2EIX

The Structure of Physarum polycephalum cytochrome b5 reductase

Structural Biology Knowledgebase: 2EIX SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.180

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2EIX

Classification: OXIDOREDUCTASE

Total Structure Weight: 57875.52

Macromolecule Entities
Molecule Chains Length Organism Details
NADH-cytochrome b5 reductase A, B 243 Physarum polycephalum EC#: 1.6.2.2 IUBMB
Fragment: residues 39-281
Gene Name(s): b5R

Small Molecules
Ligands 4 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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IOD
Query on IOD

A, B IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.180
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 101.08 α = 90.00
b = 136.37 β = 90.00
c = 45.72 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-03-14
  • Released Date: 2007-04-17
  • Deposition author(s): Kim, S.W., Suga, M., Ogasahara, K., Ikegami, T., Minami, Y., Yubisui, T., Tsukihara, T.

Revision History

  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4