[English] 日本語
Yorodumi
- PDB-1m0b: HIV-1 protease in complex with an ethyleneamine inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1m0b
TitleHIV-1 protease in complex with an ethyleneamine inhibitor
ComponentsPROTEASE RETROPEPSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HIV PROTEASE / PEPTIDOMIMETICS / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / viral penetration into host nucleus / establishment of integrated proviral latency ...HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / viral penetration into host nucleus / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / 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 / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / 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. / 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 / 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
BOC-PHE-PSI[CH2CH2NH]-PHE-GLU-PHE-NH2 / Chem-0ZQ / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsPetrokova, H. / Hasek, J. / Dohnalek, J.
CitationJournal: Eur.J.Biochem. / Year: 2004
Title: Role of hydroxyl group and R/S configuration of isostere in binding properties of HIV-1 protease inhibitors
Authors: Petrokova, H. / Duskova, J. / Dohnalek, J. / Skalova, T. / Vondrackova-Buchtelova, E. / Soucek, M. / Konvalinka, J. / Brynda, J. / Fabry, M. / Sedlacek, J. / Hasek, J.
History
DepositionJun 12, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PROTEASE RETROPEPSIN
B: PROTEASE RETROPEPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3874
Polymers21,6082
Non-polymers7802
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-26 kcal/mol
Surface area8920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.700, 62.700, 82.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Cell settinghexagonal
Space group name H-MP61

-
Components

#1: Protein PROTEASE RETROPEPSIN / E.C.3.4.23.16 / HIV-1 PROTEASE


Mass: 10803.756 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P03367, HIV-1 retropepsin
#2: Chemical ChemComp-0ZQ / N-{(3S)-3-[(tert-butoxycarbonyl)amino]-4-phenylbutyl}-L-phenylalanyl-L-alpha-glutamyl-L-phenylalaninamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 687.825 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H49N5O7 / References: BOC-PHE-PSI[CH2CH2NH]-PHE-GLU-PHE-NH2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE INHIBITOR 0ZQ DOES NOT HAVE ANY HYDROXYL GROUP IN THE ISOSTERE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: citrate buffer, pH 4.6, NaCl, VAPOR DIFFUSION, HANGING DROP at 298K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
13 mg/mlprotein1drop
250 mMsodium acetate1droppH5.8
30.5 %(v/v)2-mercaptoethanol1drop
40.2-0.6 M1reservoirNaCl
50.1 Msodium citrate1reservoirpH4.5-5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9794 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1999
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.45→25 Å / Num. all: 6801 / Num. obs: 6765 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 14.4
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 3.6 / Num. unique all: 984 / % possible all: 98.7
Reflection
*PLUS
% possible obs: 99.2 % / Num. measured all: 42257 / Rmerge(I) obs: 0.091
Reflection shell
*PLUS
Lowest resolution: 2.51 Å / % possible obs: 98.5 % / Num. unique obs: 865 / Num. measured obs: 3548 / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 3.14

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→25 Å / Rfactor Rfree error: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 377 5.6 %RANDOM
Rwork0.178 ---
all0.181 6801 --
obs0.181 6765 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 84.943 Å2 / ksol: 0.376286 e/Å3
Displacement parametersBiso mean: 29.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error free: 0.27 Å / Luzzati sigma a free: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.45→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 56 153 1725
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.131.5
X-RAY DIFFRACTIONc_mcangle_it3.222
X-RAY DIFFRACTIONc_scbond_it32
X-RAY DIFFRACTIONc_scangle_it4.412.5
LS refinement shellResolution: 2.45→2.6 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.242 65 5.8 %
Rwork0.241 1053 -
obs--98.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2INH_ALL.PARINH_ALL_FREEBOC.TOP
X-RAY DIFFRACTION3WATER.PARAM
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor all: 0.18 / Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.11

+
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://pdbjlvh1.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