[English] 日本語
Yorodumi
- PDB-5con: X-ray crystal structure of wild type HIV-1 protease in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5con
TitleX-ray crystal structure of wild type HIV-1 protease in complex with GRL-015
ComponentsHIV-1 protease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / GRL-015 / HIV-1 protease / protease-inhibitor / darunavir / Tp-THF / nonpeptidic / hydroxyl / O-methoxy. / 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
Chem-52W / Pol protein / Pol protein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsYedidi, R.S. / Hayashi, H. / Aoki, M. / Das, D. / Ghosh, A.K. / Mitsuya, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: J.Virol. / Year: 2015
Title: C-5-Modified Tetrahydropyrano-Tetrahydofuran-Derived Protease Inhibitors (PIs) Exert Potent Inhibition of the Replication of HIV-1 Variants Highly Resistant to Various PIs, including Darunavir.
Authors: Aoki, M. / Hayashi, H. / Yedidi, R.S. / Martyr, C.D. / Takamatsu, Y. / Aoki-Ogata, H. / Nakamura, T. / Nakata, H. / Das, D. / Yamagata, Y. / Ghosh, A.K. / Mitsuya, H.
History
DepositionJul 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,1983
Polymers21,6062
Non-polymers5931
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-22 kcal/mol
Surface area9380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.786, 62.786, 81.907
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein HIV-1 protease /


Mass: 10802.771 Da / Num. of mol.: 2 / Fragment: UNP residues 1-99 / Mutation: D25N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli (E. coli) / References: UniProt: G0X8E3, UniProt: G0X8E8*PLUS
#2: Chemical ChemComp-52W / (3R,3aS,4S,7aS)-3-hydroxyhexahydro-4H-furo[2,3-b]pyran-4-yl [(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-phenylbutan-2-yl]carbamate / GRL-015


Mass: 592.701 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H40N2O9S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.16 Å3/Da / Density % sol: 43.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.3 / Details: 0.6 M sodium/potassium phosphate pH6.3

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 18426 / % possible obs: 99.4 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 54.46
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 5.9 / % possible all: 98.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4 Å45.3 Å
Translation4 Å45.3 Å

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
MOLREP10.2.35phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→31.393 Å / FOM work R set: 0.8053 / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.267 857 5.06 %
Rwork0.2206 16065 -
obs0.2229 16922 99.4 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.595 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso max: 70.96 Å2 / Biso mean: 27.21 Å2 / Biso min: 10.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.1042 Å20 Å20 Å2
2--0.1042 Å2-0 Å2
3----0.2085 Å2
Refinement stepCycle: final / Resolution: 1.8→31.393 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 82 144 1742
Biso mean--22.95 33.52 -
Num. residues----198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081630
X-RAY DIFFRACTIONf_angle_d1.2592214
X-RAY DIFFRACTIONf_chiral_restr0.079262
X-RAY DIFFRACTIONf_plane_restr0.006266
X-RAY DIFFRACTIONf_dihedral_angle_d17.482634
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.91280.29971430.24542666280999
1.9128-2.06040.32631420.23442653279599
2.0604-2.26770.2951400.245826702810100
2.2677-2.59570.31011450.252726612806100
2.5957-3.26980.28241510.232726822833100
3.2698-31.39780.21741360.190327332869100

+
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