[English] 日本語
![](img/lk-miru.gif)
- PDB-3zcm: Small molecule inhibitors of the LEDGF site of HIV integrase iden... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3zcm | ||||||
---|---|---|---|---|---|---|---|
Title | Small molecule inhibitors of the LEDGF site of HIV integrase identified by fragment screening and structure based design. | ||||||
![]() | HIV INTEGRASE | ||||||
![]() | TRANSFERASE | ||||||
Function / homology | ![]() symbiont-mediated activation of host apoptosis / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...symbiont-mediated activation of host apoptosis / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / endonuclease activity / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Peat, T.S. | ||||||
![]() | ![]() Title: Small Molecule Inhibitors of the Ledgf Site of Human Immunodeficiency Virus Integrase Identified by Fragment Screening and Structure Based Design. Authors: Peat, T.S. / Rhodes, D.I. / Vandegraaff, N. / Le, G. / Smith, J.A. / Clark, L.J. / Jones, E.D. / Coates, J.A.V. / Thienthong, N. / Newman, J. / Dolezal, O. / Mulder, R. / Ryan, J.H. / ...Authors: Peat, T.S. / Rhodes, D.I. / Vandegraaff, N. / Le, G. / Smith, J.A. / Clark, L.J. / Jones, E.D. / Coates, J.A.V. / Thienthong, N. / Newman, J. / Dolezal, O. / Mulder, R. / Ryan, J.H. / Savage, G.P. / Francis, C.L. / Deadman, J.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 81.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 60.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 3zsoC ![]() 3zsqC ![]() 3zsrC ![]() 3zsvC ![]() 3zswC ![]() 3zsxC ![]() 3zsyC ![]() 3zszC ![]() 3zt0C ![]() 3zt1C ![]() 3zt2C ![]() 3zt3SC ![]() 3zt4C S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 18395.842 Da / Num. of mol.: 2 / Fragment: CORE CATALYTIC DOMAIN, RESIDUES 56-212 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q76353, UniProt: P12497*PLUS, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
---|
-Non-polymers , 5 types, 163 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PX3.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PX3.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Details
Sequence details | 3 MUTATIONS MADE FOR SOLUBILITY |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.5 % / Description: NONE |
---|---|
Crystal grow | pH: 5.5 Details: THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 22, 2009 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→45.3 Å / Num. obs: 34979 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3ZT3 Resolution: 1.8→31.33 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.999 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 21.239 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→31.33 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|