2WDR

E. coli succinate:quinone oxidoreductase (SQR) with pentachlorophenol bound

PDB DOI: https://doi.org/10.2210/pdb2WDR/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMDmpstruc

Deposited: 2009-03-25 Released: 2009-08-25
Deposition Author(s): Ruprecht, J., Yankovskaya, V., Maklashina, E., Iwata, S., Cecchini, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.228
R-Value Work: 0.197
R-Value Observed: 0.199

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure of Escherichia Coli Succinate:Quinone Oxidoreductase with an Occupied and Empty Quinone- Binding Site.

Ruprecht, J., Yankovskaya, V., Maklashina, E., Iwata, S., Cecchini, G.

(2009) J Biol Chem 284: 29836

PubMed: 19710024 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1074/jbc.M109.010058
Primary Citation of Related Structures:
2WDQ, 2WDR, 2WDV

PubMed Abstract:
Three new structures of Escherichia coli succinate-quinone oxidoreductase (SQR) have been solved. One with the specific quinone-binding site (Q-site) inhibitor carboxin present has been solved at 2.4 A resolution and reveals how carboxin inhibits the Q-site. The other new structures are with the Q-site inhibitor pentachlorophenol and with an empty Q-site. These structures reveal important details unresolved in earlier structures. Comparison of the new SQR structures shows how subtle rearrangements of the quinone-binding site accommodate the different inhibitors. The position of conserved water molecules near the quinone binding pocket leads to a reassessment of possible water-mediated proton uptake networks that complete reduction of ubiquinone. The dicarboxylate-binding site in the soluble domain of SQR is highly similar to that seen in high resolution structures of avian SQR (PDB 2H88) and soluble flavocytochrome c (PDB 1QJD) showing mechanistically significant structural features conserved across prokaryotic and eukaryotic SQRs.

Organizational Affiliation

Membrane Protein Crystallography Group, Molecular Biosciences Division, Imperial College, London SW72AZ, United Kingdom.

