[English] 日本語
Yorodumi
- PDB-3toh: HIV-1 Protease - Epoxydic Inhibitor Complex (pH 9 - Orthorombic C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3toh
TitleHIV-1 Protease - Epoxydic Inhibitor Complex (pH 9 - Orthorombic Crystal form P212121)
ComponentsGag-Pol polyprotein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HIV PR / epoxide / in-crystal reaction / hydrolase / HYDROLASE-HYDROLASE 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 / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase / RNA stem-loop binding ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase / RNA stem-loop binding / viral penetration into host nucleus / host multivesicular body / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / 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
Similarity search - Function
Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase-like, N-terminal ...Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase-like, N-terminal / 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 / RNase H type-1 domain profile. / Ribonuclease H domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / 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. / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
(S)-N-((2S,3S,4R,5R)-4-AMINO-3,5-DIHYDROXY-1,6-DIPHENYLHEXAN-2-YL)-3-METHYL-2-(2-PHENOXYACETAMIDO)BUTANAMIDE / Chem-079 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.116 Å
AuthorsGeremia, S. / Olajuyigbe, F.M. / Demitri, N.
CitationJournal: Molecules / Year: 2016
Title: Developing HIV-1 Protease Inhibitors through Stereospecific Reactions in Protein Crystals.
Authors: Olajuyigbe, F.M. / Demitri, N. / De Zorzi, R. / Geremia, S.
History
DepositionSep 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Other
Revision 1.2Oct 29, 2014Group: Structure summary
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.5Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Gag-Pol polyprotein
B: Gag-Pol polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2496
Polymers21,4812
Non-polymers7684
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-20 kcal/mol
Surface area10020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.268, 58.377, 61.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Gag-Pol polyprotein / Pr160Gag-Pol / Matrix protein p17 / MA / Capsid protein p24 / CA / Spacer peptide p2 / Nucleocapsid ...Pr160Gag-Pol / Matrix protein p17 / MA / Capsid protein p24 / CA / Spacer peptide p2 / Nucleocapsid protein p7 / NC / Transframe peptide / TF / p6-pol / p6* / Protease / PR / Retropepsin / Reverse transcriptase/ribonuclease H / Exoribonuclease H / p66 RT / p51 RT / p15 / Integrase / IN


Mass: 10740.677 Da / Num. of mol.: 2 / Fragment: UNP Residues 501-599 / Mutation: Q507K L533I L563I C567A C595A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 (BRU ISOLATE)
Gene: gag-pol / Plasmid: pET11A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P03367, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H
#2: Chemical ChemComp-079 / (S)-N-((2S,3S,4R,5R)-4-amino-3,5-dihydroxy-1,6-diphenylhexan-2-yl)-3-methyl-2-(2-phenoxyacetamido)butanamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 533.658 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H39N3O5
References: (S)-N-((2S,3S,4R,5R)-4-AMINO-3,5-DIHYDROXY-1,6-DIPHENYLHEXAN-2-YL)-3-METHYL-2-(2-PHENOXYACETAMIDO)BUTANAMIDE
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Compound detailsEPOXYDIC INHIBITOR

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: Ammonium sulfate 40%, DMSO 10%, sodium citrate 0.25M. pH has been increased through ammonia diffusion, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 11, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.116→42.26 Å / Num. all: 57890 / Num. obs: 69731 / % possible obs: 95.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 10.5
Reflection shellResolution: 1.116→1.17 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 2.9 / % possible all: 83.7

-
Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2NMZ

2nmz


Resolution: 1.116→42.26 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.083 / SU ML: 0.023 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.038 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21139 2796 4 %RANDOM
Rwork0.17683 ---
obs0.17822 66936 96.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.477 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å20 Å2
2--0.08 Å20 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.116→42.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 51 183 1746
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221624
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4862.0152202
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0045206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.55224.3453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.49615297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.082159
X-RAY DIFFRACTIONr_chiral_restr0.0950.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021156
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.2703
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21131
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2126
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3490.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5881.51035
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.18121628
X-RAY DIFFRACTIONr_scbond_it3.0163670
X-RAY DIFFRACTIONr_scangle_it4.464.5570
X-RAY DIFFRACTIONr_rigid_bond_restr1.58731705
X-RAY DIFFRACTIONr_sphericity_free5.9563183
X-RAY DIFFRACTIONr_sphericity_bonded3.83431594
LS refinement shellResolution: 1.116→1.145 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 179 -
Rwork0.308 4635 -
obs--91.59 %

+
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