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Download EndnoteCrystallographic studies of the binding of ligands to the Ubiquinone site of Mitochondrial Respiratory Complex II
Huang, L.-S., Berry, E.A.To be published.
6MYO
Avian mitochondrial complex II with flutolanyl bound
- DOI: 10.2210/pdb6MYO/pdb
- Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
- Organism(s): Gallus gallus
- Deposited: 2018-11-02 Released: 2019-11-06
- Funding Organization(s): Department of Health & Human Services
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.2 Å
- R-Value Free: 0.227
- R-Value Work: 0.189
wwPDB Validation 3D Report Full Report
This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by: Sequence | Structure
Entity ID: 1 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | A | 621 | Gallus gallus | Mutation(s): 0 Gene Names: SDHA EC: 1.3.5.1 |
Find proteins for F1NPJ4 (Gallus gallus) Go to Gene View: SDHA Go to UniProtKB: F1NPJ4 | ||||
Entity ID: 2 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial | B | 252 | Gallus gallus | Mutation(s): 0 Gene Names: SDHB EC: 1.3.5.1 |
Find proteins for Q9YHT2 (Gallus gallus) Go to Gene View: SDHB Go to UniProtKB: Q9YHT2 | ||||
Entity ID: 3 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| Succinate dehydrogenase cytochrome b, large subunit | C | 140 | Gallus gallus | Mutation(s): 0 EC: 1.3.5.1 |
Find proteins for D0VWW3 (Gallus gallus) Go to UniProtKB: D0VWW3 | ||||
Entity ID: 4 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial | D | 103 | Gallus gallus | Mutation(s): 0 Gene Names: SDHD |
Find proteins for Q5ZIS0 (Gallus gallus) Go to Gene View: SDHD Go to UniProtKB: Q5ZIS0 | ||||
Small Molecules
| Ligands 12 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| K Query on K | A | POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N |  | Ligand Interaction | |
| MN Query on MN | A | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N |  | Ligand Interaction | |
| SF4 Query on SF4 | B | IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC |  | Ligand Interaction | |
| FTN Query on FTN | C | N-[3-(1-methylethoxy)phenyl]-2-(trifluoromethyl)benzamide flutolanil, N-(3-Isopropoxy-phenyl)-2-trifluoromethylbenzamide C17 H16 F3 N O2 PTCGDEVVHUXTMP-UHFFFAOYSA-N |  | Ligand Interaction | |
| F3S Query on F3S | B | FE3-S4 CLUSTER Fe3 S4 FCXHZBQOKRZXKS-MZMDZPPWAW |  | Ligand Interaction | |
| FAD Query on FAD | A | FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N |  | Ligand Interaction | |
| FES Query on FES | B | FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N |  | Ligand Interaction | |
| OAA Query on OAA | A | OXALOACETATE ION C4 H3 O5 KHPXUQMNIQBQEV-UHFFFAOYSA-M |  | Ligand Interaction | |
| UMQ Query on UMQ | C | UNDECYL-MALTOSIDE UNDECYL-BETA-D-MALTOPYRANOSIDE C23 H44 O11 UYEMNFYVTFDKRG-ZNGNCRBCSA-N |  | Ligand Interaction | |
| HEM Query on HEM | C | PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L |  | Ligand Interaction | |
| PEG Query on PEG | A | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |  | Ligand Interaction | |
| 3PE Query on 3PE | D | 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE 3-SN-PHOSPHATIDYLETHANOLAMINE C41 H82 N O8 P LVNGJLRDBYCPGB-LDLOPFEMSA-N |  | Ligand Interaction | |
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MLZ Query on MLZ | C | L-PEPTIDE LINKING | C7 H16 N2 O2 |  | LYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.2 Å
- R-Value Free: 0.227
- R-Value Work: 0.189
- Space Group: P 21 21 21
Unit Cell:
| Length (Å) | Angle (°) |
|---|---|
| a = 69.637 | α = 90.00 |
| b = 83.783 | β = 90.00 |
| c = 289.575 | γ = 90.00 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| DENZO | data reduction |
| PHENIX | phasing |
| SCALEPACK | data scaling |
Entry History & Funding Information
Deposition Data
- Deposited Date: 2018-11-02
- Released Date: 2019-11-06
- Deposition Author(s): Berry, E.A., Huang, L.-S.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Department of Health & Human Services | United States | 1R01GM062563 |