Macromolecule Content

Total Structure Weight: 363.41 kDa
Atom Count: 24,936
Modelled Residue Count: 3,159
Deposited Residue Count: 3,210
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 FLAVOPROTEIN SUBUNIT	A, E, I	588	Escherichia coli	Mutation(s): 0 EC: 1.3.5.1 (PDB Primary Data), 1.3.99.1 (PDB Primary Data) Membrane Entity: Yes
UniProt
Find proteins for P0AC41 (Escherichia coli (strain K12)) Explore P0AC41 Go to UniProtKB: P0AC41
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0AC41
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 IRON-SULFUR SUBUNIT	B, F, J	238	Escherichia coli	Mutation(s): 0 EC: 1.3.5.1 (PDB Primary Data), 1.3.99.1 (PDB Primary Data) Membrane Entity: Yes
UniProt
Find proteins for P07014 (Escherichia coli (strain K12)) Explore P07014 Go to UniProtKB: P07014
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07014
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 B556 SUBUNIT	C, G, K	129	Escherichia coli	Mutation(s): 0 EC: 1.3.5.1 Membrane Entity: Yes
UniProt
Find proteins for P69054 (Escherichia coli (strain K12)) Explore P69054 Go to UniProtKB: P69054
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P69054
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 HYDROPHOBIC MEMBRANE ANCHOR SUBUNIT	D, H, L	115	Escherichia coli	Mutation(s): 0 EC: 1.3.5.1 Membrane Entity: Yes
UniProt
Find proteins for P0AC44 (Escherichia coli (strain K12)) Explore P0AC44 Go to UniProtKB: P0AC44
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0AC44
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 CA [auth I] SDF format, chain M [auth A] SDF format, chain U [auth E] MOL2 format, chain CA [auth I] MOL2 format, chain M [auth A] MOL2 format, chain U [auth E] mmCIF format, chain CA [auth I] mmCIF format, chain M [auth A] mmCIF format, chain U [auth E]	CA [auth I], M [auth A], U [auth E]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain CA [auth I] Focus chain M [auth A] Focus chain U [auth E]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain IA [auth K] SDF format, chain S [auth C] MOL2 format, chain AA [auth G] MOL2 format, chain IA [auth K] MOL2 format, chain S [auth C] mmCIF format, chain AA [auth G] mmCIF format, chain IA [auth K] mmCIF format, chain S [auth C]	AA [auth G], IA [auth K], S [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain AA [auth G] Focus chain IA [auth K] Focus chain S [auth C]
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain GA [auth J] SDF format, chain Q [auth B] SDF format, chain Y [auth F] MOL2 format, chain GA [auth J] MOL2 format, chain Q [auth B] MOL2 format, chain Y [auth F] mmCIF format, chain GA [auth J] mmCIF format, chain Q [auth B] mmCIF format, chain Y [auth F]	GA [auth J], Q [auth B], Y [auth F]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain GA [auth J] Focus chain Q [auth B] Focus chain Y [auth F]
F3S Query on F3S Download Ideal Coordinates CCD File SDF format, chain HA [auth J] SDF format, chain R [auth B] SDF format, chain Z [auth F] MOL2 format, chain HA [auth J] MOL2 format, chain R [auth B] MOL2 format, chain Z [auth F] mmCIF format, chain HA [auth J] mmCIF format, chain R [auth B] mmCIF format, chain Z [auth F]	HA [auth J], R [auth B], Z [auth F]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain HA [auth J] Focus chain R [auth B] Focus chain Z [auth F]
PCI Query on PCI Download Ideal Coordinates CCD File SDF format, chain BA [auth G] SDF format, chain JA [auth K] SDF format, chain T [auth C] MOL2 format, chain BA [auth G] MOL2 format, chain JA [auth K] MOL2 format, chain T [auth C] mmCIF format, chain BA [auth G] mmCIF format, chain JA [auth K] mmCIF format, chain T [auth C]	BA [auth G], JA [auth K], T [auth C]	PENTACHLOROPHENOL C₆ H Cl₅ O IZUPBVBPLAPZRR-UHFFFAOYSA-N		Interactions Focus chain BA [auth G] Focus chain JA [auth K] Focus chain T [auth C]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain FA [auth J] SDF format, chain P [auth B] SDF format, chain X [auth F] MOL2 format, chain FA [auth J] MOL2 format, chain P [auth B] MOL2 format, chain X [auth F] mmCIF format, chain FA [auth J] mmCIF format, chain P [auth B] mmCIF format, chain X [auth F]	FA [auth J], P [auth B], X [auth F]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain FA [auth J] Focus chain P [auth B] Focus chain X [auth F]
TEO Query on TEO Download Ideal Coordinates CCD File SDF format, chain DA [auth I] SDF format, chain N [auth A] SDF format, chain V [auth E] MOL2 format, chain DA [auth I] MOL2 format, chain N [auth A] MOL2 format, chain V [auth E] mmCIF format, chain DA [auth I] mmCIF format, chain N [auth A] mmCIF format, chain V [auth E]	DA [auth I], N [auth A], V [auth E]	MALATE LIKE INTERMEDIATE C₄ H₄ O₅ QFBHYOKSQPPXHZ-UWTATZPHSA-L		Interactions Focus chain DA [auth I] Focus chain N [auth A] Focus chain V [auth E]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain EA [auth I] SDF format, chain O [auth A] SDF format, chain W [auth E] MOL2 format, chain EA [auth I] MOL2 format, chain O [auth A] MOL2 format, chain W [auth E] mmCIF format, chain EA [auth I] mmCIF format, chain O [auth A] mmCIF format, chain W [auth E]	EA [auth I], O [auth A], W [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain EA [auth I] Focus chain O [auth A] Focus chain W [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.228
R-Value Work: 0.197
R-Value Observed: 0.199
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.955	α = 90
b = 186.128	β = 90
c = 204.034	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-08-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-08-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2015-02-04
Changes: Atomic model, Derived calculations, Non-polymer description, Other