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Open data
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Basic information
Entry | Database: PDB / ID: 3l71 | |||||||||
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Title | Cytochrome BC1 complex from chicken with azoxystrobin bound | |||||||||
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![]() | 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 | ![]() 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 / electron transfer 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 / electron transfer activity / oxidoreductase activity / heme binding / mitochondrion / membrane / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Huang, L. / Berry, E.A. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 827.3 KB | Display | ![]() |
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PDB format | ![]() | 660.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3l72C ![]() 3l73C ![]() 3l74C ![]() 3h1hS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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. |
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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) ![]() ![]() #2: Protein | Mass: 46683.809 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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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) ![]() ![]() #4: Protein | Mass: 26973.744 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Cytochrome b-c1 complex subunit Rieske, ... , 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) ![]() ![]() #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) ![]() ![]() |
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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) ![]() ![]() #7: Protein | Mass: 9498.735 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Protein | Mass: 9057.119 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #10: Protein | Mass: 7005.963 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Sugars , 1 types, 5 molecules ![](data/chem/img/BOG.gif)
#18: Sugar | ChemComp-BOG / |
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-Non-polymers , 9 types, 43 molecules ![](data/chem/img/PEE.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/AZO.gif)
![](data/chem/img/UQ.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/AZO.gif)
![](data/chem/img/UQ.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.01 Å3/Da / Density % sol: 69.36 % Description: THE DATA WAS COLLECTED IN TWO PASSES- HIGH RES PASS WAS INTEGRATED 2.8 TO 60 A, LOW RES 150 TO 4 A, AND BOTH PASSES WERE INTEGRATED AND SCALED SIMULTANEOUSLY IN SCALEPACK. DISTANCE 430 ...Description: THE DATA WAS COLLECTED IN TWO PASSES- HIGH RES PASS WAS INTEGRATED 2.8 TO 60 A, LOW RES 150 TO 4 A, AND BOTH PASSES WERE INTEGRATED AND SCALED SIMULTANEOUSLY IN SCALEPACK. DISTANCE 430 MM FOR HI RES, 900 MM FOR LOW RES PASS. RESOLUTION USED IN REFINEMENT WAS 25 TO 2.84 A. |
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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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 29, 2006 |
Radiation | Monochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→99 Å / Num. all: 172787 / Num. obs: 172787 / % possible obs: 92.6 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 79.9 Å2 / Rsym value: 0.108 / Net I/σ(I): 28.3 |
Reflection shell | Resolution: 2.79→2.84 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 0.994 / Num. unique all: 5617 / % possible all: 60.8 |
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Processing
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Refinement | Method to determine structure: RIGID BODY REFINEMENT Starting model: PDB ENTRY 3H1H Resolution: 2.84→24.94 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3326344.4 / 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: 24.0536 Å2 / ksol: 0.272715 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 78.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.84→24.94 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.84→2.99 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 7
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Xplor file |
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