5LDW Oxidoreductase date Jun 28, 2016
title Structure Of Mammalian Respiratory Complex I, Class1
authors K.R.Vinothkumar, J.Zhu, J.Hirst
compound source
Molecule: Nadh-Ubiquinone Oxidoreductase Chain 3
Chain: A
Synonym: Nadh Dehydrogenase Subunit 3
Ec: 1.6.5.3
Other_details: Residues 28-50 Are Disordered Or Poor Densit
 Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh Dehydrogenase [Ubiquinone] Iron-Sulfur Prote Mitochondrial;
Chain: B
Synonym: Complex I-20kd,Ci-20kd,Nadh-Ubiquinone Oxidoreduct Subunit,Psst Subunit;
Ec: 1.6.5.3,1.6.99.3
Other_details: This Chain Coordinates An Iron-Sulphur Clust
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh Dehydrogenase [Ubiquinone] Iron-Sulfur Prote Mitochondrial;
Chain: C
Synonym: Complex I-30kd,Ci-30kd,Nadh-Ubiquinone Oxidoreduct Subunit;
Ec: 1.6.5.3,1.6.99.3
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh Dehydrogenase [Ubiquinone] Iron-Sulfur Prote Mitochondrial;
Chain: D
Synonym: Complex I-49kd,Ci-49kd,Nadh-Ubiquinone Oxidoreduct Subunit;
Ec: 1.6.5.3,1.6.99.3
Other_details: Residues 51-60 Not Modelled 129 Is R For Cam Cows Instead Of Q;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh Dehydrogenase [Ubiquinone] Flavoprotein 2, Mitochondrial;
Chain: E
Synonym: Nadh Dehydrogenase Subunit II,Nadh-Ubiquinone Oxid 24 Kda Subunit;
Ec: 1.6.5.3,1.6.99.3
Other_details: This Chain Coordinates An Iron-Sulphur Clust
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh Dehydrogenase [Ubiquinone] Flavoprotein 1, Mitochondrial;
Chain: F
Synonym: Complex I-51kd,Ci-51kd,Nadh Dehydrogenase Flavopro Nadh-Ubiquinone Oxidoreductase 51 Kda Subunit;
Ec: 1.6.5.3,1.6.99.3
Other_details: This Chain Coordinates Sf4 And Also Binds Fm
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh-Ubiquinone Oxidoreductase 75 Kda Subunit, Mitochondrial,Nadh-Ubiquinone Oxidoreductase 75 Kda Subunit Mitochondrial;
Chain: G
Synonym: Complex I-75kd,Ci-75kd,Complex I-75kd,Ci-75kd
Ec: 1.6.5.3,1.6.99.3,1.6.5.3,1.6.99.3
Other_details: This Chain Coordinates 2xsf4 And 1fes. We Ar Uncertain Of The Register 210-692;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh-Ubiquinone Oxidoreductase Chain 1
Chain: H
Synonym: Nadh Dehydrogenase Subunit 1
Ec: 1.6.5.3
Other_details: Residues 201-217 Are Disordered
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh Dehydrogenase [Ubiquinone] Iron-Sulfur Prote Mitochondrial;
Chain: I
Synonym: Complex I-23kd,Ci-23kd,Nadh-Ubiquinone Oxidoreduct Subunit,Tyky Subunit;
Ec: 1.6.5.3,1.6.99.3
Other_details: This Chain Coordinates 2 Iron-Sulphur Cluste
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh-Ubiquinone Oxidoreductase Chain 6
Chain: J
Synonym: Nadh Dehydrogenase Subunit 6
Ec: 1.6.5.3
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh-Ubiquinone Oxidoreductase Chain 4l
Chain: K
Synonym: Nadh Dehydrogenase Subunit 4l
Ec: 1.6.5.3
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh-Ubiquinone Oxidoreductase Chain 5
Chain: L
Synonym: Nadh Dehydrogenase Subunit 5
Ec: 1.6.5.3
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh-Ubiquinone Oxidoreductase Chain 4
Chain: M
Synonym: Nadh Dehydrogenase Subunit 4
Ec: 1.6.5.3
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh-Ubiquinone Oxidoreductase Chain 2
Chain: N
Synonym: Nadh Dehydrogenase Subunit 2
Ec: 1.6.5.3
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh Dehydrogenase [Ubiquinone] 1 Alpha Subcomple 10, Ndufa10,Nadh Dehydrogenase [Ubiquinone] 1 Alpha Subcomp Subunit 10, Ndufa10,Nadh Dehydrogenase [Ubiquinone] 1 Alpha Subcomplex Subunit 10, Mitochondrial;
Chain: O
Synonym: Complex I-42kd,Ci-42kd,Nadh-Ubiquinone Oxidoreduct Subunit;
Other_details: We Are Uncertain Of The Register 5-90
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh Dehydrogenase [Ubiquinone] 1 Alpha Subcomple 9, Ndufa9;
Chain: P
Other_details: Residue Range 187-199, 253-279 Not Modelled Of The Residues Are Assigned As The Density Doesn'T Allow I Density For Nap Is Prominent And Has Been Modelled.;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh Dehydrogenase [Ubiquinone] Iron-Sulfur Prote Ndufs4;
