[English] 日本語
![](img/lk-miru.gif)
- PDB-6ohr: Structure of compound 5 bound human Phospholipase D1 catalytic domain -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6ohr | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of compound 5 bound human Phospholipase D1 catalytic domain | ||||||
![]() | Phospholipase D1, chimeric constuct | ||||||
![]() | hydrolase/hydrolase inhibitor / phosphodiesterase / HYDROLASE / HKD motif / hydrolase-hydrolase inhibitor complex | ||||||
Function / homology | ![]() : / Synthesis of PG / phospholipase D / N-acylphosphatidylethanolamine-specific phospholipase D activity / phosphatidic acid biosynthetic process / regulation of microvillus assembly / Synthesis of PA / phospholipase D activity / phospholipid catabolic process / cholinergic synapse ...: / Synthesis of PG / phospholipase D / N-acylphosphatidylethanolamine-specific phospholipase D activity / phosphatidic acid biosynthetic process / regulation of microvillus assembly / Synthesis of PA / phospholipase D activity / phospholipid catabolic process / cholinergic synapse / regulation of synaptic vesicle cycle / regulation of vesicle-mediated transport / small GTPase-mediated signal transduction / tertiary granule membrane / CDC42 GTPase cycle / RHOG GTPase cycle / endocytic vesicle / RHOA GTPase cycle / Role of phospholipids in phagocytosis / specific granule membrane / RAC1 GTPase cycle / phosphatidylinositol binding / positive regulation of translation / chemotaxis / late endosome membrane / Ras protein signal transduction / endosome / apical plasma membrane / lysosomal membrane / Golgi membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Metrick, C.M. / Chodaparambil, J.V. | ||||||
![]() | ![]() Title: Human PLD structures enable drug design and characterization of isoenzyme selectivity. Authors: Metrick, C.M. / Peterson, E.A. / Santoro, J.C. / Enyedy, I.J. / Murugan, P. / Chen, T. / Michelsen, K. / Cullivan, M. / Spilker, K.A. / Kumar, P.R. / May-Dracka, T.L. / Chodaparambil, J.V. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 650 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 526.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 110 KB | Display | |
Data in CIF | ![]() | 148.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ohmSC ![]() 6ohoC ![]() 6ohpC ![]() 6ohqC ![]() 6ohsC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
5 | ![]()
| ||||||||
6 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 73987.852 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Chemical | ChemComp-MKG / |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.67 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: 0.1M Tris-HCl pH 8.8, 2.81M sodium acetate pH 7.6, 0.04-0.05M glycine pH 9.5, 0.3-0.5 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 66130 / % possible obs: 99.8 % / Redundancy: 31.1 % / CC1/2: 0.99 / Net I/σ(I): 4.1 |
Reflection shell | Resolution: 3.2→4 Å / Num. unique obs: 6614 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6OHM Resolution: 3.2→48.362 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.97
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→48.362 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|