[English] 日本語
Yorodumi
- PDB-7ve2: Crystal Structure of Lopinavir bound Plasmepsin II (PMII) from Pl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ve2
TitleCrystal Structure of Lopinavir bound Plasmepsin II (PMII) from Plasmodium falciparum
ComponentsPlasmepsin II
KeywordsHYDROLASE / Inhibitor / Protease / Peptidomimetic / HIV-1 protease inhibitor / peptidase / hemoglobin degrader
Function / homology
Function and homology information


MHC class II antigen presentation / hemoglobin catabolic process / cytostome / plasmepsin II / Neutrophil degranulation / vacuolar lumen / food vacuole / vacuolar membrane / aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Pepsin-like domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
Chem-AB1 / Plasmepsin II
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsMishra, V. / Rathore, I. / Bhaumik, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)Ramalingaswami Re-entry Fellowship India
Citation
Journal: Curr Res Struct Biol / Year: 2024
Title: Inhibition of Plasmodium falciparum plasmepsins by drugs targeting HIV-1 protease: A way forward for antimalarial drug discovery.
Authors: Mishra, V. / Deshmukh, A. / Rathore, I. / Chakraborty, S. / Patankar, S. / Gustchina, A. / Wlodawer, A. / Yada, R.Y. / Bhaumik, P.
#1: Journal: Biorxiv / Year: 2023
Title: Molecular insights into the inhibition of plasmepsins by HIV-1 protease inhibitors: Implications for antimalarial drug discovery.
Authors: Mishra, V. / Rathore, I. / Bhaumik, P.
History
DepositionSep 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Mar 6, 2024Group: Database references / Category: citation / citation_author

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Plasmepsin II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9724
Polymers37,1141
Non-polymers1,8593
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-4 kcal/mol
Surface area14820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.940, 108.940, 70.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

-
Components

#1: Protein Plasmepsin II /


Mass: 37113.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PF3D7_1408000 / Plasmid: pET32b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami B(DE3)pLysS / References: UniProt: Q8I6V3, plasmepsin II
#2: Chemical ChemComp-AB1 / N-{1-BENZYL-4-[2-(2,6-DIMETHYL-PHENOXY)-ACETYLAMINO]-3-HYDROXY-5-PHENYL-PENTYL}-3-METHYL-2-(2-OXO-TETRAHYDRO-PYRIMIDIN-1-YL)-BUTYRAMIDE / ABT-378 / LOPINAVIR / Lopinavir


Mass: 628.801 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H48N4O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: antiretroviral, protease inhibitor*YM
#3: Chemical ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS / CHAPS detergent


Mass: 614.877 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 1.4 M ammonium sulfate, 0.1 M Bis-Tris pH 5.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→38.52 Å / Num. obs: 6877 / % possible obs: 99.9 % / Redundancy: 7.54 % / Biso Wilson estimate: 87.22 Å2 / CC1/2: 0.99 / Net I/σ(I): 9.95
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 7.57 % / Mean I/σ(I) obs: 1.04 / Num. unique obs: 602 / CC1/2: 0.37 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YIC

5yic


Resolution: 3.2→38.52 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.912 / SU B: 83.027 / SU ML: 0.637 / Cross valid method: THROUGHOUT / ESU R Free: 0.561 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26617 344 5 %RANDOM
Rwork0.22459 ---
obs0.2268 6531 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 127.423 Å2
Baniso -1Baniso -2Baniso -3
1-5.26 Å2-0 Å2-0 Å2
2--5.26 Å2-0 Å2
3----10.53 Å2
Refinement stepCycle: 1 / Resolution: 3.2→38.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2606 0 130 0 2736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0132813
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172625
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.6413847
X-RAY DIFFRACTIONr_angle_other_deg1.11.5736082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2625328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.21724.504131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.90815437
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.205153
X-RAY DIFFRACTIONr_chiral_restr0.0570.2378
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023096
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02614
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.374.9951315
X-RAY DIFFRACTIONr_mcbond_other1.374.9941314
X-RAY DIFFRACTIONr_mcangle_it2.4237.4881642
X-RAY DIFFRACTIONr_mcangle_other2.4237.4891643
X-RAY DIFFRACTIONr_scbond_it1.5265.7741498
X-RAY DIFFRACTIONr_scbond_other1.5225.7511496
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7248.642206
X-RAY DIFFRACTIONr_long_range_B_refined6.98498.47911258
X-RAY DIFFRACTIONr_long_range_B_other6.98598.49411259
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 24 -
Rwork0.368 455 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -32.853 Å / Origin y: -13.005 Å / Origin z: 13.987 Å
111213212223313233
T0.0423 Å2-0.1485 Å2-0.0473 Å2-0.5863 Å20.1322 Å2--1.344 Å2
L4.8121 °23.6665 °20.8592 °2-5.4686 °20.3776 °2--2.9266 °2
S-0.0028 Å °-0.5038 Å °0.5395 Å °-0.1372 Å °-0.0022 Å °1.2695 Å °0.3161 Å °-1.2567 Å °0.005 Å °

+
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