Chain: Q
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh Dehydrogenase [Ubiquinone] Iron-Sulfur Prote Ndufs6,Nadh Dehydrogenase [Ubiquinone] Iron-Sulfur Protein Mitochondrial,Nadh Dehydrogenase [Ubiquinone] Iron-Sulfur P Mitochondrial;
Chain: R
Synonym: Complex I-13kd-A,Ci-13kd-A,Nadh-Ubiquinone Oxidore Kda-A Subunit,Complex I-13kd-A,Ci-13kd-A,Nadh-Ubiquinone Oxidoreductase 13 Kda-A Subunit;
Other_details: This Chain Coordinates A Zinc Atom
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh Dehydrogenase [Ubiquinone] 1 Alpha Subcomple 2;
Chain: S
Synonym: Complex I-B8,Ci-B8,Nadh-Ubiquinone Oxidoreductase Subunit;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Acyl Carrier Protein, Mitochondrial
Chain: T, U
Synonym: Acp,Ci-Sdap,Nadh-Ubiquinone Oxidoreductase 9.6 Kda
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh Dehydrogenase [Ubiquinone] 1 Alpha Subcomple 5;
Chain: V
Synonym: Complex I Subunit B13,Complex I-13kd-B,Ci-13kd-B,N Ubiquinone Oxidoreductase 13 Kda-B Subunit;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh Dehydrogenase [Ubiquinone] 1 Alpha Subcomple 6;
Chain: W
Synonym: Complex I-B14,Ci-B14,Nadh-Ubiquinone Oxidoreductas Subunit;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh Dehydrogenase [Ubiquinone] 1 Alpha Subcomple 8,Nadh Dehydrogenase [Ubiquinone] 1 Alpha Subcomplex Subuni Dehydrogenase [Ubiquinone] 1 Alpha Subcomplex Subunit 8, Nd
Chain: X
Synonym: Complex I-19kd,Ci-19kd,Complex I-Pgiv,Ci-Pgiv,Nadh Ubiquinone Oxidoreductase 19 Kda Subunit,Complex I-19kd,Ci- Complex I-Pgiv,Ci-Pgiv,Nadh-Ubiquinone Oxidoreductase 19 Kd
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh Dehydrogenase [Ubiquinone] 1 Alpha Subcomple 11;
Chain: Y
Synonym: Complex I-B14.7,Ci-B14.7,Nadh-Ubiquinone Oxidoredu Subunit B14.7;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh Dehydrogenase [Ubiquinone] 1 Alpha Subcomple 13, Ndufa13,Nadh Dehydrogenase [Ubiquinone] 1 Alpha Subcomp Subunit 13,Nadh Dehydrogenase [Ubiquinone] 1 Alpha Subcompl 13, Ndufa13,Nadh Dehydrogenase [Ubiquinone] 1 Alpha Subcomp Subunit 13,Nadh Dehydrogenase [Ubiquinone] 1 Alpha Subcompl 13, Ndufa13,Nadh Dehydrogenase [Ubiquinone] 1 Alpha Subcomp Subunit 13,Nadh Dehydrogenase [Ubiquinone] 1 Alpha Subcompl 13, Ndufa13;
Chain: Z
Synonym: Cell Death Regulatory Protein Grim-19,Complex I-B1 B16.6,Gene Associated With Retinoic-Interferon-Induced Mort Protein,Grim-19,Nadh-Ubiquinone Oxidoreductase B16.6 Subuni Death Regulatory Protein Grim-19,Complex I-B16.6,Ci-B16.6,G Associated With Retinoic-Interferon-Induced Mortality 19 Pr Grim-19,Nadh-Ubiquinone Oxidoreductase B16.6 Subunit,Cell D Regulatory Protein Grim-19,Complex I-B16.6,Ci-B16.6,Gene As With Retinoic-Interferon-Induced Mortality 19 Protein,Grim- Ubiquinone Oxidoreductase B16.6 Subunit;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh Dehydrogenase [Ubiquinone] 1 Alpha Subcomple 1;
Chain: a
Synonym: Complex I-Mwfe,Ci-Mwfe,Nadh-Ubiquinone Oxidoreduct Subunit;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh Dehydrogenase [Ubiquinone] 1 Alpha Subcomple 3,Nadh Dehydrogenase [Ubiquinone] 1 Alpha Subcomplex Subuni Dehydrogenase [Ubiquinone] 1 Alpha Subcomplex Subunit 3, Nd
Chain: b
Synonym: Complex I-B9,Ci-B9,Nadh-Ubiquinone Oxidoreductase Subunit,Complex I-B9,Ci-B9,Nadh-Ubiquinone Oxidoreductase B
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh Dehydrogenase [Ubiquinone] 1 Subunit C1, Mitochondrial;
Chain: c
Synonym: Complex I-Kfyi,Ci-Kfyi,Nadh-Ubiquinone Oxidoreduct Subunit;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh Dehydrogenase [Ubiquinone] 1 Subunit C2, Ndu Dehydrogenase [Ubiquinone] 1 Subunit C2,Nadh Dehydrogenase [Ubiquinone] 1 Subunit C2, Ndufc2,Nadh Dehydrogenase [Ubiqu Subunit C2,Nadh Dehydrogenase [Ubiquinone] 1 Subunit C2, Nd Dehydrogenase [Ubiquinone] 1 Subunit C2,Nadh Dehydrogenase [Ubiquinone] 1 Subunit C2, Ndufc2;
Chain: d
