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- PDB-5c24: Crystal Structure of HIV-1 Reverse Transcriptase in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 5c24
TitleCrystal Structure of HIV-1 Reverse Transcriptase in Complex with 7-((4-((4-cyanophenyl)amino)-1,3,5-triazin-2-yl)amino)-6,8-dimethylindolizine-2-carbonitrile (JLJ605), a non-nucleoside inhibitor
Components(HIV-1 REVERSE TRANSCRIPTASE, ...Reverse transcriptase) x 2
KeywordsTRANSFERASE / HYDROLASE/INHIBITOR / HIV / reverse transcriptase / non-nucleoside inhibitor / indolizine / triazine / polymerase / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


: / : / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...: / : / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / 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 / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane
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 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / 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
Chem-4XO / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsFrey, K.M. / Anderson, K.S.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI27690 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI44616 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM32136 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM49551 United States
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2015
Title: Discovery and crystallography of bicyclic arylaminoazines as potent inhibitors of HIV-1 reverse transcriptase.
Authors: Lee, W.G. / Frey, K.M. / Gallardo-Macias, R. / Spasov, K.A. / Chan, A.H. / Anderson, K.S. / Jorgensen, W.L.
History
DepositionJun 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 REVERSE TRANSCRIPTASE, P66 SUBUNIT
B: HIV-1 REVERSE TRANSCRIPTASE, P51 SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,5565
Polymers110,0552
Non-polymers5013
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-50 kcal/mol
Surface area45350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.287, 72.963, 109.183
Angle α, β, γ (deg.)90.000, 100.170, 90.000
Int Tables number5
Space group name H-MC121

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Components

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HIV-1 REVERSE TRANSCRIPTASE, ... , 2 types, 2 molecules AB

#1: Protein HIV-1 REVERSE TRANSCRIPTASE, P66 SUBUNIT / Reverse transcriptase / Pr160Gag-Pol


Mass: 61801.836 Da / Num. of mol.: 1 / Fragment: UNP residues 604-1144 / Mutation: C280S, K172A, K173A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate BH10)
Strain: isolate BH10 / Gene: gag-pol / Plasmid: PCDF-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P03366, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H
#2: Protein HIV-1 REVERSE TRANSCRIPTASE, P51 SUBUNIT / Reverse transcriptase / Pr160Gag-Pol


Mass: 48253.465 Da / Num. of mol.: 1 / Fragment: UNP residues 604-1027 / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate BH10)
Strain: isolate BH10 / Gene: gag-pol / Plasmid: PCDF-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P03366, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H

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Non-polymers , 4 types, 23 molecules

#3: Chemical ChemComp-4XO / 6-({4-[(4-cyanophenyl)amino]-1,3,5-triazin-2-yl}amino)-5,7-dimethylindolizine-2-carbonitrile


Mass: 380.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H16N8
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% v/v PEG 8000, 50 mM HEPES (pH 7.0),100 mM ammonium sulfate, 15 mM magnesium sulfate, and 5 mM spermine-HCl using hanging drop vaporization

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 22, 2014
RadiationMonochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.6→43.011 Å / Num. obs: 39121 / % possible obs: 99.5 % / Redundancy: 3.8 % / Rpim(I) all: 0.047 / Rrim(I) all: 0.092 / Rsym value: 0.079 / Χ2: 2.176 / Net I/av σ(I): 31.481 / Net I/σ(I): 11.3 / Num. measured all: 146748
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.643.70.6252.57119490.7660.3750.730.79799.1
2.64-2.693.80.56319360.7860.3350.6560.84699.2
2.69-2.743.80.47119310.8450.280.5480.89999.2
2.74-2.83.80.40719630.890.2420.4740.93199.2
2.8-2.863.80.33419120.9070.1990.3891.08399.4
2.86-2.933.80.28319340.9350.1680.3291.15399.4
2.93-33.80.24819370.9460.1470.2881.24699.4
3-3.083.80.21619570.9550.1290.2521.30499.5
3.08-3.173.80.18119520.9620.1080.2111.45499.5
3.17-3.283.80.14819260.9660.0890.1731.63299.6
3.28-3.393.80.12819570.9790.0760.1492.01699.6
3.39-3.533.80.11419520.9830.0680.1332.3599.7
3.53-3.693.80.09719680.9840.0580.1142.64599.7
3.69-3.883.80.08519700.9890.0510.0993.199.8
3.88-4.133.80.07819410.9890.0470.0913.53899.7
4.13-4.453.80.07519720.990.0450.0873.91999.8
4.45-4.893.70.07119800.9910.0420.0834.206100
4.89-5.63.70.06319810.9920.0380.0743.574100
5.6-7.053.60.05519810.9930.0340.0652.81699.9
7.05-503.60.05520220.9930.0340.0644.04198.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERPhenixphasing
RefinementResolution: 2.6→43.011 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.258 2000 5.11 %Random
Rwork0.2214 37115 --
obs0.2233 39115 98.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.89 Å2 / Biso min: 32.95 Å2
Refinement stepCycle: final / Resolution: 2.6→43.011 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7695 0 35 20 7750
Biso mean--71.35 60.11 -
Num. residues----949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037943
X-RAY DIFFRACTIONf_angle_d0.72310819
X-RAY DIFFRACTIONf_chiral_restr0.0291177
X-RAY DIFFRACTIONf_plane_restr0.0041362
X-RAY DIFFRACTIONf_dihedral_angle_d13.0192950
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.64860.3211250.26832310243587
2.6486-2.72020.32571440.26982671281599
2.7202-2.80030.31891430.27522665280899
2.8003-2.89060.3241420.26852634277699
2.8906-2.99390.32041430.2772644278799
2.9939-3.11380.3111420.281326492791100
3.1138-3.25540.30991440.26626662810100
3.2554-3.4270.32351450.254426802825100
3.427-3.64160.28731430.247826742817100
3.6416-3.92260.27171440.218926672811100
3.9226-4.3170.27611450.203226832828100
4.317-4.94090.22041450.199527072852100
4.9409-6.2220.22531470.210927192866100
6.222-43.01660.20511480.18752746289499

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