[English] 日本語
Yorodumi
- PDB-3dcr: X-ray structure of HIV-1 protease and hydrated form of ketomethyl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3dcr
TitleX-ray structure of HIV-1 protease and hydrated form of ketomethylene isostere inhibitor
ComponentsChemical analogue HIV-1 protease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HIV-1 protease / homodimer / beta-turn / beta-strand / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Retropepsin-like catalytic domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily ...Retropepsin-like catalytic domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
N~2~-[(2R,5S)-5-({(2S,3S)-2-[(N-acetyl-L-threonyl)amino]-3-methylpent-4-enoyl}amino)-2-butyl-4,4-dihydroxynonanoyl]-L-glutaminyl-L-argininamide / Chem-KVS / Protease
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsTorbeev, V.Y. / Mandal, K. / Terechko, V.A. / Kent, S.B.H.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2008
Title: Crystal structure of chemically synthesized HIV-1 protease and a ketomethylene isostere inhibitor based on the p2/NC cleavage site
Authors: Torbeev, V.Y. / Mandal, K. / Terechko, V.A. / Kent, S.B.H.
History
DepositionJun 4, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 16, 2013Group: Non-polymer description
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0Aug 7, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / entity / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.type / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Nov 1, 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_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chemical analogue HIV-1 protease
B: Chemical analogue HIV-1 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3223
Polymers21,5212
Non-polymers8011
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-23 kcal/mol
Surface area10010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.200, 58.077, 61.658
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Chemical analogue HIV-1 protease


Mass: 10760.625 Da / Num. of mol.: 2 / Fragment: HIV-1 protease / Source method: obtained synthetically
Details: total chemical protein synthesis utilizing solid phase peptide synthesis and native chemical ligation
References: UniProt: O38732*PLUS, HIV-1 retropepsin
#2: Chemical ChemComp-KVS / N~2~-[(2R,5S)-5-({(2S,3S)-2-[(N-acetyl-L-threonyl)amino]-3-methylpent-4-enoyl}amino)-2-butyl-4,4-dihydroxynonanoyl]-L-glutaminyl-L-argininamide


Type: Peptide-like / Class: Inhibitor / Mass: 800.986 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H68N10O10
References: N~2~-[(2R,5S)-5-({(2S,3S)-2-[(N-acetyl-L-threonyl)amino]-3-methylpent-4-enoyl}amino)-2-butyl-4,4-dihydroxynonanoyl]-L-glutaminyl-L-argininamide
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE OF ENTITY 1 WAS BASED ON UNP DB CODE POL_HV1A2, ACCESSION P03369, RESIDUES 491-589.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.21 % / Mosaicity: 0.645 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M CITRATE, 0.2M SODIUM PHOPHATE, 30% (W/V) AMMONIUM SULFATE, 10% (V/V) DMSO, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 26, 2007
Details: Si(111) Double Crystal Monochrometer. Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 37058 / Num. obs: 37029 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.084 / Χ2: 1.565 / Net I/σ(I): 32
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 6.3 / Num. unique all: 3623 / Χ2: 1.861 / % possible all: 99.9

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
Locallymodified Blu-Ice GUI interface to EPICS controldata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4HVP

4hvp


Resolution: 1.4→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.925 / SU B: 1.883 / SU ML: 0.038 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1846 5 %RANDOM
Rwork0.204 ---
obs0.204 36899 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.995 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å20 Å2
2---0.25 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1518 0 56 113 1687
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221598
X-RAY DIFFRACTIONr_bond_other_d0.0010.021089
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.9972160
X-RAY DIFFRACTIONr_angle_other_deg0.90532681
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1655197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.27725.08857
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.0415283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.947158
X-RAY DIFFRACTIONr_chiral_restr0.1020.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021690
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02281
X-RAY DIFFRACTIONr_nbd_refined0.3390.2227
X-RAY DIFFRACTIONr_nbd_other0.1980.21042
X-RAY DIFFRACTIONr_nbtor_refined0.1690.2742
X-RAY DIFFRACTIONr_nbtor_other0.0870.2840
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.267
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1210.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.170.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.27
X-RAY DIFFRACTIONr_mcbond_it1.2641.51031
X-RAY DIFFRACTIONr_mcbond_other0.3381.5416
X-RAY DIFFRACTIONr_mcangle_it1.85821634
X-RAY DIFFRACTIONr_scbond_it2.7153634
X-RAY DIFFRACTIONr_scangle_it4.0914.5526
LS refinement shellResolution: 1.398→1.434 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 124 -
Rwork0.276 2510 -
all-2634 -
obs--97.45 %
Refinement TLS params.Method: refined / Origin x: -4.914 Å / Origin y: 1.1888 Å / Origin z: -18.0563 Å
111213212223313233
T-0.0096 Å2-0.0096 Å20.0083 Å2--0.0402 Å2-0.0033 Å2---0.0542 Å2
L0.8592 °20.1397 °20.2131 °2-0.8442 °2-0.2519 °2--0.6302 °2
S0.0206 Å °-0.0618 Å °0.0007 Å °-0.071 Å °0.0007 Å °-0.0016 Å °0.0646 Å °-0.0588 Å °-0.0213 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 991 - 99
2X-RAY DIFFRACTION1BC1011 - 6
3X-RAY DIFFRACTION1BB1 - 991 - 99

+
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