4GAP

Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with NAD+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.276
  • R-Value Work: 0.237

Literature

Macromolecules
Sequence Display for 4GAP

Classification: OXIDOREDUCTASE

Total Structure Weight: 108499.07

Macromolecule Entities
Molecule Chains Length Organism Details
Rotenone-insensitive NADH-ubiquinone oxidoreductase A, B 471 Saccharomyces cerevisiae EC#: 1.6.5.9 IUBMB
Gene Name(s): NDI1 YML120C YM7056.06C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: inferred by homology | Group: MONOTOPIC MEMBRANE PROTEINS

Subgroup Name: Dehydrogenases

Protein Name: Ndi1 NADH Dehydrogenase


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

A, B FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAD
Query on NAD

A, B NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.276
  • R-Value Work: 0.237
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 116.01 α = 90.00
b = 164.48 β = 90.00
c = 70.19 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-07-25
  • Released Date: 2012-09-05
  • Deposition author(s): Iwata, M., Lee, Y., Yamashita, T., Yagi, T., Iwata, S., Cameron, A.D., Maher, M.J.

Revision History

  • Version 1_0: 2012-09-05

    Type: Initial release

  • Version 1_1: 2012-10-03

    Type: Database references