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- PDB-2ynf: HIV-1 Reverse Transcriptase Y188L mutant in complex with inhibito... -

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Basic information

Entry
Database: PDB / ID: 2ynf
TitleHIV-1 Reverse Transcriptase Y188L mutant in complex with inhibitor GSK560
Components
  • P51 RT
  • REVERSE TRANSCRIPTASE/RIBONUCLEASE H
KeywordsHYDROLASE / NNRTI
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 / 2-LTR circle formation / Uncoating of the HIV Virion / 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 / 2-LTR circle formation / Uncoating of the HIV Virion / 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 / retroviral ribonuclease H / Budding and maturation of HIV virion / exoribonuclease H / exoribonuclease H activity / protein processing / host multivesicular body / 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 / peptidase activity / 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 / 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 / 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
D(-)-TARTARIC ACID / Chem-WHU / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHIV-1 M\:B_HXB2R (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsChong, P. / Sebahar, P. / Youngman, M. / Garrido, D. / Zhang, H. / Stewart, E.L. / Nolte, R.T. / Wang, L. / Ferris, R.G. / Edelstein, M. ...Chong, P. / Sebahar, P. / Youngman, M. / Garrido, D. / Zhang, H. / Stewart, E.L. / Nolte, R.T. / Wang, L. / Ferris, R.G. / Edelstein, M. / Weaver, K. / Mathis, A. / Peat, A.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Rational Design of Potent Non-Nucleoside Inhibitors of HIV-1 Reverse Transcriptase.
Authors: Chong, P. / Sebahar, P. / Youngman, M. / Garrido, D. / Zhang, H. / Stewart, E.L. / Nolte, R.T. / Wang, L. / Ferris, R.G. / Edelstein, M. / Weaver, K. / Mathis, A. / Peat, A.
History
DepositionOct 14, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: REVERSE TRANSCRIPTASE/RIBONUCLEASE H
B: P51 RT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,8067
Polymers117,0842
Non-polymers7225
Water7,819434
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint-52 kcal/mol
Surface area43840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.578, 154.508, 157.026
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein REVERSE TRANSCRIPTASE/RIBONUCLEASE H / EXORIBONUCLEASE H / P66 RT


Mass: 64845.301 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 M\:B_HXB2R (virus) / Plasmid: PKK233-2 VARIANT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P04585, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H
#2: Protein P51 RT


Mass: 52238.875 Da / Num. of mol.: 1 / Fragment: RESIDUES 588-1015
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 M\:B_HXB2R (virus) / Plasmid: PKK233-2 VARIANT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04585

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Non-polymers , 4 types, 439 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-TAR / D(-)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#5: Chemical ChemComp-WHU / 2-azanyl-N-[[4-bromanyl-3-(3-chloranyl-5-cyano-phenoxy)-2-fluoranyl-phenyl]methyl]-4-chloranyl-1H-imidazole-5-carboxamide


Mass: 499.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H11BrCl2FN5O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 434 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsPRESUMED MG IONS D(-)-TARTARIC ACID (TAR): TARTRATE FROM CRYSTALLIZATION CONDITION
Sequence detailsY188L MUTATION POLY HIS TAG ADDED AT THE N-TERMINUS FOR PURIFICATION

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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: 3.2 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 7.5
Details: 100MM HEPES PH7.5, 10MM SPERMIDINE, 1.1M SODIUM POTASSIUM TARTRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 3, 2008 / Details: BERYLLIUM LENSES
RadiationMonochromator: DIAMOND LAUE MONOCHROMATORS SUPPLIED BY JJ X-RAY
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 59250 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.4
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4.15 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HMV

1hmv


Resolution: 2.36→47.57 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.902 / SU B: 12.266 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.277 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23631 1783 3 %RANDOM
Rwork0.19722 ---
obs0.1984 57009 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.099 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2--0.31 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.36→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7728 0 42 434 8204
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.028008
X-RAY DIFFRACTIONr_bond_other_d0.0010.025441
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.96210920
X-RAY DIFFRACTIONr_angle_other_deg0.85313362
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9245966
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.77225.029342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.108151379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9481529
X-RAY DIFFRACTIONr_chiral_restr0.0720.21201
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218717
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021540
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.364→2.425 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 105 -
Rwork0.231 3302 -
obs--80.6 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0446-0.7011-1.56951.70421.87633.21160.16290.11030.00370.1853-0.3116-0.0053-0.1155-0.3630.14880.32510.1076-0.00730.226-0.03410.1995-29.64962.5341.839
25.3652-1.927-3.27812.49621.87042.32220.92870.23711.4203-0.5960.0475-0.9452-0.8054-0.1909-0.97610.65970.22530.27350.25530.00370.8376-14.36567.2421.408
33.1755-1.49062.59071.9231-0.82966.86390.1396-0.33990.36470.07470.2633-0.5859-0.04720.2992-0.40290.1436-0.0388-0.0120.2987-0.17060.43978.74451.11130.106
41.8543-2.1362-0.58977.1985-1.2111.66390.0171-0.14340.14770.3866-0.0218-0.4639-0.19950.18830.00470.20630.00620.06540.21710.00550.32126.07643.67617.915
50.5299-0.74970.34732.4368-1.27951.50250.0931-0.04650.1772-0.125-0.1606-0.33370.16790.27660.06740.19320.08760.02510.28590.02780.270810.16721.55221.886
65.3238-0.01972.27842.5251-0.42583.7680.3733-0.2751-0.3551-0.4403-0.0168-0.02481.1342-0.1476-0.35660.56630.1636-0.04780.2370.04920.23410.3872.928.707
73.34111.3385-0.72763.97840.02982.93670.0671-0.03040.0082-0.0811-0.22210.0176-0.0237-0.11780.1550.18370.0868-0.02470.2572-0.06730.1619-28.35839.32316.267
80.72830.73570.66222.37721.10831.45070.0757-0.16390.1247-0.1351-0.07960.29840.1075-0.22770.00390.2340.0387-0.040.2836-0.01170.2248-36.23328.48910.509
97.3802-3.3063.64182.2238-1.87031.99460.19590.10540.0785-0.369-0.10940.00930.41480.0318-0.08640.64690.0563-0.12430.24210.00050.1399-19.37511.2614.283
104.943-1.85850.15072.998-0.23260.6734-0.1337-0.2245-0.1965-0.13260.2561-0.08520.7261-0.1278-0.12240.8586-0.0227-0.110.2330.00410.1194-7.5921.117.163
115.83860.887-0.15863.7799-0.02972.07920.2735-0.2630.3452-0.242-0.1191-0.47510.10210.1641-0.15440.21930.04490.04250.2104-0.01880.2344-14.34121.89513.237
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 155
2X-RAY DIFFRACTION2A156 - 253
3X-RAY DIFFRACTION3A254 - 325
4X-RAY DIFFRACTION4A326 - 363
5X-RAY DIFFRACTION5A364 - 527
6X-RAY DIFFRACTION6A528 - 558
7X-RAY DIFFRACTION7B5 - 89
8X-RAY DIFFRACTION8B90 - 194
9X-RAY DIFFRACTION9B195 - 270
10X-RAY DIFFRACTION10B271 - 347
11X-RAY DIFFRACTION11B348 - 428

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