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- PDB-4obg: Crystal Structure of Nelfinavir-Resistant, Inactive HIV-1 Proteas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4obg | ||||||
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Title | Crystal Structure of Nelfinavir-Resistant, Inactive HIV-1 Protease (D30N/N88D) in Complex with the p1-p6 substrate. | ||||||
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![]() | HYDROLASE / Co-evolution / Resistance | ||||||
Function / homology | ![]() host cellular component / Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cell nuclear membrane / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / viral budding via host ESCRT complex ...host cellular component / Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cell nuclear membrane / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / viral budding via host ESCRT complex / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / Membrane binding and targetting of GAG proteins / Assembly Of The HIV Virion / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / Budding and maturation of HIV virion / 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 / 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 / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Kolli, M. | ||||||
![]() | ![]() Title: HIV-1 protease-substrate coevolution in nelfinavir resistance. Authors: Kolli, M. / Ozen, A. / Kurt-Yilmaz, N. / Schiffer, C.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128.8 KB | Display | ![]() |
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PDB format | ![]() | 100.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 492.1 KB | Display | ![]() |
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Full document | ![]() | 496.8 KB | Display | |
Data in XML | ![]() | 20.1 KB | Display | |
Data in CIF | ![]() | 27.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4obdC ![]() 4obfC ![]() 4obhC ![]() 4objC ![]() 4obkC ![]() 1t3rS 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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2 | ![]()
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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 6 molecules ABCDEF
#1: Protein | Mass: 10814.804 Da / Num. of mol.: 4 / Mutation: Q7K, D25N, D30N, N88D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 1173.325 Da / Num. of mol.: 2 / Fragment: UNP residues 446-455 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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-Non-polymers , 4 types, 213 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.24 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 28% PEG 5000, 0.1M ammonium sulfate, 0.5M MES monohydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 9, 2009 / Details: Mirrors |
Radiation | Monochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→50 Å / Num. obs: 34288 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rsym value: 0.068 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.78→1.86 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.88 / Rsym value: 0.355 / % possible all: 99.7 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Rfactor: 47.01 / Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1T3R Resolution: 1.78→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.01 / SU B: 4.999 / SU ML: 0.121 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.977 Å2
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Refinement step | Cycle: LAST / Resolution: 1.78→50 Å
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Refine LS restraints |
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