[English] 日本語
Yorodumi
- PDB-1hef: The crystal structures at 2.2 angstroms resolution of hydroxyethy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hef
TitleThe crystal structures at 2.2 angstroms resolution of hydroxyethylene-based inhibitors bound to human immunodeficiency virus type 1 protease show that the inhibitors are present in two distinct orientations
Components
  • HIV-1 PROTEASE
  • SKF 108738 PEPTIDE INHIBITOR
KeywordsHYDROLASE/HYDROLASE INHIBITOR / 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 / 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 / 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 / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA 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
methyl N-{(2S,4S,5S)-5-[(L-alanyl-L-alanyl)amino]-2-benzyl-4-hydroxy-6-phenylhexanoyl}-L-valyl-L-valinate / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsMurthy, K. / Winborne, E.L. / Minnich, M.D. / Culp, J.S. / Debouck, C.
CitationJournal: J.Biol.Chem. / Year: 1992
Title: The crystal structures at 2.2-A resolution of hydroxyethylene-based inhibitors bound to human immunodeficiency virus type 1 protease show that the inhibitors are present in two distinct orientations.
Authors: Murthy, K.H. / Winborne, E.L. / Minnich, M.D. / Culp, J.S. / Debouck, C.
History
DepositionSep 21, 1992Processing site: BNL
Revision 1.0May 31, 1994Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Remark 300HIV-1 PROTEASE IS A SYMMETRIC DIMER, WHILE THE INHIBITOR IS AN ASYMMETRIC MOLECULE. FURTHERMORE, ...HIV-1 PROTEASE IS A SYMMETRIC DIMER, WHILE THE INHIBITOR IS AN ASYMMETRIC MOLECULE. FURTHERMORE, THE INHIBITOR IS SMALL ENOUGH TO BE ENTIRELY CONTAINED WITHIN THE ACTIVE SITE OF THE ENZYME AND, THEREFORE, DOES NOT CONTRIBUTE TO INTER-DIMER CONTACTS. THUS, OF THE TWO POSSIBLE ORIENTATIONS OF THE INHIBITOR, NEITHER IS THERMODYNAMICALLY PREFERRED. IN THE CRYSTAL STRUCTURE, THEREFORE, BOTH ARE REPRESENTED EQUALLY. THE ASYMMETRIC UNIT OF THE CRYSTAL THUS CONSISTS OF ONE PROTEASE MONOMER, AND ONE COPY OF EACH OF TWO POSSIBLE ORIENTATIONS OF THE INHIBITOR. EACH COPY OF THE INHIBITOR REPRESENTS HALF THE TOTAL OCCUPANCY FOR THE INHIBITOR.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: HIV-1 PROTEASE
I: SKF 108738 PEPTIDE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)11,4542
Polymers11,4542
Non-polymers00
Water41423
1
E: HIV-1 PROTEASE
I: SKF 108738 PEPTIDE INHIBITOR

E: HIV-1 PROTEASE
I: SKF 108738 PEPTIDE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)22,9094
Polymers22,9094
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+2/31
Unit cell
Length a, b, c (Å)63.070, 63.070, 83.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11E-100-

HOH

-
Components

#1: Protein HIV-1 PROTEASE /


Mass: 10786.663 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Production host: Escherichia coli (E. coli) / References: UniProt: P03366
#2: Protein/peptide SKF 108738 PEPTIDE INHIBITOR


Type: Peptide-like / Class: Inhibitor / Mass: 667.835 Da / Num. of mol.: 1 / Source method: obtained synthetically
References: methyl N-{(2S,4S,5S)-5-[(L-alanyl-L-alanyl)amino]-2-benzyl-4-hydroxy-6-phenylhexanoyl}-L-valyl-L-valinate
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS VARIANT OF THE HIV 1 PROTEASE HAS ASN AT THE POSITION 36 IN CHAIN E AS CONFIRMED BY INSPECTION ...THIS VARIANT OF THE HIV 1 PROTEASE HAS ASN AT THE POSITION 36 IN CHAIN E AS CONFIRMED BY INSPECTION OF THE ELECTRON DENSITY. SEE REFERENCES 14,15, AND 16 CITED IN J.BIOL.CHEM. V.267:22770, (1992).

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.08 %
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
114-24 %satammonium sulfate1reservoir
2200 mMacetate1reservoir
350 mMsodium acetate1drop
4200 mMsodium chloride1drop
55 mMdithiothreitol1drop
62 mMEDTA1drop
7protein-inhibitor complex1drop0.002ml

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.2→5 Å / σ(I): 2
Details: THE INHIBITOR ALA-ALA-PJJ-VAL-VME IS DISORDERED AROUND THE TWO-FOLD CYRSTALLOGRAPHIC AXIS. APPLICATION OF CRYSTALLOGRAPHIC SYMMETRY RESULTS IN THE OVERLAP OF THE TWO ORIENTATIONS. THE ...Details: THE INHIBITOR ALA-ALA-PJJ-VAL-VME IS DISORDERED AROUND THE TWO-FOLD CYRSTALLOGRAPHIC AXIS. APPLICATION OF CRYSTALLOGRAPHIC SYMMETRY RESULTS IN THE OVERLAP OF THE TWO ORIENTATIONS. THE OCCUPANCY OF EACH ORIENTATION IS 1/2.
RfactorNum. reflection
obs0.159 3649
Refinement stepCycle: LAST / Resolution: 2.2→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms806 0 0 23 829
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.025
X-RAY DIFFRACTIONp_angle_d0.0440.05
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0550.06
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.2190.2
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor1.72
X-RAY DIFFRACTIONp_staggered_tor23.715
X-RAY DIFFRACTIONp_orthonormal_tor3025
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.159
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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