+Open data
-Basic information
Entry | Database: PDB / ID: 2c30 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure Of The Human P21-Activated Kinase 6 | ||||||
Components | SERINE/THREONINE-PROTEIN KINASE PAK 6 | ||||||
Keywords | TRANSFERASE / CRIB DOMAIN / ATP-BINDING / NUCLEOTIDE-BINDING | ||||||
Function / homology | Function and homology information neuron projection arborization / RHOD GTPase cycle / Activation of RAC1 / neuron projection extension / RHOV GTPase cycle / regulation of MAPK cascade / RHOH GTPase cycle / CDC42 GTPase cycle / cytoskeleton organization / RAC1 GTPase cycle ...neuron projection arborization / RHOD GTPase cycle / Activation of RAC1 / neuron projection extension / RHOV GTPase cycle / regulation of MAPK cascade / RHOH GTPase cycle / CDC42 GTPase cycle / cytoskeleton organization / RAC1 GTPase cycle / locomotory behavior / learning / memory / fibrillar center / cell junction / postsynaptic density / non-specific serine/threonine protein kinase / intracellular signal transduction / cadherin binding / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / regulation of DNA-templated transcription / nucleoplasm / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Filippakopoulos, P. / Berridge, G. / Bray, J. / Burgess, N. / Colebrook, S. / Das, S. / Eswaran, J. / Gileadi, O. / Papagrigoriou, E. / Savitsky, P. ...Filippakopoulos, P. / Berridge, G. / Bray, J. / Burgess, N. / Colebrook, S. / Das, S. / Eswaran, J. / Gileadi, O. / Papagrigoriou, E. / Savitsky, P. / Smee, C. / Turnbull, A. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / von Delft, F. / Knapp, S. | ||||||
Citation | Journal: Structure / Year: 2007 Title: Crystal Structures of the P21-Activated Kinases Pak4, Pak5, and Pak6 Reveal Catalytic Domain Plasticity of Active Group II Paks. Authors: Eswaran, J. / Lee, W.H. / Debreczeni, J.E. / Filippakopoulos, P. / Turnbull, A. / Fedorov, O. / Deacon, S.W. / Peterson, J.R. / Knapp, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2c30.cif.gz | 82.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2c30.ent.gz | 60.3 KB | Display | PDB format |
PDBx/mmJSON format | 2c30.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/2c30 ftp://data.pdbj.org/pub/pdb/validation_reports/c3/2c30 | HTTPS FTP |
---|
-Related structure data
Related structure data | 2bvaSC 2cdzC 2f57C 1f3mS 1yhvS 1yhwS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 36679.270 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 383-681 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9NQU5, EC: 2.7.1.37 |
---|---|
#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 51.68 % Description: ENSEMBLE OF MODELS WAS USED IN PHASER AS SEARCH MODEL. |
---|---|
Crystal grow | Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1.60M MGSO4 0.1M MES PH 6.5 SITTING DROPS, 150NL AND 50NL PROTEIN AND RESERVOIR MIX. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9764 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 3, 2005 / Details: DYNAMICALLY BENDABLE MIRROR |
Radiation | Monochromator: LN2 COOLED FIXED-EXIT SI (111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9764 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→55 Å / Num. obs: 177870 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.1 / % possible all: 93.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 2BVA, 1YHW, 1YHV, 1F3M Resolution: 1.6→54.96 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.633 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. UNEXPLAINED SIGMAA DENSITY REMAINS UNMODELLED AFTER THE LAST MODELLED RESIDUE, AND AROUND SIDECHAIN A615.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.82 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→54.96 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|