Synonym: Complex I-B14.5b,Ci-B14.5b,Nadh-Ubiquinone Oxidore Subunit B14.5b,Complex I-B14.5b,Ci-B14.5b,Nadh-Ubiquinone Oxidoreductase Subunit B14.5b,Complex I-B14.5b,Ci-B14.5b,Na Ubiquinone Oxidoreductase Subunit B14.5b;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh Dehydrogenase [Ubiquinone] Iron-Sulfur Prote
Chain: e
Synonym: Complex I-15 Kda,Ci-15 Kda,Nadh-Ubiquinone Oxidore Kda Subunit;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh Dehydrogenase [Ubiquinone] 1 Beta Subcomplex 1;
Chain: f
Synonym: Complex I-Mnll,Ci-Mnll,Nadh-Ubiquinone Oxidoreduct Subunit;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh Dehydrogenase [Ubiquinone] 1 Beta Subcomplex 11, Mitochondrial;
Chain: g
Synonym: Complex I-Esss,Ci-Esss,Nadh-Ubiquinone Oxidoreduct Subunit;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh Dehydrogenase [Ubiquinone] 1 Beta Subcomplex 5, Mitochondrial,Nadh Dehydrogenase [Ubiquinone] 1 Beta Sub Subunit 5, Mitochondrial,Nadh Dehydrogenase [Ubiquinone] 1 Subcomplex Subunit 5, Ndufb5;
Chain: h
Synonym: Complex I-Sgdh,Ci-Sgdh,Nadh-Ubiquinone Oxidoreduct Subunit,Complex I-Sgdh,Ci-Sgdh,Nadh-Ubiquinone Oxidoreducta Subunit;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh Dehydrogenase [Ubiquinone] 1 Beta Subcomplex 6,Nadh Dehydrogenase [Ubiquinone] 1 Beta Subcomplex Subunit Dehydrogenase [Ubiquinone] 1 Beta Subcomplex Subunit 6, Ndu
Chain: I
Synonym: Complex I-B17,Ci-B17,Nadh-Ubiquinone Oxidoreductas Subunit,Complex I-B17,Ci-B17,Nadh-Ubiquinone Oxidoreductase Subunit;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh Dehydrogenase [Ubiquinone] 1 Beta Subcomplex 2, Ndufb2;
Chain: j
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh Dehydrogenase [Ubiquinone] 1 Beta Subcomplex 3, Ndufb3;
Chain: k
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh Dehydrogenase [Ubiquinone] 1 Beta Subcomplex 8, Ndufb8;
Chain: l
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh Dehydrogenase [Ubiquinone] 1 Beta Subcomplex 4, Ndufb4,Nadh Dehydrogenase [Ubiquinone] 1 Beta Subcomplex 4, Ndufb4,Nadh Dehydrogenase [Ubiquinone] 1 Beta Subcomplex 4;
Chain: m
Synonym: Complex I-B15,Ci-B15,Nadh-Ubiquinone Oxidoreductas Subunit;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh Dehydrogenase [Ubiquinone] 1 Beta Subcomplex 9,Nadh Dehydrogenase [Ubiquinone] 1 Beta Subcomplex Subunit Dehydrogenase [Ubiquinone] 1 Beta Subcomplex Subunit 9, Ndu
Chain: n
Synonym: Complex I-B22,Ci-B22,Nadh-Ubiquinone Oxidoreductas Subunit,Complex I-B22,Ci-B22,Nadh-Ubiquinone Oxidoreductase Subunit;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh Dehydrogenase [Ubiquinone] 1 Beta Subcomplex 7;
Chain: o
Synonym: Complex I-B18,Ci-B18,Nadh-Ubiquinone Oxidoreductas Subunit;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh Dehydrogenase [Ubiquinone] 1 Beta Subcomplex 10, Ndufb10,Nadh Dehydrogenase [Ubiquinone] 1 Beta Subcompl 10,Nadh Dehydrogenase [Ubiquinone] 1 Beta Subcomplex Subuni Ndufb10,Nadh Dehydrogenase [Ubiquinone] 1 Beta Subcomplex S Nadh Dehydrogenase [Ubiquinone] 1 Beta Subcomplex Subunit 1 Ndufb10,Nadh Dehydrogenase [Ubiquinone] 1 Beta Subcomplex S Nadh Dehydrogenase [Ubiquinone] 1 Beta Subcomplex Subunit 1 Ndufb10;
Chain: p
Synonym: Complex I-Pdsw,Ci-Pdsw,Nadh-Ubiquinone Oxidoreduct Subunit,Complex I-Pdsw,Ci-Pdsw,Nadh-Ubiquinone Oxidoreducta Subunit,Complex I-Pdsw,Ci-Pdsw,Nadh-Ubiquinone Oxidoreducta Subunit;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh Dehydrogenase [Ubiquinone] 1 Alpha Subcomple 12;
Chain: q
Synonym: Complex I-B17.2,Cib17.2,Nadh-Ubiquinone Oxidoreduc Subunit B17.2;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh Dehydrogenase [Ubiquinone] 1 Alpha Subcomple 7, Ndufa7;
Chain: r
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Nadh Dehydrogenase [Ubiquinone] Flavoprotein 3, N
Chain: s
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 4.27 Å
ligand FES, FMN, NAP, SF4, ZN enzyme Oxidoreductase E.C.1.6.5.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


