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- PDB-6vx2: HIV Integrase core domain in complex with inhibitor (5-methyl-1-b... -

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Basic information

Entry
Database: PDB / ID: 6vx2
TitleHIV Integrase core domain in complex with inhibitor (5-methyl-1-benzofuran-3-yl)acetic acid
ComponentsIntegrase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Inhibitor / HIV Integrase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / endonuclease activity / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / 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 / RNase H type-1 domain profile. / Ribonuclease H domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Retroviral matrix protein / Retrovirus capsid, C-terminal / 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. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
IODIDE ION / (5-methyl-1-benzofuran-3-yl)acetic acid / Integrase / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsGorman, M.A. / Parker, M.W.
CitationJournal: To Be Published
Title: HIV Integrase core domain in complex with inhibitor (5-methyl-1-benzofuran-3-yl)acetic acid
Authors: Gorman, M.A. / Parker, M.W.
History
DepositionFeb 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,17611
Polymers17,9051
Non-polymers1,27110
Water543
1
A: Integrase
hetero molecules

A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,35222
Polymers35,8112
Non-polymers2,54120
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5650 Å2
ΔGint-64 kcal/mol
Surface area13100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.288, 46.288, 140.096
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Integrase


Mass: 17905.354 Da / Num. of mol.: 1 / Mutation: Q53E,C56S,G124S,A125T,W131E,V151I,F185K,Q209E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli (E. coli)
References: UniProt: F2WR39, UniProt: P12497*PLUS, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-RQG / (5-methyl-1-benzofuran-3-yl)acetic acid


Mass: 190.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.1 Å3/Da / Density % sol: 41.3 % / Description: Cubic Bi-pyramid
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.2 M ammonium sulfate, 100 mM potassium iodide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 25, 2014
RadiationMonochromator: AXCO capillary / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.38→46.16 Å / Num. obs: 6539 / % possible obs: 99.9 % / Redundancy: 7.9 % / Biso Wilson estimate: 33.5 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.03 / Rrim(I) all: 0.084 / Χ2: 0.96 / Net I/σ(I): 16.9
Reflection shellResolution: 2.38→2.47 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 666 / CC1/2: 0.947 / Rpim(I) all: 0.158 / Rrim(I) all: 0.454 / Χ2: 0.92 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimlessdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.4→43.95 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.879 / SU B: 18.855 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.543 / ESU R Free: 0.332 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2949 768 12 %RANDOM
Rwork0.21635 ---
obs0.22577 5603 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.075 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å20 Å2
2---0.94 Å20 Å2
3---1.89 Å2
Refinement stepCycle: 1 / Resolution: 2.4→43.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1085 0 31 3 1119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131127
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171061
X-RAY DIFFRACTIONr_angle_refined_deg1.9571.6531523
X-RAY DIFFRACTIONr_angle_other_deg1.3241.5912459
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4635139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.91923.67349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.40215194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.889154
X-RAY DIFFRACTIONr_chiral_restr0.1210.2151
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021231
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02220
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_it2.1182.922562
X-RAY DIFFRACTIONr_mcbond_other2.1172.919561
X-RAY DIFFRACTIONr_mcangle_it3.4784.357699
X-RAY DIFFRACTIONr_mcangle_other3.4764.361700
X-RAY DIFFRACTIONr_scbond_it2.513.274563
X-RAY DIFFRACTIONr_scbond_other2.3753.219556
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9754.681812
X-RAY DIFFRACTIONr_long_range_B_refined7.4333.2531219
X-RAY DIFFRACTIONr_long_range_B_other7.42833.2461220
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å
RfactorNum. reflection% reflection
Rfree0.35 54 -
Rwork0.242 387 -
obs--94.64 %
Refinement TLS params.Method: refined / Origin x: 18.2263 Å / Origin y: 5.7011 Å / Origin z: 3.907 Å
111213212223313233
T0.0941 Å2-0.0097 Å2-0.0098 Å2-0.1201 Å2-0.006 Å2--0.0245 Å2
L0.7545 °2-0.6905 °20.3726 °2-0.676 °2-0.3797 °2--1.1404 °2
S-0.0408 Å °-0.0731 Å °0.1243 Å °0.0189 Å °0.0139 Å °-0.1236 Å °0.2035 Å °0.0712 Å °0.0269 Å °

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