[English] 日本語
Yorodumi
- PDB-6w6q: WT HTLV-1 Protease in Complex with Darunavir (DRV) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6w6q
TitleWT HTLV-1 Protease in Complex with Darunavir (DRV)
ComponentsHTLV-1 Protease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HTLV / PROTEASE / PROTEASE INHIBITOR / COMPLEX / HYDROLASE INHIBITOR COMPLEX / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
Chem-017 / Pro protein
Similarity search - Component
Biological speciesHuman T-cell leukemia virus type I
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLockbaum, G.J. / Henes, M. / Kosovrasti, K. / Nalivaika, E.A. / Ali, A. / KurtYilmaz, N. / Schiffer, C.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01-GM109767 United States
CitationJournal: To Be Published
Title: To Be Determined
Authors: Lockbaum, G.J. / Henes, M. / Kosovrasti, K. / Nalivaika, E.A. / Ali, A. / KurtYilmaz, N. / Schiffer, C.A.
History
DepositionMar 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: HTLV-1 Protease
A: HTLV-1 Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6813
Polymers25,1332
Non-polymers5481
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-35 kcal/mol
Surface area10220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.499, 78.499, 160.560
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11B-319-

HOH

-
Components

#1: Protein HTLV-1 Protease


Mass: 12566.579 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human T-cell leukemia virus type I / Gene: pro / Details (production host): pXC35 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Y1C9N2
#2: Chemical ChemComp-017 / (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE / Darunavir / TMC114 / UIC-94017


Mass: 547.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C27H37N3O7S / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 39-41% (v/v) PEG 300, 0.1M Phosphate/Citrate Buffer pH 4.2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.07812 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07812 Å / Relative weight: 1
ReflectionResolution: 2.1→42.1 Å / Num. obs: 17823 / % possible obs: 99.84 % / Redundancy: 9.1 % / Biso Wilson estimate: 55.16 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.09417 / Rpim(I) all: 0.03357 / Net I/σ(I): 12.61
Reflection shellResolution: 2.1→2.175 Å / Rmerge(I) obs: 1.996 / Mean I/σ(I) obs: 1.16 / Num. unique obs: 16621 / CC1/2: 0.366 / Rpim(I) all: 0.6757

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
Aimlessdata scaling
PHASERphasing
Coot0.8.8model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3wsj

3wsj


Resolution: 2.1→42.052 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2636 891 5 %
Rwork0.2291 16923 -
obs0.2308 17814 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 167.65 Å2 / Biso mean: 70.5757 Å2 / Biso min: 33.64 Å2
Refinement stepCycle: final / Resolution: 2.1→42.052 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1674 0 150 52 1876
Biso mean--78.24 71.05 -
Num. residues----232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061804
X-RAY DIFFRACTIONf_angle_d0.9072496
X-RAY DIFFRACTIONf_dihedral_angle_d4.4121241
X-RAY DIFFRACTIONf_chiral_restr0.05322
X-RAY DIFFRACTIONf_plane_restr0.004309
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.1-2.23160.36761440.33572742
2.2316-2.40390.34831440.31512733
2.4039-2.64570.31471460.25932768
2.6457-3.02850.29531480.24172807
3.0285-3.81520.25711470.23332831
3.8152-42.050.23941620.20563042

+
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