C


D


E


F


G


H


I


J


K


L


M


N


S


T, U


V


W


X


Y


a


b


c


d


e


f


i


m


n


o


q
  • electron transfer activity


    • Primary referenceStructure of mammalian respiratory complex I., Zhu J, Vinothkumar KR, Hirst J, Nature. 2016 Aug 18;536(7616):354-8. PMID:27509854
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1042 Kb) [Save to disk]
  • Biological Unit Coordinates (5ldw.pdb1.gz) 1017 Kb
  • LPC: Ligand-Protein Contacts for 5LDW
  • CSU: Contacts of Structural Units for 5LDW
  • Retrieve 5LDW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5LDW from S2C, [Save to disk]
    • View 5LDW 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 5LDW
  • 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: [5ldw_Q] [5ldw_b] [5ldw_c] [5ldw_e] [5ldw_J] [5ldw_F] [5ldw_Y] [5ldw_a] [5ldw_k] [5ldw_I] [5ldw_g] [5ldw_d] [5ldw_i] [5ldw_V] [5ldw_M] [5ldw_G] [5ldw_o] [5ldw_A] [5ldw_s] [5ldw_j] [5ldw_K] [5ldw_R] [5ldw_H] [5ldw_B] [5ldw_h] [5ldw_q] [5ldw_O] [5ldw_D] [5ldw_T] [5ldw_L] [5ldw_m] [5ldw_p] [5ldw_W] [5ldw_l] [5ldw_S] [5ldw_N] [5ldw_Z] [5ldw] [5ldw_n] [5ldw_P] [5ldw_U] [5ldw_f] [5ldw_C] [5ldw_X] [5ldw_r] [5ldw_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5LDW: [L51_S25_CI-B8] [NADH-G_4Fe-4S_3] [NADH_4Fe-4S ] by SMART
    • Other resources with information on 5LDW
  • Community annotation for 5LDW at PDBWiki (http://pdbwiki.org)

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