[English] 日本語
Yorodumi
- PDB-7t9o: HIV Integrase in complex with Compound-25 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7t9o
TitleHIV Integrase in complex with Compound-25
ComponentsIntegrase
KeywordsDNA BINDING PROTEIN / Viral Protein / DNA Integration / AIDS / RNASEH / LEDGF / ENDONUCLEASE / HIV-1 integrase
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-GEI / Integrase
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKhan, J.A. / Lewis, H. / Kish, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: Design, Synthesis, and Preclinical Profiling of GSK3739936 (BMS-986180), an Allosteric Inhibitor of HIV-1 Integrase with Broad-Spectrum Activity toward 124/125 Polymorphs.
Authors: Naidu, B.N. / Patel, M. / McAuliffe, B. / Ding, B. / Cianci, C. / Simmermacher, J. / Jenkins, S. / Parker, D.D. / Sivaprakasam, P. / Khan, J.A. / Kish, K. / Lewis, H. / Hanumegowda, U. / ...Authors: Naidu, B.N. / Patel, M. / McAuliffe, B. / Ding, B. / Cianci, C. / Simmermacher, J. / Jenkins, S. / Parker, D.D. / Sivaprakasam, P. / Khan, J.A. / Kish, K. / Lewis, H. / Hanumegowda, U. / Krystal, M. / Meanwell, N.A. / Kadow, J.F.
History
DepositionDec 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6286
Polymers19,6851
Non-polymers9435
Water1,11762
1
A: Integrase
hetero molecules

A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,25712
Polymers39,3712
Non-polymers1,88610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4850 Å2
ΔGint-91 kcal/mol
Surface area11680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.919, 70.919, 66.920
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-431-

HOH

-
Components

#1: Protein Integrase


Mass: 19685.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Plasmid: pET15b / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q76353
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GEI / (2S)-tert-butoxy[4-(4,4-dimethylpiperidin-1-yl)-5-{4-[2-(4-fluorophenyl)ethoxy]phenyl}-2,6-dimethylpyridin-3-yl]acetic acid


Mass: 562.715 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H43FN2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 4.6%(w/v) PEG 3350, 261 mM ammonium acetate, 0.81% glycerol(v/v), 91 mM magnesium chloride and 100 mM MES pH 6.0
PH range: 6.0?

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 14550 / % possible obs: 99.9 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 34.5
Reflection shellResolution: 1.95→2.02 Å / Rmerge(I) obs: 0.587 / Num. unique obs: 1435

-
Processing

Software
NameVersionClassification
BUSTER2.11.7 (17-DEC-2019)refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NCJ

6ncj


Resolution: 1.95→45.25 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.95 / SU R Cruickshank DPI: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.133 / SU Rfree Blow DPI: 0.123 / SU Rfree Cruickshank DPI: 0.122
RfactorNum. reflection% reflectionSelection details
Rfree0.2189 732 5.04 %RANDOM
Rwork0.1908 ---
obs0.1921 14527 99.8 %-
Displacement parametersBiso max: 107.03 Å2 / Biso mean: 41.89 Å2 / Biso min: 26.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.7999 Å20 Å20 Å2
2---0.7999 Å20 Å2
3---1.5998 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: final / Resolution: 1.95→45.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1045 0 70 62 1177
Biso mean--51.53 53.12 -
Num. residues----138
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d394SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes224HARMONIC5
X-RAY DIFFRACTIONt_it1147HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion154SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1059SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1198HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg1676HARMONIC20.89
X-RAY DIFFRACTIONt_omega_torsion3.29
X-RAY DIFFRACTIONt_other_torsion13.14
LS refinement shellResolution: 1.95→1.97 Å / Rfactor Rfree error: 0 / Total num. of bins used: 37
RfactorNum. reflection% reflection
Rfree0.2387 23 5.69 %
Rwork0.1864 381 -
all0.1891 404 -
obs--94.61 %
Refinement TLS params.Method: refined / Origin x: 12.2345 Å / Origin y: 33.9313 Å / Origin z: -6.2698 Å
111213212223313233
T-0.0485 Å2-0.0072 Å2-0.0132 Å2--0.0323 Å20.0077 Å2---0.0729 Å2
L2.3019 °2-0.7905 °2-0.0906 °2-1.0775 °20.1867 °2--1.5547 °2
S0.017 Å °0.2254 Å °0.075 Å °-0.0409 Å °-0.0616 Å °0.0301 Å °-0.1279 Å °-0.0755 Å °0.0445 Å °
Refinement TLS groupSelection details: { A|* }

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more