+
Open data
-
Basic information
Entry | Database: PDB / ID: 3n5j | ||||||
---|---|---|---|---|---|---|---|
Title | Human fpps complex with NOV_311 | ||||||
![]() | FARNESYL PYROPHOSPHATE SYNTHASE | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / BISPHOSPHONATE / FRAGMENT-BASED SCREENING / TRANSFERASE / ISOPRENE BIOSYNTHESIS / CHOLESTEROL BIOSYNTHESIS / RANSFERASE-TRANSFERASE INHIBITOR complex / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | ![]() geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / Cholesterol biosynthesis / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / RNA binding ...geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / Cholesterol biosynthesis / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / RNA binding / nucleoplasm / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rondeau, J.-M. | ||||||
![]() | ![]() Title: Allosteric non-bisphosphonate FPPS inhibitors identified by fragment-based discovery. Authors: Jahnke, W. / Rondeau, J.M. / Cotesta, S. / Marzinzik, A. / Pelle, X. / Geiser, M. / Strauss, A. / Gotte, M. / Bitsch, F. / Hemmig, R. / Henry, C. / Lehmann, S. / Glickman, J.F. / Roddy, T.P. ...Authors: Jahnke, W. / Rondeau, J.M. / Cotesta, S. / Marzinzik, A. / Pelle, X. / Geiser, M. / Strauss, A. / Gotte, M. / Bitsch, F. / Hemmig, R. / Henry, C. / Lehmann, S. / Glickman, J.F. / Roddy, T.P. / Stout, S.J. / Green, J.R. #1: ![]() Title: Structural basis for the exceptional in vivo efficacy of bisphosphonate drugs Authors: Rondeau, J.M. / Bitsch, F. / Bourgier, E. / Geiser, M. / Hemmig, R. / Kroemer, M. / Lehmann, S. / Ramage, P. / Rieffel, S. / Strauss, A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 86.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 64.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 3n1vC ![]() 3n1wC ![]() 3n3lC ![]() 3n45C ![]() 3n46C ![]() 3n49C ![]() 3n5hC ![]() 3n6kC C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 40183.855 Da / Num. of mol.: 1 / Fragment: Residues 72-419 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P14324, dimethylallyltranstransferase, (2E,6E)-farnesyl diphosphate synthase | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-PO4 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59.07 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.3 Details: 1.2M sodium potassium phosphate, 25% glycerol, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 105 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 2, 2004 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97936 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. all: 20763 / Num. obs: 20763 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 47.1 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 2.35→2.41 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 9.1 / Num. unique all: 1490 / % possible all: 99.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.3635 Å2 / ksol: 0.384751 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→41.95 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.35→2.5 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
|