+Open data
-Basic information
Entry | Database: PDB / ID: 3l73 | |||||||||
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Title | Cytochrome BC1 complex from chicken with triazolone inhibitor | |||||||||
Components |
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Keywords | OXIDOREDUCTASE / CYTOCHROME BC1 / MEMBRANE PROTEIN / HEME PROTEIN / RIESKE IRON SULFUR PROTEIN / CYTOCHROME B / CYTOCHROME C1 / COMPLEX III / MITOCHONDRIAL PROCESSING PROTEIN / UBIQUINONE / AZOXYSTROBIN OXIDOREDUCTASE / REDOX ENZYME RESPIRATORY CHAIN / ELECTRON TRANSPORT / HEME / INNER MEMBRANE / MEMBRANE / STROBILURINS BINDING / MITOCHONDRION / TRANSMEMBRANE / STIGMATELLIN / IRON / MITOCHONDRIAL INNER MEMBRANE / RESPIRATORY CHAIN / IRON-SULFUR / TRANSIT PEPTIDE / Metal-binding / Mitochondrion inner membrane / Transport / Disulfide bond | |||||||||
Function / homology | Function and homology information Respiratory electron transport / quinol-cytochrome-c reductase / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / response to oxidative stress / oxidoreductase activity ...Respiratory electron transport / quinol-cytochrome-c reductase / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / response to oxidative stress / oxidoreductase activity / electron transfer activity / heme binding / mitochondrion / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | GALLUS GALLUS (chicken) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / RIGID BODY REFINEMENT / Resolution: 3.04 Å | |||||||||
Authors | Huang, L. / Berry, E.A. | |||||||||
Citation | Journal: To be Published Title: Famoxadone and related inhibitors bind like methoxy acrylate inhibitors in the Qo site of the BC1 compl and fix the rieske iron-sulfur protein in a positio close to but distinct from that seen ...Title: Famoxadone and related inhibitors bind like methoxy acrylate inhibitors in the Qo site of the BC1 compl and fix the rieske iron-sulfur protein in a positio close to but distinct from that seen with stigmatellin and other "DISTAL" Qo inhibitors. Authors: Huang, L. / Berry, E.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3l73.cif.gz | 827.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l73.ent.gz | 661 KB | Display | PDB format |
PDBx/mmJSON format | 3l73.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3l73_validation.pdf.gz | 6.6 MB | Display | wwPDB validaton report |
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Full document | 3l73_full_validation.pdf.gz | 6.8 MB | Display | |
Data in XML | 3l73_validation.xml.gz | 163.2 KB | Display | |
Data in CIF | 3l73_validation.cif.gz | 212.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l7/3l73 ftp://data.pdbj.org/pub/pdb/validation_reports/l7/3l73 | HTTPS FTP |
-Related structure data
Related structure data | 3l71C 3l72C 3l74C 3h1hS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The deposited coordinates (20 chains plus hetero groups) make up the asymmetric unit which is the biological assembly. One other subunit of the biological assembly (Subunit 11) is lost during purification or crystallization and is not present in the deposited structure. |
-Components
-MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN ... , 2 types, 4 molecules ANBO
#1: Protein | Mass: 49503.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: D0VX31, quinol-cytochrome-c reductase #2: Protein | Mass: 46683.809 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: D0VX29, quinol-cytochrome-c reductase |
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-Protein , 2 types, 4 molecules CPDQ
#3: Protein | Mass: 42622.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: P18946, quinol-cytochrome-c reductase #4: Protein | Mass: 26973.744 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: D0VX26, quinol-cytochrome-c reductase |
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-CYTOCHROME B-C1 COMPLEX SUBUNIT ... , 2 types, 4 molecules ERIV
#5: Protein | Mass: 21506.188 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 77-272 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: Q5ZLR5, quinol-cytochrome-c reductase #9: Protein/peptide | Mass: 4785.649 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 45-76 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: Q5ZLR5, quinol-cytochrome-c reductase |
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-MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE ... , 4 types, 8 molecules FSGTHUJW
#6: Protein | Mass: 13394.397 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: D0VX30, quinol-cytochrome-c reductase #7: Protein | Mass: 9498.735 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: D0VX32, quinol-cytochrome-c reductase #8: Protein | Mass: 9057.119 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: D0VX28, quinol-cytochrome-c reductase #10: Protein | Mass: 7005.963 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: D0VX27, quinol-cytochrome-c reductase |
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-Sugars , 1 types, 5 molecules
#18: Sugar | ChemComp-BOG / |
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-Non-polymers , 9 types, 43 molecules
#11: Chemical | ChemComp-PEE / #12: Chemical | ChemComp-HEM / #13: Chemical | #14: Chemical | #15: Chemical | #16: Chemical | #17: Chemical | ChemComp-CDL / #19: Chemical | #20: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE COMPLETE SEQUENCE OF CHAIN I AND V IS ...THE COMPLETE SEQUENCE OF CHAIN I AND V IS MLSVAARSGP |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.02 Å3/Da / Density % sol: 69.38 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.77 Details: FINAL CONCENTRATIONS BEFORE DIFFUSION: 50 MM CACODYLATE, 9.4 MM TRISHCL, 10 MM MGCL2, 50 G/L GLYCEROL, 30 G/L PEG 3350DA, 0.23 MM EDTA, 0.47 G/L UNDECYL MALTOSIDE, 31 MM OCTYL GLUCOSIDE, PH ...Details: FINAL CONCENTRATIONS BEFORE DIFFUSION: 50 MM CACODYLATE, 9.4 MM TRISHCL, 10 MM MGCL2, 50 G/L GLYCEROL, 30 G/L PEG 3350DA, 0.23 MM EDTA, 0.47 G/L UNDECYL MALTOSIDE, 31 MM OCTYL GLUCOSIDE, PH 6.77, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 / Wavelength: 1 Å | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 26, 2006 | |||||||||
Radiation | Monochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.9→25 Å / Num. all: 167200 / Num. obs: 167200 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 80.8 Å2 / Rsym value: 0.085 / Net I/σ(I): 19.38 | |||||||||
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.072 / Num. unique all: 8264 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: RIGID BODY REFINEMENT Starting model: PDB ENTRY 3H1H Resolution: 3.04→24.97 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3513358.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 21.5201 Å2 / ksol: 0.241878 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 86.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.04→24.97 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.04→3.2 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 7
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Xplor file |
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