4G6H

Crystal structure of NDH with NADH

Structural Biology Knowledgebase: 4G6H SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.225
  • R-Value Work: 0.193

Literature

Macromolecules
Sequence Display for 4G6H

Classification: OXIDOREDUCTASE

Total Structure Weight: 115197.27

Macromolecule Entities
Molecule Chains Length Organism Details
Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial A, B 502 Saccharomyces cerevisiae EC#: 1.6.5.9 IUBMB
Gene Name(s): NDI1 YML120C YM7056.06C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: mpstruc | Group: MONOTOPIC MEMBRANE PROTEINS

Subgroup Name: Dehydrogenases

Protein Name: Ndi1 NADH Dehydrogenase


Small Molecules
Ligands 3 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)
NAI
Query on NAI

A, B 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
NADH (Synonym)
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.225
  • R-Value Work: 0.193
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 126.19 α = 90.00
b = 229.59 β = 90.00
c = 111.87 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-07-19
  • Released Date: 2012-10-24
  • Deposition author(s): Li, W., Feng, Y., Ge, J., Yang, M.

Revision History

  • 2013-11-06
    Type: Non-polymer description | Details: update ligand code
  • 2012-12-05
    Type: Citation | Details: Citation update