3AE8

Crystal structure of porcine heart mitochondrial complex II bound with N-(3-Isopropoxy-phenyl)-2-trifluoromethylbenzamide

PDB DOI: https://doi.org/10.2210/pdb3AE8/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.288
R-Value Work: 0.239
R-Value Observed: 0.242

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of porcine heart mitochondrial complex II bound with N-(3-Isopropoxy-phenyl)-2-trifluoromethylbenzamide

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.

Macromolecule Content

Total Structure Weight: 126.58 kDa
Atom Count: 8,662
Modelled Residue Count: 1,092
Deposited Residue Count: 1,117
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q0QF01
Protein Feature View Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q007T0
Protein Feature View Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D0VWV4
Protein Feature View Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A5GZW8
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Ligand Interaction
EPH Query on EPH Download Ideal Coordinates CCD File SDF format, chain K [auth D] MOL2 format, chain K [auth D]	K [auth D]	L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE C₃₉ H₆₈ N O₈ P MABRTXOVHMDVAT-AAEGOEIASA-N		Ligand Interaction
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain J [auth C] MOL2 format, chain J [auth C]	J [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Ligand Interaction
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B]	G [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-VKOJMFJBAC		Ligand Interaction
FTN Query on FTN Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B]	I [auth B]	N-[3-(1-methylethoxy)phenyl]-2-(trifluoromethyl)benzamide C₁₇ H₁₆ F₃ N O₂ PTCGDEVVHUXTMP-UHFFFAOYSA-N		Ligand Interaction
F3S Query on F3S Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B]	H [auth B]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-MZMDZPPWAW		Ligand Interaction
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B]	F [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.288
R-Value Work: 0.239
R-Value Observed: 0.242
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.655	α = 90
b = 83.994	β = 90
c = 295.317	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