subunit 14
Chain: N, V
Synonym: Nadh Dehydrogenase I Chain 14,Ndh-1 Subunit 14
Ec: 7.1.1.-

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Nadh-Quinone Oxidoreductase Subunit 8
Chain: H, Q
Synonym: Nadh Dehydrogenase I Subunit 8,Ndh-1 Subunit 8
Ec: 7.1.1.-

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274
symmetry Space Group: P 1 21 1
R_factor 0.204 R_Free 0.229
crystal
cell
length a length b length c angle alpha angle beta angle gamma
96.280 340.890 263.300 90.00 100.57 90.00
method X-Ray Diffractionresolution 3.11 Å
ligand FES, FMN, SF4 enzyme E.C.7.1.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
1, B


2, C


3, D


6, G


7, I


A, P


E, 4


F, 5


N, V


O, 9


Q, H


S, K


T, M, L, J, R, U


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (3187 Kb) [Save to disk]
  • Biological Unit Coordinates (6y11.pdb1.gz) 1546 Kb
  • Biological Unit Coordinates (6y11.pdb2.gz) 1550 Kb
  • LPC: Ligand-Protein Contacts for 6Y11
  • CSU: Contacts of Structural Units for 6Y11
  • Structure Factors (3206 Kb)
  • Retrieve 6Y11 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6Y11 from S2C, [Save to disk]
  • View 6Y11 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 6Y11
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6y11 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6y11_E] [6y11_S] [6y11_O] [6y11_R] [6y11_M] [6y11_U] [6y11_6] [6y11_1] [6y11_B] [6y11_D] [6y11_3] [6y11_H] [6y11_J] [6y11_X] [6y11_W] [6y11_2] [6y11_L] [6y11_V] [6y11_I] [6y11_7] [6y11_T] [6y11_Q] [6y11_A] [6y11_P] [6y11_F] [6y11_C] [6y11_N] [6y11_9] [6y11_G] [6y11_5] [6y11_4] [6y11_K]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6Y11
  • Community annotation for 6Y11 at PDBWiki (http://pdbwiki.org)

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