7TAY | pdb_00007tay

Bos Taurus Mitochondrial BC1 in complex with Pyramoxadone

PDB DOI: https://doi.org/10.2210/pdb7TAY/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bos taurus
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2021-12-21 Released: 2023-01-18
Deposition Author(s): Xia, D., Zhou, F., Esser, L.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free:
0.258 (Depositor), 0.258 (DCC)
R-Value Work:
0.227 (Depositor), 0.229 (DCC)
R-Value Observed:
0.228 (Depositor)

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

Conformation Switch of Rieske ISP subunit is revealed by the Crystal Structure of Bacterial Cytochrome bc1 in Complex with Azoxystrobin

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

To be published.

Macromolecule Content

Total Structure Weight: 250.98 kDa
Atom Count: 16,843
Modeled Residue Count: 2,076
Deposited Residue Count: 2,166
Unique protein chains: 11

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 1, mitochondrial	A	446	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P31800 (Bos taurus) Explore P31800 Go to UniProtKB: P31800
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P31800
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Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 2, mitochondrial	B	439	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P23004 (Bos taurus) Explore P23004 Go to UniProtKB: P23004
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P23004
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Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b	C	379	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00157 (Bos taurus) Explore P00157 Go to UniProtKB: P00157
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00157
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Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c1, heme protein, mitochondrial	D	241	Bos taurus	Mutation(s): 0 EC: 7.1.1.8 Membrane Entity: Yes
UniProt
Find proteins for P00125 (Bos taurus) Explore P00125 Go to UniProtKB: P00125
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00125
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Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit Rieske, mitochondrial	E	196	Bos taurus	Mutation(s): 0 EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P13272 (Bos taurus) Explore P13272 Go to UniProtKB: P13272
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P13272
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Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 7	F	110	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00129 (Bos taurus) Explore P00129 Go to UniProtKB: P00129
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00129
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Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 8	G	80	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P13271 (Bos taurus) Explore P13271 Go to UniProtKB: P13271
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P13271
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Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 6, mitochondrial	H	78	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00126 (Bos taurus) Explore P00126 Go to UniProtKB: P00126
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00126
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Reference Sequence

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| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit Rieske, mitochondrial	I	78	Bos taurus	Mutation(s): 0 EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P13272 (Bos taurus) Explore P13272 Go to UniProtKB: P13272
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P13272
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 9	J	63	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00130 (Bos taurus) Explore P00130 Go to UniProtKB: P00130
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00130
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 10	K	56	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P07552 (Bos taurus) Explore P07552 Go to UniProtKB: P07552
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07552
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain S [auth C] SDF format, chain M [auth A] MOL2 format, chain V [auth D] MOL2 format, chain S [auth C] MOL2 format, chain M [auth A] mmCIF format, chain V [auth D] mmCIF format, chain S [auth C] mmCIF format, chain M [auth A]	M [auth A], S [auth C], V [auth D]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain M [auth A] Focus chain S [auth C] Focus chain V [auth D] Interactions & Density Focus chain M [auth A] Focus chain S [auth C] Focus chain V [auth D]
PEF Query on PEF Download:Ideal Coordinates CCD File SDF format, chain R [auth C] MOL2 format, chain R [auth C] mmCIF format, chain R [auth C]	R [auth C]	DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE C₃₇ H₇₄ N O₈ P SLKDGVPOSSLUAI-PGUFJCEWSA-N		Interactions Focus chain R [auth C] Interactions & Density Focus chain R [auth C]
8PE Query on 8PE Download:Ideal Coordinates CCD File SDF format, chain Q [auth C] MOL2 format, chain Q [auth C] mmCIF format, chain Q [auth C]	Q [auth C]	(2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate C₃₇ H₇₄ N O₈ P RFJQNULIDFTTLL-PGUFJCEWSA-N		Interactions Focus chain Q [auth C] Interactions & Density Focus chain Q [auth C]
PX4 Query on PX4 Download:Ideal Coordinates CCD File SDF format, chain X [auth J] MOL2 format, chain X [auth J] mmCIF format, chain X [auth J]	X [auth J]	1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₃₆ H₇₃ N O₈ P CITHEXJVPOWHKC-UUWRZZSWSA-O		Interactions Focus chain X [auth J] Interactions & Density Focus chain X [auth J]
HEC Query on HEC Download:Ideal Coordinates CCD File SDF format, chain U [auth D] MOL2 format, chain U [auth D] mmCIF format, chain U [auth D]	U [auth D]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain U [auth D] Interactions & Density Focus chain U [auth D]
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C]	N [auth C], O [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain N [auth C] Focus chain O [auth C] Interactions & Density Focus chain N [auth C] Focus chain O [auth C]
6PE Query on 6PE Download:Ideal Coordinates CCD File SDF format, chain Y [auth K] SDF format, chain L [auth A] MOL2 format, chain Y [auth K] MOL2 format, chain L [auth A] mmCIF format, chain Y [auth K] mmCIF format, chain L [auth A]	L [auth A], Y [auth K]	1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE C₁₇ H₃₃ N O₈ P PELYUHWUVHDSSU-OAHLLOKOSA-M		Interactions Focus chain L [auth A] Focus chain Y [auth K] Interactions & Density Focus chain L [auth A] Focus chain Y [auth K]
PQU (Subject of Investigation/LOI) Query on PQU Download:Ideal Coordinates CCD File SDF format, chain P [auth C] MOL2 format, chain P [auth C] mmCIF format, chain P [auth C]	P [auth C]	(5S)-3-anilino-5-methyl-5-(6-phenoxypyridin-3-yl)-1,3-oxazolidine-2,4-dione C₂₁ H₁₇ N₃ O₄ QOFLFGUNPBNKDO-NRFANRHFSA-N		Interactions Focus chain P [auth C] Interactions & Density Focus chain P [auth C]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain W [auth E] MOL2 format, chain W [auth E] mmCIF format, chain W [auth E]	W [auth E]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain W [auth E] Interactions & Density Focus chain W [auth E]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain T [auth C] MOL2 format, chain T [auth C] mmCIF format, chain T [auth C]	T [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain T [auth C] Interactions & Density Focus chain T [auth C]