7TCE

Crystal structure of delta sub IV Rhodobacter Sphaeroides bc1 with the antimalarial drug atovaquone.

PDB DOI: https://doi.org/10.2210/pdb7TCE/pdb

Classification: OXIDOREDUCTASE
Organism(s): Cereibacter sphaeroides
Expression System: Cereibacter sphaeroides
Mutation(s): No
Membrane Protein: Yes OPMPDBTM

Deposited: 2021-12-23 Released: 2023-01-18
Deposition Author(s): Esser, L., Xia, D., Zhou, F.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.85 Å
R-Value Free: 0.273
R-Value Work: 0.241
R-Value Observed: 0.242

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of delta sub IV Rhodobacter Sphaeroides bc1 with the antimalarial drug atovaquone.

Esser, L., Xia, D., Zhou, F.

To be published.

Macromolecule Content

Total Structure Weight: 410.47 kDa
Atom Count: 27,786
Modelled Residue Count: 3,456
Deposited Residue Count: 3,604
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b	A, D [auth E], G [auth K], J [auth O]	445	Cereibacter sphaeroides	Mutation(s): 0 Gene Names: petB, fbcB Membrane Entity: Yes
UniProt
Find proteins for Q02761 (Cereibacter sphaeroides) Explore Q02761 Go to UniProtKB: Q02761
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q02761
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c1	B, E [auth F], H [auth L], K [auth P]	269	Cereibacter sphaeroides	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q02760 (Cereibacter sphaeroides) Explore Q02760 Go to UniProtKB: Q02760
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q02760
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquinol-cytochrome c reductase iron-sulfur subunit	C, F [auth G], I [auth M], L [auth Q]	187	Cereibacter sphaeroides	Mutation(s): 0 Gene Names: petA, fbcF EC: 7.1.1.8 Membrane Entity: Yes
UniProt
Find proteins for Q02762 (Cereibacter sphaeroides) Explore Q02762 Go to UniProtKB: Q02762
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q02762
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain JA [auth L] SDF format, chain RA [auth P] SDF format, chain S [auth B] MOL2 format, chain BA [auth F] MOL2 format, chain JA [auth L] MOL2 format, chain RA [auth P] MOL2 format, chain S [auth B] mmCIF format, chain BA [auth F] mmCIF format, chain JA [auth L] mmCIF format, chain RA [auth P] mmCIF format, chain S [auth B]	BA [auth F], JA [auth L], RA [auth P], S [auth B]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain BA [auth F] Focus chain JA [auth L] Focus chain RA [auth P] Focus chain S [auth B] Interactions & Density Focus chain BA [auth F] Focus chain JA [auth L] Focus chain RA [auth P] Focus chain S [auth B]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain EA [auth K] SDF format, chain FA [auth K] SDF format, chain M [auth A] SDF format, chain MA [auth O] SDF format, chain N [auth A] SDF format, chain NA [auth O] SDF format, chain V [auth E] SDF format, chain W [auth E] MOL2 format, chain EA [auth K] MOL2 format, chain FA [auth K] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth O] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth O] MOL2 format, chain V [auth E] MOL2 format, chain W [auth E] mmCIF format, chain EA [auth K] mmCIF format, chain FA [auth K] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth O] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth O] mmCIF format, chain V [auth E] mmCIF format, chain W [auth E]	EA [auth K] FA [auth K] M [auth A] MA [auth O] N [auth A] EA [auth K], FA [auth K], M [auth A], MA [auth O], N [auth A], NA [auth O], V [auth E], W [auth E]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain EA [auth K] Focus chain FA [auth K] Focus chain M [auth A] Focus chain MA [auth O] Focus chain N [auth A] Focus chain NA [auth O] Focus chain V [auth E] Focus chain W [auth E] Interactions & Density Focus chain EA [auth K] Focus chain FA [auth K] Focus chain M [auth A] Focus chain MA [auth O] Focus chain N [auth A] Focus chain NA [auth O] Focus chain V [auth E] Focus chain W [auth E]
