3VRA | pdb_00003vra

Mitochondrial rhodoquinol-fumarate reductase from the parasitic nematode Ascaris suum with the specific inhibitor Atpenin A5

PDB DOI: https://doi.org/10.2210/pdb3VRA/pdb

Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
Organism(s): Ascaris suum
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD

Deposited: 2012-04-07 Released: 2013-04-10
Deposition Author(s): Shimizu, H., Shiba, T., Inaoka, D.K., Osanai, A., Kita, K., Sakamoto, K., Harada, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.44 Å
R-Value Free:
0.281 (Depositor), 0.278 (DCC)
R-Value Work:
0.205 (Depositor), 0.203 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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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 mitochondrial quinol-fumarate reductase from parasitic nematode Ascaris suum

Shimizu, H., Shiba, T., Inaoka, D.K., Osanai, A., Kita, K., Sakamoto, K., Harada, S.

To be published.

Macromolecule Content

Total Structure Weight: 289.13 kDa
Atom Count: 18,262
Modeled Residue Count: 2,288
Deposited Residue Count: 2,542
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flavoprotein subunit of complex II	A, E	645	Ascaris suum	Mutation(s): 0 EC: 1.3.5.1 Membrane Entity: Yes
UniProt
Find proteins for Q33862 (Ascaris suum) Explore Q33862 Go to UniProtKB: Q33862
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q33862
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Iron-sulfur subunit of succinate dehydrogenase	B, F	282	Ascaris suum	Mutation(s): 0 EC: 1.3.5.1 Membrane Entity: Yes
UniProt
Find proteins for O44074 (Ascaris suum) Explore O44074 Go to UniProtKB: O44074
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O44074
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-large subunit	C, G	188	Ascaris suum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P92506 (Ascaris suum) Explore P92506 Go to UniProtKB: P92506
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P92506
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial	D, H	156	Ascaris suum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P92507 (Ascaris suum) Explore P92507 Go to UniProtKB: P92507
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P92507
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain R [auth E] MOL2 format, chain J [auth A] MOL2 format, chain R [auth E] mmCIF format, chain J [auth A] mmCIF format, chain R [auth E]	J [auth A], R [auth E]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain J [auth A] Focus chain R [auth E] Interactions & Density Focus chain J [auth A] Focus chain R [auth E]
EPH Query on EPH Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain X [auth H] MOL2 format, chain P [auth D] MOL2 format, chain X [auth H] mmCIF format, chain P [auth D] mmCIF format, chain X [auth H]	P [auth D], X [auth H]	L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE C₃₉ H₆₈ N O₈ P MABRTXOVHMDVAT-AAEGOEIASA-N		Interactions Focus chain P [auth D] Focus chain X [auth H] Interactions & Density Focus chain P [auth D] Focus chain X [auth H]
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain V [auth G] MOL2 format, chain N [auth C] MOL2 format, chain V [auth G] mmCIF format, chain N [auth C] mmCIF format, chain V [auth G]	N [auth C], V [auth G]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain N [auth C] Focus chain V [auth G] Interactions & Density Focus chain N [auth C] Focus chain V [auth G]
AT5 Query on AT5 Download:Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain W [auth G] MOL2 format, chain O [auth C] MOL2 format, chain W [auth G] mmCIF format, chain O [auth C] mmCIF format, chain W [auth G]	O [auth C], W [auth G]	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 O [auth C] Focus chain W [auth G] Interactions & Density Focus chain O [auth C] Focus chain W [auth G]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain T [auth F] MOL2 format, chain L [auth B] MOL2 format, chain T [auth F] mmCIF format, chain L [auth B] mmCIF format, chain T [auth F]	L [auth B], T [auth F]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain T [auth F] Interactions & Density Focus chain L [auth B] Focus chain T [auth F]
F3S Query on F3S Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain U [auth F] MOL2 format, chain M [auth B] MOL2 format, chain U [auth F] mmCIF format, chain M [auth B] mmCIF format, chain U [auth F]	M [auth B], U [auth F]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain U [auth F] Interactions & Density Focus chain M [auth B] Focus chain U [auth F]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain S [auth F] MOL2 format, chain K [auth B] MOL2 format, chain S [auth F] mmCIF format, chain K [auth B] mmCIF format, chain S [auth F]	K [auth B], S [auth F]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain S [auth F] Interactions & Density Focus chain K [auth B] Focus chain S [auth F]
MLI Query on MLI Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain Q [auth E] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth E] mmCIF format, chain I [auth A] mmCIF format, chain Q [auth E]	I [auth A], Q [auth E]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain Q [auth E] Interactions & Density Focus chain I [auth A] Focus chain Q [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.44 Å
R-Value Free: 0.281 (Depositor), 0.278 (DCC)
R-Value Work: 0.205 (Depositor), 0.203 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.823	α = 90
b = 132.25	β = 90
c = 220.577	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-04-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-04-10
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-20
Changes: Structure summary

3VRA | pdb_00003vra

Mitochondrial rhodoquinol-fumarate reductase from the parasitic nematode Ascaris suum with the specific inhibitor Atpenin A5

Literature

Crystal structure of mitochondrial quinol-fumarate reductase from parasitic nematode Ascaris suum

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

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Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)