3AEG

Crystal structure of porcine heart mitochondrial complex II bound with N-Biphenyl-3-yl-2-iodo-benzamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.27 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of porcine heart mitochondrial complex II bound with N-Biphenyl-3-yl-2-iodo-benzamide

Harada, S.Sasaki, T.Shindo, M.Kido, Y.Inaoka, D.K.Omori, J.Osanai, A.Sakamoto, K.Mao, J.Matsuoka, S.Inoue, M.Honma, T.Tanaka, A.Kita, K.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
A
622Sus scrofaMutation(s): 0 
Gene Names: SDHA
EC: 1.3.5.1
Find proteins for Q0QF01 (Sus scrofa)
Go to Gene View: SDHA
Go to UniProtKB:  Q0QF01
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
B
252Sus scrofaMutation(s): 0 
Gene Names: SDHB
EC: 1.3.5.1
Find proteins for Q007T0 (Sus scrofa)
Go to Gene View: SDHB
Go to UniProtKB:  Q007T0
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Succinate dehydrogenase cytochrome b560 subunit, mitochondrial
C
140Sus scrofaMutation(s): 0 
Gene Names: SDHC
Find proteins for D0VWV4 (Sus scrofa)
Go to Gene View: SDHC
Go to UniProtKB:  D0VWV4
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
D
103Sus scrofaMutation(s): 0 
Gene Names: SDHD
Find proteins for A5GZW8 (Sus scrofa)
Go to Gene View: SDHD
Go to UniProtKB:  A5GZW8
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
B
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

Download SDF File 
Download CCD File 
B
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
FAD
Query on FAD

Download SDF File 
Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
FES
Query on FES

Download SDF File 
Download CCD File 
B
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
C
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
11J
Query on 11J

Download SDF File 
Download CCD File 
C
N-biphenyl-3-yl-2-iodobenzamide
C19 H14 I N O
HKKUOXBTPBBQJA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.27 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.244 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 71.862α = 90.00
b = 83.874β = 90.00
c = 294.862γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data reduction
HKL-2000data scaling
DENZOdata reduction
HKL-2000data collection
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-02-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-11
    Type: Refinement description