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- PDB-1qs4: Core domain of HIV-1 integrase complexed with Mg++ and 1-(5-chlor... -

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Basic information

Entry
Database: PDB / ID: 1qs4
TitleCore domain of HIV-1 integrase complexed with Mg++ and 1-(5-chloroindol-3-yl)-3-hydroxy-3-(2H-tetrazol-5-yl)-propenone
ComponentsPROTEIN (HIV-1 INTEGRASE (E.C.2.7.7.49))
KeywordsTRANSFERASE / DNA INTEGRATION / INTEGRASE / HIV / ASPARTYL PROTEASE / ENDONUCLEASE
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 / viral penetration into host nucleus / establishment of integrated proviral latency ...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 / viral penetration into host nucleus / establishment of integrated proviral latency / 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 / 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 / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / 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. / 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. / Nucleotidyltransferase; domain 5 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-100 / Gag-Pol polyprotein / Integrase
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsGoldgur, Y. / Craigie, R. / Fujiwara, T. / Yoshinaga, T. / Davies, D.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Structure of the HIV-1 integrase catalytic domain complexed with an inhibitor: a platform for antiviral drug design.
Authors: Goldgur, Y. / Craigie, R. / Cohen, G.H. / Fujiwara, T. / Yoshinaga, T. / Fujishita, T. / Sugimoto, H. / Endo, T. / Murai, H. / Davies, D.R.
History
DepositionJun 25, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Nov 3, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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.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 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (HIV-1 INTEGRASE (E.C.2.7.7.49))
B: PROTEIN (HIV-1 INTEGRASE (E.C.2.7.7.49))
C: PROTEIN (HIV-1 INTEGRASE (E.C.2.7.7.49))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8027
Polymers50,4403
Non-polymers3634
Water9,800544
1
A: PROTEIN (HIV-1 INTEGRASE (E.C.2.7.7.49))
B: PROTEIN (HIV-1 INTEGRASE (E.C.2.7.7.49))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9655
Polymers33,6262
Non-polymers3383
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-30 kcal/mol
Surface area13990 Å2
MethodPISA, PQS
2
C: PROTEIN (HIV-1 INTEGRASE (E.C.2.7.7.49))
hetero molecules

C: PROTEIN (HIV-1 INTEGRASE (E.C.2.7.7.49))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6754
Polymers33,6262
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)76.233, 46.735, 141.361
Angle α, β, γ (deg.)90.00, 105.55, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PROTEIN (HIV-1 INTEGRASE (E.C.2.7.7.49))


Mass: 16813.219 Da / Num. of mol.: 3 / Fragment: Catalytic core domain / Mutation: F185K, W131E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q76353, UniProt: P12497*PLUS, RNA-directed DNA polymerase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-100 / 1-(5-CHLOROINDOL-3-YL)-3-HYDROXY-3-(2H-TETRAZOL-5-YL)-PROPENONE


Mass: 289.677 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H8ClN5O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 544 / 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: 2.4 Å3/Da / Density % sol: 48.84 %
Crystal growpH: 7
Details: 30% PEG 4000, 100 MM HEPES, 5 MM MGCL2, 5 MM DTT, 1% GLYCEROL, pH 7.00
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Details: Goldgur, Y., (1998) Proc. Natl. Acad. Sci. U.S.A., 95, 9150.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.5 mg/mlprotein1drop
220 mMTris-HCl1drop
30.5 M1dropNaCl
41 mMEDTA1drop
55 mMdithiothreitol1drop
630 %PEG40001reservoir
7100 mMHEPES1reservoir
85 mM1reservoirMgCl2
95 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→38.07 Å / Num. obs: 26564 / % possible obs: 94.2 % / Observed criterion σ(I): -3 / Redundancy: 2.12 % / Biso Wilson estimate: 29.64 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 10.4
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.274 / % possible all: 81.2
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / Observed criterion σ(I): -3
Reflection shell
*PLUS
% possible obs: 81 % / Mean I/σ(I) obs: 2.86

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.1→38.07 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1282 5 %RANDOM
Rwork0.209 ---
obs0.209 25282 94.2 %-
Solvent computationSolvent model: BABINET'S PRINCIPLE / Bsol: 73.9058 Å2 / ksol: 0.3627 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.732 Å20 Å21.644 Å2
2---10.3 Å20 Å2
3---5.567 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3469 0 23 544 4036
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.19
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shellResolution: 2.1→2.13 Å / Total num. of bins used: 25
Rfactor% reflection
Rfree0.3287 5 %
Rwork0.2963 -
obs-81.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4100.par100.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.1 Å / % reflection Rfree: 5 %

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