[English] 日本語
Yorodumi
- PDB-5krs: HIV-1 Integrase Catalytic Core Domain in Complex with an Alloster... -

+
Open data


ID or keywords:

Loading...

-
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 / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / endonuclease activity / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / proteolysis / DNA binding / RNA 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 / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / 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 / Water


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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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 )

+
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