[English] 日本語
![](img/lk-miru.gif)
- PDB-5fpd: Structure of heat shock-related 70kDA protein 2 with small-molecu... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5fpd | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of heat shock-related 70kDA protein 2 with small-molecule ligand pyrazine-2-carboxamide (AT513) in an alternate binding site. | ||||||
![]() | HEAT SHOCK-RELATED 70KDA PROTEIN 2 | ||||||
![]() | CHAPERONE / HEAT SHOCK-RELATED PROTEIN / HEAT SHOCK / HSP70 / HSPA2 / PROTEIN-LIGAND COMPLEX / FRAGMENT SCREENING / ALTERNATE BINDING SITE / AT513. | ||||||
Function / homology | ![]() CatSper complex / glycolipid binding / synaptonemal complex disassembly / negative regulation of inclusion body assembly / male meiotic nuclear division / synaptonemal complex / meiotic spindle / male meiosis I / chaperone cofactor-dependent protein refolding / response to unfolded protein ...CatSper complex / glycolipid binding / synaptonemal complex disassembly / negative regulation of inclusion body assembly / male meiotic nuclear division / synaptonemal complex / meiotic spindle / male meiosis I / chaperone cofactor-dependent protein refolding / response to unfolded protein / spermatid development / Regulation of HSF1-mediated heat shock response / Attenuation phase / protein folding chaperone / heat shock protein binding / positive regulation of G2/M transition of mitotic cell cycle / Meiotic synapsis / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to cold / male germ cell nucleus / ATP-dependent protein folding chaperone / tau protein binding / PKR-mediated signaling / disordered domain specific binding / unfolded protein binding / protein-folding chaperone binding / response to heat / protein refolding / spermatogenesis / blood microparticle / positive regulation of protein phosphorylation / enzyme binding / cell surface / ATP hydrolysis activity / extracellular exosome / ATP binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Jhoti, H. / Ludlow, R.F. / Patel, S. / Saini, H.K. / Tickle, I.J. / Verdonk, M. | ||||||
![]() | ![]() Title: Detection of Secondary Binding Sites in Proteins Using Fragment Screening. Authors: Ludlow, R.F. / Verdonk, M.L. / Saini, H.K. / Tickle, I.J. / Jhoti, H. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 310.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 252.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 443.5 KB | Display | |
Data in XML | ![]() | 36.2 KB | Display | |
Data in CIF | ![]() | 56.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5fp5C ![]() 5fp6C ![]() 5fpeC ![]() 5fpmC ![]() 5fpnC ![]() 5fpoC ![]() 5fprC ![]() 5fpsC ![]() 5fptC ![]() 5fpyC ![]() 1s3xS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (1, 0.00025, 0.00087), Vector: |
-
Components
#1: Protein | Mass: 42383.000 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | PYRAZINE-2-CARBOXAMIDE (L02): ASTEX COMPOUND REGISTRY AT513. PYRAZINE-2-CARBOXAMIDE (L01): ASTEX ...PYRAZINE-2-CARBOXAMID | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.3 % / Description: NONE |
---|---|
Crystal grow | pH: 8 Details: 1.0M NACL, 0.1M TRIS/HCL PH=8, 20.0% W/V PEG 8000. PROTEIN CONC. = 9MG/ML. |
-Data collection
Diffraction | Mean temperature: 93 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN CCD / Detector: CCD / Date: May 30, 2008 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→38.3 Å / Num. obs: 53188 / % possible obs: 97.9 % / Observed criterion σ(I): -3.7 / Redundancy: 2 % / Biso Wilson estimate: 22.79 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.97→2.03 Å / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 3.7 / % possible all: 88.4 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1S3X Resolution: 1.97→38.34 Å / Cor.coef. Fo:Fc: 0.9504 / Cor.coef. Fo:Fc free: 0.9179 / Cross valid method: THROUGHOUT / σ(F): 0
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.45 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→38.34 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.97→2.02 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|