4WZ7

Crystal structure of mitochondrial NADH:ubiquinone oxidoreductase from Yarrowia lipolytica.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.341
  • R-Value Work: 0.316

Literature

Macromolecules
Sequence Display for 4WZ7

Classification: oxidoreductase

Total Structure Weight: 656099.63

Macromolecule Entities
Molecule Chains Length Organism Details
NADH-ubiquinone oxidoreductase chain 1 1 327 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
NADH dehydrogenase subunit 2 2 438 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
NADH-ubiquinone oxidoreductase chain 3 3 89 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
NADH-ubiquinone oxidoreductase chain 4 4 470 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
NADH-ubiquinone oxidoreductase chain 5 5 619 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
NADH-ubiquinone oxidoreductase chain 6 6 185 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
Gene Name(s): ND6
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
NUAM protein A 628 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
NUBM protein B 370 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
NUCM protein C 444 Yarrowia lipolytica EC#: 1.6.99.3 IUBMB
Fragment: UNP residues 23-466
39-kDa subunit E 195 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
NUGM protein G 133 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
Subunit NUHM of protein NADH:Ubiquinone Oxidoreductase (Complex I) H 154 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
Subunit NUIM of protein NADH:Ubiquinone Oxidoreductase (Complex I) I 137 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
Subunit NUKM of protein NADH:Ubiquinone Oxidoreductase (Complex I) K 183 Yarrowia lipolytica EC#: 1.6.99.3 IUBMB
Gene Name(s): nukm
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
NADH-ubiquinone oxidoreductase chain 4L L 89 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
Gene Name(s): ND4L
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
unknown subunits 1 D, Z 57 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
unknown subunits 2 F 54 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
unknown subunits J 63 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
unknown subunits M 29 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
unknown subunits N 50 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
unknown subunits O 70 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
unknown subunits P 46 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
unknown subunits Q 51 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
unknown subunits R 30 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
unknown subunits S 69 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
unknown subunits AH, T 15 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
unknown subunits U 26 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
unknown subunits V 22 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
unknown subunits AB, AY, BE, W 9 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
unknown subunits AJ, AV, BH, X 16 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
unknown subunits AR, AT, Y 13 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
unknown subunits AA, AW, BB, BG 18 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
unknown subunits AC, AD 47 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
unknown subunits AE 48 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
unknown subunits AF 35 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
unknown subunits AG 25 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
unknown subunits AI, AL 36 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
unknown subunits AK, AN 76 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
unknown subunits AM 17 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
unknown subunits AO 32 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
unknown subunits AP, AS 11 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
unknown subunits AQ, BA 8 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
unknown subunits AU 58 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
unknown subunits AX 39 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
unknown subunits AZ 40 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
unknown subunits BC 20 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
unknown subunits BD, BF 19 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB
unknown subunits BI 905 Yarrowia lipolytica EC#: 1.6.5.3 IUBMB

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Electron Transport Chain Complexes: Complex I

Protein Name: Mitochondrial Complex I


Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SF4
Query on SF4

A, B, I, K IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FES
Query on FES

A, H FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
UNK
Query on UNK
1, 2, 3, 4, 5, A, AA, AB, AC, AD, AE, AF, AG, AH, AI, AJ, AK, AL, AM, AN, AO, AP, AQ, AR, AS, AT, AU, AV, AW, AX, AY, AZ, B, BA, BB, BC, BD, BE, BF, BG, BH, BI, C, D, E, F, G, H, I, J, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z L-PEPTIDE LINKING C4 H9 N O2 --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.341
  • R-Value Work: 0.316
  • Space Group: H 3 2

Unit Cell:

Length (Å) Angle (°)
a = 317.74 α = 90.00
b = 317.74 β = 90.00
c = 818.97 γ = 120.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2014-11-18
  • Released Date: 2015-03-25
  • Deposition author(s): Wirth, C., Zickermann, V., Brandt, U., Hunte, C.

Revision History

No revisions since initial release