- PDB-3di6: HIV-1 RT with pyridazinone non-nucleoside inhibitor -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3di6
Title
HIV-1 RT with pyridazinone non-nucleoside inhibitor
Components
Reverse transcriptase/ribonuclease H
p51 RT
Keywords
TRANSFERASE / HIV / RT / REVERSE TRANSCRIPTASE / TRANSFERASE RNA-DIRECTED DNA POLYMERASE / NUCLEOTIDYLTRANSFERASE / AIDS / Cytoplasm / Hydrolase / Viral nucleoprotein
Function / homology
Function and homology information
integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / 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 / viral life cycle / Assembly Of The HIV Virion / HIV-1 retropepsin / : / Budding and maturation of HIV virion / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / protein processing / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / peptidase activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / DNA binding / RNA binding / zinc ion binding / membrane / identical protein binding Similarity search - Function
HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. ...HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology
Mass: 64710.121 Da / Num. of mol.: 1 / Fragment: UNP residues 588-1148 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 (HXB2 isolate) Gene: gag-pol / Production host: Escherichia coli (E. coli) References: UniProt: P04585, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H
#2: Protein
p51RT
Mass: 51399.047 Da / Num. of mol.: 1 / Fragment: UNP residues 588-1027 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 (HXB2 isolate) Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P04585
Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.99 Å3/Da / Density % sol: 58.86 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 1.15 M sodium malonate, 50 mM potassium phosphate, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K
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Data collection
Diffraction
Mean temperature: 100 K
Diffraction source
Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.976067 Å
Detector
Detector: CCD / Date: Aug 1, 2003
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.976067 Å / Relative weight: 1
Reflection
Resolution: 2.65→50 Å / Num. obs: 40591 / % possible obs: 99.5 % / Redundancy: 5.8 % / Rsym value: 0.0307 / Net I/σ(I): 45
Reflection shell
Resolution: 2.65→2.74 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 8.6 / Num. unique all: 4012 / Rsym value: 0.186 / % possible all: 99.8
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Processing
Software
Name
Version
Classification
PHASER
phasing
REFMAC
5.2.0019
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→46.88 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.26537
2064
5.1 %
RANDOM
Rwork
0.21721
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all
0.21969
40591
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obs
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38450
99.6 %
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Displacement parameters
Biso mean: 43.462 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.03 Å2
0 Å2
0 Å2
2-
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-1.49 Å2
0 Å2
3-
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2.52 Å2
Refinement step
Cycle: LAST / Resolution: 2.65→46.88 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
7788
0
23
97
7908
Refine LS restraints
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
r_bond_refined_d
0.008
X-RAY DIFFRACTION
r_bond_other_d
0.001
X-RAY DIFFRACTION
r_angle_refined_deg
1.068
X-RAY DIFFRACTION
r_angle_other_deg
0.784
X-RAY DIFFRACTION
r_chiral_restr
0.062
LS refinement shell
Resolution: 2.65→2.719 Å
Rfactor
Num. reflection
% reflection
Rfree
0.373
139
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Rwork
0.3
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obs
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2800
98.8 %
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