3AEE

Crystal structure of porcine heart mitochondrial complex II bound with Atpenin A5

PDB DOI: https://doi.org/10.2210/pdb3AEE/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: 3.22 Å
R-Value Free: 0.282
R-Value Work: 0.232
R-Value Observed: 0.235

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of porcine heart mitochondrial complex II bound with Atpenin A5

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: 125.91 kDa
Atom Count: 8,618
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 EC: 1.3.5.1 (PDB Primary Data), 1.1.5 (UniProt) 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
Sequence Annotations 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 EC: 1.3.5.1 (PDB Primary Data), 1.1.5 (UniProt) 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
Sequence Annotations 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 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
Sequence Annotations Expand
Reference Sequence

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(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 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
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 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] mmCIF format, chain E [auth A]	E [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain I [auth C] MOL2 format, chain I [auth C] mmCIF format, chain I [auth C]	I [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain I [auth C] Interactions & Density Focus chain I [auth C]
AT5 Query on AT5 Download Ideal Coordinates CCD File SDF format, chain J [auth C] MOL2 format, chain J [auth C] mmCIF format, chain J [auth C]	J [auth C]	3-[(2S,4S,5R)-5,6-DICHLORO-2,4-DIMETHYL-1-OXOHEXYL]-4-HYDROXY-5,6-DIMETHOXY-2(1H)-PYRIDINONE C₁₅ H₂₁ Cl₂ N O₅ OVULNOOPECCZRG-CIUDSAMLSA-N		Interactions Focus chain J [auth C] Interactions & Density Focus chain J [auth C]
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
F3S Query on F3S Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.22 Å
R-Value Free: 0.282
R-Value Work: 0.232
R-Value Observed: 0.235
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.751	α = 90
b = 83.841	β = 90
c = 293.735	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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-02-09

Deposition Author(s):

Revision History (Full details and data files)

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
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-11-13
Changes: Structure summary