3AEG

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

• PDB DOI:  https://doi.org/10.2210/pdb3AEG/pdb

• Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
• Organism(s): Sus scrofa
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2010-02-04 Released: 2011-02-09 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.27 Å
• R-Value Free: 0.312 
• R-Value Work: 0.244 
• R-Value Observed: 0.248 

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 125.94 kDa 
• Atom Count: 8,617 
• Modelled Residue Count: 1,092 
• Deposited Residue Count: 1,117 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial	A	622	Sus scrofa	Mutation(s): 0  Gene Names: SDHA EC: 1.3.5.1 Membrane Entity: Yes
UniProt
Find proteins for Q0QF01 (Sus scrofa) Explore Q0QF01  Go to UniProtKB:  Q0QF01

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial	B	252	Sus scrofa	Mutation(s): 0  Gene Names: SDHB EC: 1.3.5.1 Membrane Entity: Yes
UniProt
Find proteins for Q007T0 (Sus scrofa) Explore Q007T0  Go to UniProtKB:  Q007T0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase cytochrome b560 subunit, mitochondrial	C	140	Sus scrofa	Mutation(s): 0  Gene Names: SDHC Membrane Entity: Yes
UniProt
Find proteins for D0VWV4 (Sus scrofa) Explore D0VWV4  Go to UniProtKB:  D0VWV4

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial	D	103	Sus scrofa	Mutation(s): 0  Gene Names: SDHD Membrane Entity: Yes
UniProt
Find proteins for A5GZW8 (Sus scrofa) Explore A5GZW8  Go to UniProtKB:  A5GZW8

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	E [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
HEM	I [auth C]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
11J	J [auth C]	N-biphenyl-3-yl-2-iodobenzamide C19 H14 I N O HKKUOXBTPBBQJA-UHFFFAOYSA-N
SF4	G [auth B]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC
F3S	H [auth B]	FE3-S4 CLUSTER Fe3 S4 FCXHZBQOKRZXKS-MZMDZPPWAW
FES	F [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.27 Å
• R-Value Free: 0.312 
• R-Value Work: 0.244 
• R-Value Observed: 0.248 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.862	α = 90
b = 83.874	β = 90
c = 294.862	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-09 
Deposition Author(s): 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.

Revision History  

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