[English] 日本語
Yorodumi
- PDB-9tsm: ProteinMPNN mutated PF3D7_1475600 (PfBDP4-BRD, 77.8% sequence ide... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9tsm
TitleProteinMPNN mutated PF3D7_1475600 (PfBDP4-BRD, 77.8% sequence identity) in complex with GSK9311
ComponentsBromodomain protein, putative
KeywordsTRANSCRIPTION / plasmodium / bromodomain / inhibitor / complex / mutation
Function / homology: / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Chem-8VI / (R,R)-2,3-BUTANEDIOL / Bromodomain protein, putative
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsAmann, M. / Straesser, T. / Einsle, O. / Guenther, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)278002225 Germany
CitationJournal: Protein Sci. / Year: 2026
Title: Stabilizing Plasmodium falciparum proteins for small molecule drug discovery.
Authors: Amann, M. / Strasser, T. / Einsle, O. / Gunther, S.
History
DepositionDec 30, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bromodomain protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0334
Polymers14,4441
Non-polymers5903
Water5,783321
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint5 kcal/mol
Surface area7500 Å2
Unit cell
Length a, b, c (Å)37.408, 32.153, 60.426
Angle α, β, γ (deg.)90.00, 101.92, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Bromodomain protein, putative


Mass: 14443.724 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PF3D7_1475600 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IK82
#2: Chemical ChemComp-8VI / N-[1,3-dimethyl-6-[(2R)-2-methylpiperazin-1-yl]-2-oxidanylidene-benzimidazol-5-yl]-N-ethyl-2-methoxy-benzamide


Mass: 437.535 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H31N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 2, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.25→59.12 Å / Num. obs: 38945 / % possible obs: 99.3 % / Redundancy: 6 % / Biso Wilson estimate: 10.68 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.021 / Rrim(I) all: 0.052 / Χ2: 1 / Net I/σ(I): 20.8
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 5.5 / Num. unique obs: 1813 / CC1/2: 0.949 / Rpim(I) all: 0.128 / Rrim(I) all: 0.288 / Χ2: 0.71 / % possible all: 94.9

-
Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→29.56 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1313 1959 5.03 %
Rwork0.1089 --
obs0.11 38925 99.29 %
Refinement stepCycle: LAST / Resolution: 1.25→29.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms990 0 42 321 1353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122177
X-RAY DIFFRACTIONf_angle_d1.0823969
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.280.12571410.1142519X-RAY DIFFRACTION95
1.28-1.320.16091600.11222598X-RAY DIFFRACTION100
1.32-1.350.14031370.11052641X-RAY DIFFRACTION100
1.35-1.40.16371490.10852637X-RAY DIFFRACTION100
1.4-1.450.14231330.1092623X-RAY DIFFRACTION100
1.45-1.510.12921450.09622609X-RAY DIFFRACTION99
1.51-1.570.11061360.09342657X-RAY DIFFRACTION100
1.57-1.660.14511620.09362605X-RAY DIFFRACTION100
1.66-1.760.13691180.1022689X-RAY DIFFRACTION100
1.76-1.90.13351270.10552690X-RAY DIFFRACTION100
1.9-2.090.12821440.10232631X-RAY DIFFRACTION99
2.09-2.390.11431300.09892669X-RAY DIFFRACTION99
2.39-3.010.12261330.11472661X-RAY DIFFRACTION99
3.01-29.560.13571440.12262737X-RAY DIFFRACTION99

+
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