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- PDB-5krs: HIV-1 Integrase Catalytic Core Domain in Complex with an Alloster... -

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Basic information

Entry
Database: PDB / ID: 5krs
TitleHIV-1 Integrase Catalytic Core Domain in Complex with an Allosteric Inhibitor, 3-(1H-pyrrol-1-yl)-2-thiophenecarboxylic acid
ComponentsIntegrase
Keywordshydrolase / transferase/inhibitor / HIV-1 Integrase Catalytic Core Domain / p75/LEDGF inhibitor / 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 / viral penetration into host nucleus / symbiont-mediated suppression of host gene expression / 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
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 ...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 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / 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. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
3-pyrrol-1-ylthiophene-2-carboxylic acid / Gag-Pol polyprotein / Integrase
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPatel, D. / Bauman, J.D. / Arnold, E.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103368 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI110310 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI127282 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: A New Class of Allosteric HIV-1 Integrase Inhibitors Identified by Crystallographic Fragment Screening of the Catalytic Core Domain.
Authors: Patel, D. / Antwi, J. / Koneru, P.C. / Serrao, E. / Forli, S. / Kessl, J.J. / Feng, L. / Deng, N. / Levy, R.M. / Fuchs, J.R. / Olson, A.J. / Engelman, A.N. / Bauman, J.D. / Kvaratskhelia, M. / Arnold, E.
History
DepositionJul 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Nov 16, 2016Group: Database references
Revision 1.3Mar 23, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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)17,4474
Polymers16,9821
Non-polymers4653
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.908, 71.908, 67.684
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-445-

HOH

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Components

#1: Protein Integrase


Mass: 16982.039 Da / Num. of mol.: 1 / Mutation: F185K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q76353, UniProt: P12497*PLUS
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-6XI / 3-pyrrol-1-ylthiophene-2-carboxylic acid


Mass: 193.222 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H7NO2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.07 Å3/Da / Density % sol: 59.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 1 mM manganese chloride, 100 mM MES pH 6.7, 10% (w/v) PEG 8000, and 5 mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.917 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 1.7→35.954 Å / Num. obs: 42447 / % possible obs: 98.5 % / Redundancy: 3.9 % / Net I/σ(I): 16.77

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Processing

Software
NameVersionClassification
PHENIX1.8.2-1309refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→35.954 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.65
RfactorNum. reflection% reflection
Rfree0.1856 3815 8.99 %
Rwork0.1677 --
obs0.1693 42443 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→35.954 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1150 0 30 136 1316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091211
X-RAY DIFFRACTIONf_angle_d1.1851641
X-RAY DIFFRACTIONf_dihedral_angle_d15.27694
X-RAY DIFFRACTIONf_chiral_restr0.063179
X-RAY DIFFRACTIONf_plane_restr0.006205
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7002-1.72170.29441410.2581419X-RAY DIFFRACTION98
1.7217-1.74440.22261430.24971447X-RAY DIFFRACTION99
1.7444-1.76830.30561540.24131475X-RAY DIFFRACTION100
1.7683-1.79350.27461350.22831436X-RAY DIFFRACTION99
1.7935-1.82030.24921460.22641447X-RAY DIFFRACTION100
1.8203-1.84880.26841420.20831431X-RAY DIFFRACTION99
1.8488-1.87910.22431400.2021425X-RAY DIFFRACTION99
1.8791-1.91150.19291480.19571455X-RAY DIFFRACTION100
1.9115-1.94620.18281460.18291479X-RAY DIFFRACTION99
1.9462-1.98360.21151440.18131404X-RAY DIFFRACTION100
1.9836-2.02410.18691280.17281447X-RAY DIFFRACTION100
2.0241-2.06810.17751360.16341453X-RAY DIFFRACTION99
2.0681-2.11620.16041460.16471451X-RAY DIFFRACTION99
2.1162-2.16920.20331420.16111431X-RAY DIFFRACTION100
2.1692-2.22780.14111450.15551421X-RAY DIFFRACTION100
2.2278-2.29330.16711520.14421450X-RAY DIFFRACTION99
2.2933-2.36740.15161420.15441403X-RAY DIFFRACTION99
2.3674-2.45190.17821380.15731443X-RAY DIFFRACTION99
2.4519-2.55010.17971280.15611454X-RAY DIFFRACTION98
2.5501-2.66610.16331430.151435X-RAY DIFFRACTION98
2.6661-2.80660.17971400.15721396X-RAY DIFFRACTION98
2.8066-2.98240.15391380.16251430X-RAY DIFFRACTION98
2.9824-3.21250.18181520.15751392X-RAY DIFFRACTION97
3.2125-3.53560.2021370.16811435X-RAY DIFFRACTION97
3.5356-4.04660.17111420.14631400X-RAY DIFFRACTION97
4.0466-5.09590.17261330.1511400X-RAY DIFFRACTION96
5.0959-35.9620.19481340.18571369X-RAY DIFFRACTION94
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)
10.6321-1.07140.14541.8134-0.13941.1169-0.05060.1164-0.0434-0.23060.02210.0351-0.03670.018-00.1593-0.0075-0.010.12880.00790.158335.3357130.783412.7451
21.3995-0.55710.5840.3577-0.34090.57340.15430.0593-0.246-0.0834-0.01110.11550.0592-0.05470.04690.13830.0119-0.00230.1602-0.00820.152133.0079132.864922.8717
30.6162-0.34760.47930.5404-0.27950.4394-0.03450.19210.1345-0.1275-0.0521-0.081-0.17910.1258-0.00010.1986-0.0093-0.01230.17360.020.143237.8684141.456116.6216
40.5248-0.17960.09030.32070.07860.50410.01420.44150.1161-0.8747-0.03130.1019-0.01570.3310.00380.46930.0479-0.0370.31760.0070.237134.626122.0474.4766
51.0141-0.20350.34030.2557-0.17160.65940.21340.0459-0.2336-0.3729-0.02820.3390.2286-0.05890.06180.1625-0.0024-0.02740.11010.00250.201133.8393117.28813.1044
60.2842-0.19520.09950.53230.20611.5076-0.08390.2079-0.0505-0.11010.2581-0.6022-0.07420.4771-0.00950.16250.03010.0280.2624-0.08010.297551.5357122.824814.065
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 55 through 93 )
2X-RAY DIFFRACTION2chain 'A' and (resid 94 through 107 )
3X-RAY DIFFRACTION3chain 'A' and (resid 108 through 149 )
4X-RAY DIFFRACTION4chain 'A' and (resid 150 through 168 )
5X-RAY DIFFRACTION5chain 'A' and (resid 169 through 185 )
6X-RAY DIFFRACTION6chain 'A' and (resid 186 through 207 )

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