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- PDB-2yng: HIV-1 Reverse Transcriptase in complex with inhibitor GSK560 -

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Basic information

Entry
Database: PDB / ID: 2yng
TitleHIV-1 Reverse Transcriptase 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 / 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 / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / Assembly Of The HIV Virion / Budding and maturation of HIV virion / protein processing / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / host multivesicular body / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / peptidase activity / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / DNA binding / zinc ion binding / identical protein 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. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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. / Aspartic peptidase domain superfamily / Ribonuclease H 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
S,R MESO-TARTARIC ACID / Chem-WHU / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHIV-1 M\:B_HXB2R (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 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 18, 2013Group: Structure summary
Revision 1.2Dec 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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)117,8567
Polymers117,1342
Non-polymers7225
Water11,890660
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-55.9 kcal/mol
Surface area44590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.876, 154.627, 156.958
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: 64895.316 Da / Num. of mol.: 1
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, 665 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SRT / S,R MESO-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


Mass: 18.015 Da / Num. of mol.: 660 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsPOLY 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: 58 % / Description: NONE
Crystal growpH: 7.5
Details: 100MM HEPES PH 7.5, 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: Jun 26, 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: 2.12→80 Å / Num. obs: 80302 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 27
Reflection shellResolution: 2.12→2.18 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4.7 / % 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 2YNF

2ynf


Resolution: 2.12→78.57 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / SU B: 9.601 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24071 2455 3 %RANDOM
Rwork0.19607 ---
obs0.19742 79353 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.024 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2---0.58 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.12→78.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7821 0 42 660 8523
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.028144
X-RAY DIFFRACTIONr_bond_other_d0.0010.025540
X-RAY DIFFRACTIONr_angle_refined_deg1.2881.96211107
X-RAY DIFFRACTIONr_angle_other_deg0.822313612
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9245982
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26125.239355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.095151408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1481527
X-RAY DIFFRACTIONr_chiral_restr0.070.21209
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218893
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021562
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: 2.12→2.175 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 163 -
Rwork0.256 5545 -
obs--99.74 %
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)
11.4471-0.4313-0.32854.14832.56216.27290.18070.1540.02940.4438-0.58060.38830.03-0.69730.39990.1222-0.00080.04810.1463-0.06720.0885-34.17363.99746.006
23.2377-0.7879-2.51320.23510.61731.95230.1687-0.00840.145-0.01-0.0329-0.1363-0.1434-0.0051-0.13580.2670.06880.00050.11230.05510.278-19.56961.35635.142
34.36780.5247-5.40422.218-0.74448.26860.26490.33180.0676-0.0481-0.3706-0.0542-0.3894-0.51460.10570.09020.1042-0.02390.176-0.03530.0912-28.43763.47131.836
42.8487-0.9332-1.24891.7940.861.23750.2877-0.23350.9428-0.07290.2374-0.6246-0.6935-0.0926-0.52520.62460.23150.10770.1438-0.10410.3795-9.07369.31423.562
52.1297-1.02360.57632.60381.17956.4572-0.0085-0.43730.20460.21750.159-0.52070.11440.2798-0.15050.0432-0.00950.00370.1271-0.03270.21148.11849.97425.783
65.274-3.8787-0.58137.0684-0.26290.56850.13220.1421-0.429-0.1435-0.21630.16920.174-0.05170.08410.101-0.01520.02120.0354-0.00670.08693.22735.07913.157
72.86820.94741.33564.7133-1.56731.74510.4107-0.2130.19-0.3099-0.4584-0.22590.52290.30640.04780.19240.16-0.01930.3332-0.15120.174915.1499.66228.765
84.4558-0.24341.37526.8805-3.38227.37190.2391-0.24040.19290.1361-0.2415-0.00620.42240.37440.00240.13040.0972-0.00360.142-0.02440.010712.5611.21528.021
97.0521.3867-2.36786.5009-0.67218.0080.19090.1341-0.0453-0.2335-0.32110.2580.18470.06420.13020.0480.0436-0.03850.0436-0.0420.0522-28.00842.29615.054
100.78151.11691.05843.71682.12042.09550.0638-0.21690.0968-0.0562-0.06250.26980.1498-0.2552-0.00130.0651-0.0078-0.04470.1325-0.00770.0816-35.13929.03512.148
1119.3835-22.913-7.85738.53484.77235.013-0.0421-0.16460.4624-1.38080.61490.67160.5552-0.0489-0.57280.2479-0.0916-0.22940.04470.08830.2265-39.30622.348-6.367
1221.4712.54766.59862.14844.21198.4137-0.9040.65361.9285-0.24840.66080.0372-0.45291.34010.24330.6056-0.013-0.00160.42760.01050.2675-24.8719.664-0.565
1313.43420.36761.06171.4165-0.03354.9006-0.01310.462-0.7280.04550.1860.00471.1293-0.6658-0.17290.89380.0327-0.10210.1953-0.030.148-0.149-5.02415.379
1410.23145.80190.231816.5344-5.89092.74650.212-0.3045-0.2720.55350.06580.4573-0.1742-0.1035-0.27780.1978-0.00850.01050.18350.06670.0489-25.3616.54921.275
1519.0457.0239-4.751811.617-1.631.19250.1507-1.0589-0.3209-0.3307-0.2173-1.1418-0.00960.28790.06670.20050.1123-0.00880.1501-0.03540.135-11.81813.81215.42
167.32632.2909-0.56955.77420.26222.25110.2253-0.36470.1976-0.3039-0.0712-0.74970.19460.2696-0.15420.06440.0160.05740.0491-0.0250.138-14.24121.86313.193
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 59
2X-RAY DIFFRACTION2A60 - 114
3X-RAY DIFFRACTION3A115 - 194
4X-RAY DIFFRACTION4A195 - 253
5X-RAY DIFFRACTION5A254 - 354
6X-RAY DIFFRACTION6A355 - 421
7X-RAY DIFFRACTION7A422 - 473
8X-RAY DIFFRACTION8A474 - 558
9X-RAY DIFFRACTION9B5 - 71
10X-RAY DIFFRACTION10B72 - 194
11X-RAY DIFFRACTION11B195 - 212
12X-RAY DIFFRACTION12B213 - 240
13X-RAY DIFFRACTION13B241 - 312
14X-RAY DIFFRACTION14B313 - 325
15X-RAY DIFFRACTION15B325 - 347
16X-RAY DIFFRACTION16B348 - 428

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