6PE Query on 6PE Download Ideal Coordinates CCD File SDF format, chain HA [auth K] SDF format, chain P [auth A] SDF format, chain PA [auth O] SDF format, chain Y [auth E] MOL2 format, chain HA [auth K] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth O] MOL2 format, chain Y [auth E] mmCIF format, chain HA [auth K] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth O] mmCIF format, chain Y [auth E]	HA [auth K], P [auth A], PA [auth O], Y [auth E]	1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE C₁₇ H₃₃ N O₈ P PELYUHWUVHDSSU-OAHLLOKOSA-M		Interactions Focus chain HA [auth K] Focus chain P [auth A] Focus chain PA [auth O] Focus chain Y [auth E] Interactions & Density Focus chain HA [auth K] Focus chain P [auth A] Focus chain PA [auth O] Focus chain Y [auth E]
AOQ (Subject of Investigation/LOI) Query on AOQ Download Ideal Coordinates CCD File SDF format, chain GA [auth K] SDF format, chain O [auth A] SDF format, chain OA [auth O] SDF format, chain X [auth E] MOL2 format, chain GA [auth K] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth O] MOL2 format, chain X [auth E] mmCIF format, chain GA [auth K] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth O] mmCIF format, chain X [auth E]	GA [auth K], O [auth A], OA [auth O], X [auth E]	2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione C₂₂ H₁₉ Cl O₃ KUCQYCKVKVOKAY-CTYIDZIISA-N		Interactions Focus chain GA [auth K] Focus chain O [auth A] Focus chain OA [auth O] Focus chain X [auth E] Interactions & Density Focus chain GA [auth K] Focus chain O [auth A] Focus chain OA [auth O] Focus chain X [auth E]
BOG Query on BOG Download Ideal Coordinates CCD File SDF format, chain IA [auth K] SDF format, chain QA [auth O] SDF format, chain R [auth A] SDF format, chain Z [auth E] MOL2 format, chain IA [auth K] MOL2 format, chain QA [auth O] MOL2 format, chain R [auth A] MOL2 format, chain Z [auth E] mmCIF format, chain IA [auth K] mmCIF format, chain QA [auth O] mmCIF format, chain R [auth A] mmCIF format, chain Z [auth E]	IA [auth K], QA [auth O], R [auth A], Z [auth E]	octyl beta-D-glucopyranoside C₁₄ H₂₈ O₆ HEGSGKPQLMEBJL-RKQHYHRCSA-N		Interactions Focus chain IA [auth K] Focus chain QA [auth O] Focus chain R [auth A] Focus chain Z [auth E] Interactions & Density Focus chain IA [auth K] Focus chain QA [auth O] Focus chain R [auth A] Focus chain Z [auth E]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain DA [auth G] SDF format, chain LA [auth M] SDF format, chain TA [auth Q] SDF format, chain U [auth C] MOL2 format, chain DA [auth G] MOL2 format, chain LA [auth M] MOL2 format, chain TA [auth Q] MOL2 format, chain U [auth C] mmCIF format, chain DA [auth G] mmCIF format, chain LA [auth M] mmCIF format, chain TA [auth Q] mmCIF format, chain U [auth C]	DA [auth G], LA [auth M], TA [auth Q], U [auth C]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain DA [auth G] Focus chain LA [auth M] Focus chain TA [auth Q] Focus chain U [auth C] Interactions & Density Focus chain DA [auth G] Focus chain LA [auth M] Focus chain TA [auth Q] Focus chain U [auth C]
SR Query on SR Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain CA [auth F] SDF format, chain KA [auth L] SDF format, chain Q [auth A] SDF format, chain SA [auth P] SDF format, chain T [auth B] MOL2 format, chain AA [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain KA [auth L] MOL2 format, chain Q [auth A] MOL2 format, chain SA [auth P] MOL2 format, chain T [auth B] mmCIF format, chain AA [auth E] mmCIF format, chain CA [auth F] mmCIF format, chain KA [auth L] mmCIF format, chain Q [auth A] mmCIF format, chain SA [auth P] mmCIF format, chain T [auth B]	AA [auth E] CA [auth F] KA [auth L] Q [auth A] SA [auth P] AA [auth E], CA [auth F], KA [auth L], Q [auth A], SA [auth P], T [auth B]	STRONTIUM ION Sr PWYYWQHXAPXYMF-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain CA [auth F] Focus chain KA [auth L] Focus chain Q [auth A] Focus chain SA [auth P] Focus chain T [auth B] Interactions & Density Focus chain AA [auth E] Focus chain CA [auth F] Focus chain KA [auth L] Focus chain Q [auth A] Focus chain SA [auth P] Focus chain T [auth B]