+Open data
-Basic information
Entry | Database: PDB / ID: 1mkj | ||||||
---|---|---|---|---|---|---|---|
Title | Human Kinesin Motor Domain With Docked Neck Linker | ||||||
Components | KINESIN HEAVY CHAIN | ||||||
Keywords | TRANSPORT PROTEIN / NECK LINKER / SWITCH II / MOTOR PROTEIN / MYOSIN / RELAY HELIX / MICROTUBULE / ATPASE | ||||||
Function / homology | Function and homology information cytoplasm organization / cytolytic granule membrane / plus-end-directed vesicle transport along microtubule / mitocytosis / anterograde dendritic transport of neurotransmitter receptor complex / anterograde neuronal dense core vesicle transport / anterograde axonal protein transport / retrograde neuronal dense core vesicle transport / vesicle transport along microtubule / lysosome localization ...cytoplasm organization / cytolytic granule membrane / plus-end-directed vesicle transport along microtubule / mitocytosis / anterograde dendritic transport of neurotransmitter receptor complex / anterograde neuronal dense core vesicle transport / anterograde axonal protein transport / retrograde neuronal dense core vesicle transport / vesicle transport along microtubule / lysosome localization / positive regulation of potassium ion transport / Kinesins / plus-end-directed microtubule motor activity / RHO GTPases activate KTN1 / stress granule disassembly / mitochondrion transport along microtubule / centrosome localization / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / ciliary rootlet / natural killer cell mediated cytotoxicity / kinesin complex / synaptic vesicle transport / Insulin processing / microtubule-based movement / centriolar satellite / axon cytoplasm / phagocytic vesicle / MHC class II antigen presentation / dendrite cytoplasm / positive regulation of protein localization to plasma membrane / regulation of membrane potential / axon guidance / positive regulation of synaptic transmission, GABAergic / cellular response to type II interferon / Signaling by ALK fusions and activated point mutants / microtubule binding / vesicle / microtubule / cadherin binding / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Sindelar, C.V. / Budny, M.J. / Rice, S. / Naber, N. / Fletterick, R. / Cooke, R. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2002 Title: Two conformations in the human kinesin power stroke defined by X-ray crystallography and EPR spectroscopy. Authors: Sindelar, C.V. / Budny, M.J. / Rice, S. / Naber, N. / Fletterick, R. / Cooke, R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1mkj.cif.gz | 80.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1mkj.ent.gz | 60 KB | Display | PDB format |
PDBx/mmJSON format | 1mkj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mkj_validation.pdf.gz | 771.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1mkj_full_validation.pdf.gz | 776.8 KB | Display | |
Data in XML | 1mkj_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 1mkj_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mk/1mkj ftp://data.pdbj.org/pub/pdb/validation_reports/mk/1mkj | HTTPS FTP |
-Related structure data
Related structure data | 2kinS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 39318.406 Da / Num. of mol.: 1 / Fragment: Residues 1-349 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P33176 | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-MG / | ||||
#3: Chemical | #4: Chemical | ChemComp-ADP / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.34 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / pH: 7.5 Details: 1.5-2 M Li2SO4, 25 mM HEPES pH 7.5, 0-50 mM KCl, pH 7.50, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.8 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 4, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. obs: 12579 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 28.7 Å2 / Rsym value: 0.079 / Net I/σ(I): 23 |
Reflection shell | Highest resolution: 2.7 Å / Mean I/σ(I) obs: 6.9 / Rsym value: 0.27 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 14266 / Num. measured all: 247497 / Rmerge(I) obs: 0.079 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.27 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2KIN Resolution: 2.7→20.03 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 147240.76 / Data cutoff high rms absF: 147240.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 23.5303 Å2 / ksol: 0.358848 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.1 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→20.03 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Highest resolution: 2.7 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / Rfactor obs: 0.209 / Rfactor Rfree: 0.259 / Rfactor Rwork: 0.211 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.295 / Rfactor Rwork: 0.28 |