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- PDB-2aog: Crystal structure analysis of HIV-1 protease mutant V82A with a s... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2aog | ||||||
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Title | Crystal structure analysis of HIV-1 protease mutant V82A with a substrate analog P2-NC | ||||||
![]() | HIV-1 PROTEASE (RETROPEPSIN) | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / ![]() ![]() ![]() | ||||||
Function / homology | ![]() RNA stem-loop binding / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tie, Y. / Boross, P.I. / Wang, Y.F. / Gaddis, L. / Liu, F. / Chen, X. / Tozser, J. / Harrison, R.W. / Weber, I.T. | ||||||
![]() | ![]() Title: Molecular basis for substrate recognition and drug resistance from 1.1 to 1.6 angstroms resolution crystal structures of HIV-1 protease mutants with substrate analogs. Authors: Tie, Y. / Boross, P.I. / Wang, Y.F. / Gaddis, L. / Liu, F. / Chen, X. / Tozser, J. / Harrison, R.W. / Weber, I.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.4 KB | Display | ![]() |
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PDB format | ![]() | 89.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2aocC ![]() 2aodSC ![]() 2aoeC ![]() 2aofC ![]() 2aohC ![]() 2aoiC ![]() 2aojC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 10712.623 Da / Num. of mol.: 2 / Mutation: Q7K, L33I, L63I, C67A, V82A, C95A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Genus: Lentivirus ![]() ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 276 molecules ![](data/chem/img/2NC.gif)
![](data/chem/img/UNX.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/UNX.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-2NC / | ||||
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#3: Chemical | ChemComp-UNX / | ||||
#4: Chemical | ChemComp-GOL / ![]() #5: Chemical | ChemComp-ACY / | ![]() #6: Water | ChemComp-HOH / | ![]() |
-Details
Nonpolymer details | IN THE DEPOSITED FILE, THE INHIBITOR 2NC HAD AN EXTRA O7 ATOM IN CONFORMATION B WHICH ACCORDING TO ...IN THE DEPOSITED FILE, THE INHIBITOR 2NC HAD AN EXTRA O7 ATOM IN CONFORMATI |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: SODIUM CHLORIDE 0.4M, DMSO 5%,CITRATE PHOSPHATE BUFFER, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 1, 2003 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.1→50 Å / Num. all: 95318 / % possible obs: 94.8 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 10.4 | |||||||||
Reflection shell | Resolution: 1.1→1.14 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2.1 / % possible all: 68.4 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB Entry 2AOD Resolution: 1.1→10 Å / Num. parameters: 18897 / Num. restraintsaints: 25007 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Refine analyze | Num. disordered residues: 45 / Occupancy sum hydrogen: 1652.1 / Occupancy sum non hydrogen: 1808.44 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→10 Å
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Refine LS restraints |
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