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- PDB-8zha: HIV-1 integrase core domain in complex with compound 15 -

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Basic information

Entry
Database: PDB / ID: 8zha
TitleHIV-1 integrase core domain in complex with compound 15
ComponentsIntegrase
KeywordsVIRAL PROTEIN / HIV / integrase / inhibitor
Function / homology
Function and homology information


HIV-1 retropepsin / 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 / viral penetration into host nucleus ...HIV-1 retropepsin / 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 / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / 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 / 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. / 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. / 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
: / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsFuruzono, T. / Orita, T. / Nomura, A. / Adachi, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2024
Title: Design and synthesis of novel and potent allosteric HIV-1 integrase inhibitors with a spirocyclic moiety.
Authors: Adachi, K. / Manabe, T. / Yamasaki, T. / Suma, A. / Orita, T. / Furuzono, T. / Adachi, T. / Ohata, Y. / Akiyama, Y. / Miyazaki, S.
History
DepositionMay 10, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2024Provider: 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)19,4345
Polymers18,5641
Non-polymers8704
Water1,18966
1
A: Integrase
hetero molecules

A: Integrase
hetero molecules


  • defined by author&software
  • Evidence: gel filtration
  • 38.9 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)38,86710
Polymers37,1272
Non-polymers1,7408
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5050 Å2
ΔGint-54 kcal/mol
Surface area13330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.740, 72.740, 66.450
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Integrase / IN


Mass: 18563.674 Da / Num. of mol.: 1 / Mutation: F185H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
Gene: gag-pol / Production host: Escherichia coli (E. coli)
References: UniProt: P12497, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-A1L1W / (2~{S})-2-[7-(cycloheptylcarbamoyl)-4',5-dimethyl-spiro[1,2-dihydroindene-3,1'-cyclohexane]-4-yl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid


Mass: 483.683 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H45NO4
#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.: 66 / 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: 2.73 Å3/Da / Density % sol: 55.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1M sodium cacodylate, 0.2M ammonium sulfate, 7% (w/v) PEG 8000, 5mM DTT, soaking the crystal with 1mM compound 15

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1 Å
DetectorType: MAR CCD 300 mm / Detector: CCD / Date: Jun 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→66.45 Å / Num. obs: 15195 / % possible obs: 99.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 32.81 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.037 / Rrim(I) all: 0.099 / Net I/σ(I): 13.2
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 0.681 / Mean I/σ(I) obs: 3 / Num. unique obs: 1054 / CC1/2: 0.744 / Rpim(I) all: 0.268 / Rrim(I) all: 0.733 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→45.72 Å / SU ML: 0.2637 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 25.6169
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.211 702 4.63 %
Rwork0.1902 14464 -
obs0.1912 15166 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.23 Å2
Refinement stepCycle: LAST / Resolution: 1.95→45.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1128 0 58 66 1252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00381216
X-RAY DIFFRACTIONf_angle_d0.63331655
X-RAY DIFFRACTIONf_chiral_restr0.0467180
X-RAY DIFFRACTIONf_plane_restr0.0035197
X-RAY DIFFRACTIONf_dihedral_angle_d16.1612447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.10.28041540.25072846X-RAY DIFFRACTION99.97
2.1-2.310.27061210.21712854X-RAY DIFFRACTION100
2.31-2.650.21361290.21432891X-RAY DIFFRACTION100
2.65-3.330.25031410.20582908X-RAY DIFFRACTION100
3.34-45.720.17521570.16142965X-RAY DIFFRACTION99.11
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)
15.268592363975.44000644682-5.464723412525.64191750764-5.687530956055.74747621342-0.4054243979570.175397926795-0.363405451358-0.6907615912560.172552320086-0.5799257986710.639866242390.4114281675610.2108048266070.285157199389-0.008037059345920.0460776062480.292065446779-0.02174566847860.32296402733824.398411550920.1086272981-7.68252813229
28.088890569432.37430452905-1.467389322512.07640310993-2.821759574764.41468063710.01276691566520.6581726873520.4188344336280.1142125794860.009666691120290.120819723032-0.2546323012070.06614111320740.01640977879840.2215540710740.02984902799140.03333812156970.267137263250.01062701058610.1892261107922.640946813430.8553762075-11.8471166081
38.073588293924.675164898776.520344394466.535434512545.626499268049.09285792970.178664638002-0.3250939164480.285158439832-0.106671270947-0.701260078871-0.0713196094162-0.359325416480.09203208357010.4914597816840.2616372944830.0005081927855490.01338128133480.2573185157220.1036887656440.32032721383725.773974894835.0707211637-7.05208748163
48.032601619575.76939577997-4.725784786357.61012474875-4.690894852563.42403701780.341466605818-0.2205584065640.3525146430230.324032431812-0.4484821859180.200277854193-0.2854335220940.05019956257080.1154930333950.2557015859440.0211595517887-0.02069227195710.25784196627-0.02172073920940.22140157136526.962586162930.14988404330.853126481309
54.494286230212.85068985769-5.342645758714.13873513232-2.063009265227.14026348807-0.4352040800350.903515430635-0.800815046518-0.0878724577549-0.165031740159-0.5784150209950.318625574941-0.6571423880190.4937224190460.2233998793760.0427916655781-0.022832277720.291530620499-0.05741604972360.30416235649527.026065107120.6990592803-6.06243212389
62.08850289378-1.33020758808-3.059559307910.9917217897991.064766739129.81303388938-0.0424191332865-0.1542578015590.1299467497610.1217868794330.137426720986-0.280892236734-0.7669351459280.20787923829-0.04109407757170.240321462884-0.01064054209540.02597990124120.378890031142-0.01371370620270.31285535661337.584218132227.0480683338-2.96722074763
72.29090685504-0.5360215837411.485073009493.24070771887-1.325979018417.00441506204-0.232077364580.75675753923-0.263211110899-0.6369272460460.159273187213-0.02317800045480.9512625298590.78475070063-0.09890026398390.4028870565-0.05952518201760.0270162379640.529600994455-0.1024328039530.33170399675831.913198070818.4679607512-6.98918512609
86.743965093732.58181025448-0.428070182772.81771052783-1.892804430536.353400895860.1366959081531.162823545890.16330719751-0.327038389559-0.1311196785590.170462676006-0.363134388654-0.174007086878-0.04700706000090.2558546138170.092032178989-0.002192017149860.4657455091990.04732349915840.24890512810714.433080241436.3588536763-14.0986612853
92.59998424284-0.3647553540520.4238573147116.11575069469-2.48565139445.821815472920.1045938293480.398007821412-0.580799264231-0.20146380853-0.1435132866170.8052740532610.678630811852-0.493532041084-0.1989840675480.316561881036-0.123293248393-0.01837069148750.299845794987-0.1281456015640.5303684103299.9106560968216.9396935713-6.72624040331
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 57 through 64 )57 - 642 - 9
22chain 'A' and (resid 66 through 83 )66 - 8311 - 28
33chain 'A' and (resid 84 through 93 )84 - 9329 - 38
44chain 'A' and (resid 94 through 107 )94 - 10739 - 52
55chain 'A' and (resid 108 through 117 )108 - 11753 - 62
66chain 'A' and (resid 118 through 129 )118 - 12963 - 74
77chain 'A' and (resid 131 through 153 )131 - 15376 - 91
88chain 'A' and (resid 154 through 185 )154 - 18592 - 123
99chain 'A' and (resid 186 through 209 )186 - 209124 - 143

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