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- PDB-3i6o: Crystal structure of wild type HIV-1 protease with macrocyclic in... -

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Basic information

Entry
Database: PDB / ID: 3i6o
TitleCrystal structure of wild type HIV-1 protease with macrocyclic inhibitor GRL-0216A
ComponentsProtease
KeywordsHYDROLASE / HIV-1 / wild type protease / protease inhibitor / macrocyclic ligand / AIDS / Aspartyl protease
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / 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 / 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 / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
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 ...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 / Cathepsin D, subunit A; domain 1 / Acid Proteases / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / 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 / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-GR6 / IODIDE ION / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 Å
AuthorsChumanevich, A.A. / Wang, Y.-F. / Kovalevsky, A.Y. / Weber, I.T.
CitationJournal: J.Med.Chem. / Year: 2009
Title: Design, Synthesis, Protein-Ligand X-ray Structure, and Biological Evaluation of a Series of Novel Macrocyclic Human Immunodeficiency Virus-1 Protease Inhibitors to Combat Drug Resistance.
Authors: Ghosh, A.K. / Kulkarni, S. / Anderson, D.D. / Hong, L. / Baldridge, A. / Wang, Y.F. / Chumanevich, A.A. / Kovalevsky, A.Y. / Tojo, Y. / Amano, M. / Koh, Y. / Tang, J. / Weber, I.T. / Mitsuya, H.
History
DepositionJul 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,75326
Polymers21,4812
Non-polymers3,27224
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-21.4 kcal/mol
Surface area9470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.764, 86.328, 45.976
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Protease


Mass: 10740.677 Da / Num. of mol.: 2 / Fragment: UNP residues 501-599 / Mutation: Q7K, L33I, L63I, C67A, C95A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 (BRU ISOLATE)
Gene: gag-pol / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03367, HIV-1 retropepsin

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Non-polymers , 5 types, 205 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-GR6 / (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl {(1S,2R)-1-benzyl-2-hydroxy-3-[(7E)-13-methoxy-1,1-dioxido-3,4,5,6,9,10-hexahydro-2H-11,1,2-benzoxathiazacyclotridecin-2-yl]propyl}carbamate


Mass: 630.749 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H42N2O9S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.71 Å3/Da / Density % sol: 54.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Protein solution: 1:15 molar ratio of protease at 2.0 mg/mL and inhibitor GRL-0216A dissolved in dimethylsulfoxide (DMSO). Reservoir solution: 5% Glycerol, 0.5 M NaI in 0.2 M MES buffer, pH ...Details: Protein solution: 1:15 molar ratio of protease at 2.0 mg/mL and inhibitor GRL-0216A dissolved in dimethylsulfoxide (DMSO). Reservoir solution: 5% Glycerol, 0.5 M NaI in 0.2 M MES buffer, pH 6.0. Crystal mounted on a nylon loop in the liquid nitrogen with additional 28% v/v Glycerol as cryoprotectant, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.8 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 21, 2007
RadiationMonochromator: Si(220) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.17→50 Å / Num. all: 72239 / Num. obs: 72239 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 11.8 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 14.7
Reflection shellResolution: 1.17→1.21 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4137 / % possible all: 52.6

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Processing

Software
NameVersionClassification
MAR345CCDdata collection
PHASERphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3B7V

3b7v


Resolution: 1.17→10 Å / Num. parameters: 17764 / Num. restraintsaints: 24272 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1957 3607 5 %RANDOM
Rwork0.1594 ---
all0.1614 72049 --
obs0.1614 72049 90.9 %-
Refine analyzeNum. disordered residues: 26 / Occupancy sum hydrogen: 1602 / Occupancy sum non hydrogen: 1722.65
Refinement stepCycle: LAST / Resolution: 1.17→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 77 181 1770
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0309
X-RAY DIFFRACTIONs_zero_chiral_vol0.08
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.075
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.03
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.035
X-RAY DIFFRACTIONs_approx_iso_adps0.091

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