[English] 日本語
Yorodumi
- PDB-4gb2: HIV-1 protease (mutant Q7K L33I L63I) in complex with a bicyclic ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gb2
TitleHIV-1 protease (mutant Q7K L33I L63I) in complex with a bicyclic pyrrolidine inhibitor
ComponentsGag-Pol polyprotein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Dimer / ASPARTYL PROTEASE / INHIBITOR / 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 / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / RNA stem-loop binding / 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 / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane
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-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain ...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. / Retropepsin-like catalytic domain / RNase H type-1 domain profile. / Ribonuclease H domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Retroviral matrix protein / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Cathepsin D, subunit A; domain 1 / Acid Proteases / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-0LQ / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.788 Å
AuthorsStieler, M. / Heine, A. / Klebe, G.
CitationJournal: To be Published
Title: Cocrystallization of potent pyrrolidine based HIV-1 protease inhibitors
Authors: Stieler, M. / Klee, N. / Heine, A. / Doerr, S. / Diederich, W. / Klebe, G.
History
DepositionJul 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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)22,3888
Polymers21,6102
Non-polymers7786
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-49 kcal/mol
Surface area9290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.661, 86.637, 45.892
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
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: 10804.808 Da / Num. of mol.: 2 / Fragment: UNP residues 501-599 / Mutation: Q7K, L33I, L63I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 (BRU ISOLATE)
Gene: gag-pol / Plasmid: PET24A / Production host: Escherichia coli (E. coli)
References: UniProt: P03367, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-0LQ / (4aS,7aS)-1,4-bis(diphenylmethyl)hexahydro-1H-pyrrolo[3,4-b]pyrazine-2,3-dione


Mass: 487.592 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H29N3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.7 Å3/Da / Density % sol: 54.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100mM sodium citrate, 3 mM NaN3, 100 mM DTT, 1150 mM NaCl, pH 5.5, VAPOR, DIFFUSION, SITTING DROP, temperature 291K, VAPOR DIFFUSION, SITTING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 12, 2011 / Details: Mirrors
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR KMC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.78→25 Å / Num. all: 22404 / Num. obs: 22404 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 20.9 Å2 / Rsym value: 0.051 / Net I/σ(I): 29.4
Reflection shellResolution: 1.78→1.83 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 1831 / Rsym value: 0.479 / % possible all: 97.5

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QNN

2qnn


Resolution: 1.788→24.714 Å / SU ML: 0.42 / Cross valid method: R-free / σ(F): 1.34 / Phase error: 19.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1147 5.12 %random
Rwork0.1733 ---
obs0.1757 22381 98.18 %-
all-22381 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.76 Å2 / ksol: 0.342 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.8708 Å20 Å20 Å2
2--1.3626 Å2-0 Å2
3---1.5082 Å2
Refinement stepCycle: LAST / Resolution: 1.788→24.714 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1494 0 52 223 1769
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091586
X-RAY DIFFRACTIONf_angle_d1.442157
X-RAY DIFFRACTIONf_dihedral_angle_d15.931592
X-RAY DIFFRACTIONf_chiral_restr0.09258
X-RAY DIFFRACTIONf_plane_restr0.006269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7878-1.86910.27431420.22072473X-RAY DIFFRACTION94
1.8691-1.96760.21591410.18392620X-RAY DIFFRACTION98
1.9676-2.09090.20531380.17252623X-RAY DIFFRACTION99
2.0909-2.25220.2181360.16882629X-RAY DIFFRACTION99
2.2522-2.47870.25091620.1732629X-RAY DIFFRACTION99
2.4787-2.83690.25241650.18872652X-RAY DIFFRACTION99
2.8369-3.57240.22371240.17372741X-RAY DIFFRACTION99
3.5724-24.71650.1931390.16042867X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -13.8869 Å / Origin y: -17.0945 Å / Origin z: 3.6789 Å
111213212223313233
T0.0807 Å2-0.0001 Å2-0.016 Å2-0.0827 Å20.0372 Å2--0.0729 Å2
L1.329 °2-0.8208 °2-0.5499 °2-1.6152 °20.8742 °2--0.9038 °2
S-0.0228 Å °-0.0509 Å °-0.0123 Å °0.0912 Å °0.0399 Å °-0.0495 Å °0.0607 Å °-0.0042 Å °-0.0058 Å °
Refinement TLS groupSelection details: all

+
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