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- PDB-7sia: HIV Integrase core domain in complex with inhibitor 2-[2-(2-{3-[(... -

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Basic information

Entry
Database: PDB / ID: 7sia
TitleHIV Integrase core domain in complex with inhibitor 2-[2-(2-{3-[(4-{2-[(3-{2-[3-(carboxymethyl)-5-methyl-1-benzofuran-2-yl]ethynyl}phenyl)formamido]ethyl}piperazin-1-yl)methyl]phenyl}ethynyl)-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


DNA integration / RNA stem-loop binding / RNA-directed DNA polymerase activity / endonuclease activity / DNA recombination / symbiont entry into host cell / DNA binding / zinc ion binding
Similarity search - Function
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. / Integrase core domain / Integrase, catalytic core ...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. / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
Chem-9I4 / IODIDE ION / Integrase
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsGorman, M.A. / Parker, M.W.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: To Be Published
Title: HIV Integrase core domain in complex with inhibitor
Authors: Gorman, M.A. / Parker, M.W.
History
DepositionOct 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

Downloads & links

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Assembly

Deposited unit
A: Integrase
B: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,04612
Polymers35,3102
Non-polymers1,73610
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-91 kcal/mol
Surface area12870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.277, 46.277, 139.003
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Integrase


Mass: 17655.059 Da / Num. of mol.: 2 / Fragment: core domain (UNP residues 50-212)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q76353, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-9I4 / (2-{[3-({4-[2-(3-{[3-(carboxymethyl)-5-methyl-1-benzofuran-2-yl]ethynyl}benzamido)ethyl]piperazin-1-yl}methyl)phenyl]ethynyl}-5-methyl-1-benzofuran-3-yl)acetic acid


Mass: 747.834 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H41N3O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#4: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.09 Å3/Da / Density % sol: 41.03 % / Description: Bi-pyamind
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: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.956 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.956 Å / Relative weight: 1
ReflectionResolution: 1.85→46.33 Å / Num. obs: 47732 / % possible obs: 99.4 % / Redundancy: 7.3 % / Biso Wilson estimate: 27 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.066 / Χ2: 1.08 / Net I/σ(I): 20
Reflection shellResolution: 1.85→1.89 Å / Rmerge(I) obs: 0.749 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1392 / CC1/2: 0.828 / Rpim(I) all: 0.307 / Rrim(I) all: 0.812 / Χ2: 0.97

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7RQ0

7rq0


Resolution: 1.85→46.28 Å / Cross valid method: THROUGHOUT / σ(F): 7.62 / Phase error: 35.54 / Stereochemistry target values: TWIN_LSQ_F / Details: TLS, Anomalous, Individual isotropic B factors
RfactorNum. reflection% reflection
Rfree0.2642 3934 8.24 %
Rwork0.2291 --
obs0.2331 47732 97.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→46.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2157 0 85 45 2287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112280
X-RAY DIFFRACTIONf_angle_d1.853086
X-RAY DIFFRACTIONf_dihedral_angle_d15.107304
X-RAY DIFFRACTIONf_chiral_restr0.066343
X-RAY DIFFRACTIONf_plane_restr0.01378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.880.40591720.37291970X-RAY DIFFRACTION82
1.88-1.920.60931700.58451954X-RAY DIFFRACTION78
1.92-1.950.47531730.48741958X-RAY DIFFRACTION81
1.95-1.990.30652040.30352262X-RAY DIFFRACTION92
1.99-2.040.29822060.26222269X-RAY DIFFRACTION92
2.04-2.090.2471920.24522249X-RAY DIFFRACTION92
2.09-2.140.27022020.25182213X-RAY DIFFRACTION92
2.14-2.20.27192070.24332342X-RAY DIFFRACTION92
2.2-2.260.42281750.43921945X-RAY DIFFRACTION82
2.26-2.330.40581890.29632228X-RAY DIFFRACTION90
2.33-2.420.2622080.25672246X-RAY DIFFRACTION91
2.42-2.510.32821890.24162253X-RAY DIFFRACTION92
2.51-2.630.26051940.22492236X-RAY DIFFRACTION92
2.63-2.770.24482030.22312255X-RAY DIFFRACTION92
2.77-2.940.27482060.21112275X-RAY DIFFRACTION92
2.94-3.170.19382000.20832210X-RAY DIFFRACTION92
3.17-3.480.2591960.19442296X-RAY DIFFRACTION92
3.48-3.990.19721880.16952206X-RAY DIFFRACTION91
3.99-5.020.18282040.15172282X-RAY DIFFRACTION91
5.03-46.280.25361970.20832208X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: 11.1266 Å / Origin y: 12.0226 Å / Origin z: -18.4032 Å
111213212223313233
T0.0994 Å20.0518 Å2-0.0048 Å2-0.0844 Å2-0.0107 Å2--0.0288 Å2
L1.0675 °20.7039 °20.5575 °2-0.8422 °20.3796 °2--1.4882 °2
S0.0826 Å °-0.1171 Å °0.1469 Å °0.1379 Å °-0.0613 Å °-0.0228 Å °-0.0098 Å °-0.0928 Å °-0.0384 Å °
Refinement TLS groupSelection details: all

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