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- PDB-9hhd: Crystal Structure of the Plasmodium falciparum Bromodomain PfBDP1... -

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Basic information

Entry
Database: PDB / ID: 9hhd
TitleCrystal Structure of the Plasmodium falciparum Bromodomain PfBDP1 in complex with RMM2
ComponentsBromodomain protein 1
KeywordsTRANSCRIPTION / plasmodium / bromodomain / inhibitor / complex
Function / homology
Function and homology information


Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. ...Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
: / Bromodomain protein 1
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsAmann, M. / Huegle, M. / Einsle, O. / Guenther, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)RTG2202 Germany
CitationJournal: Chemmedchem / Year: 2025
Title: A Novel Inhibitor against the Bromodomain Protein 1 of the Malaria Pathogen Plasmodium Falciparum.
Authors: Amann, M. / Warstat, R. / Rechten, K.K. / Theuer, P. / Schustereder, M. / Clavey, S. / Breit, B. / Einsle, O. / Hugle, M. / Petter, M. / Gunther, S.
History
DepositionNov 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0812
Polymers15,8271
Non-polymers2531
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7890 Å2
Unit cell
Length a, b, c (Å)38.447, 88.106, 108.046
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Bromodomain protein 1


Mass: 15827.206 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PF3D7_1033700 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IJ72
#2: Chemical ChemComp-A1IUZ / 3-methyl-1-(2-methylphenyl)-5,6,7,8-tetrahydro-2~{H}-cyclohepta[c]pyrrol-4-one


Mass: 253.339 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19NO / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.3 M LiSO4, 15% PEG3350, 0.1 M Tris pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.000033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000033 Å / Relative weight: 1
ReflectionResolution: 2.26→44.05 Å / Num. obs: 8932 / % possible obs: 99.7 % / Redundancy: 13.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.318 / Net I/σ(I): 8.7
Reflection shellResolution: 2.26→2.33 Å / Num. unique obs: 782 / CC1/2: 0.685 / Rpim(I) all: 0.748

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→44.05 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2493 441 4.94 %
Rwork0.2085 --
obs0.2106 8924 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.26→44.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1038 0 19 123 1180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071106
X-RAY DIFFRACTIONf_angle_d0.7931501
X-RAY DIFFRACTIONf_dihedral_angle_d17.189406
X-RAY DIFFRACTIONf_chiral_restr0.044162
X-RAY DIFFRACTIONf_plane_restr0.005192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.590.31481350.28332761X-RAY DIFFRACTION99
2.59-3.260.29261350.23382802X-RAY DIFFRACTION100
3.26-44.050.21741710.17672920X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.78490.0678-0.22374.4828-1.04434.203-0.4255-0.1592-0.46270.59530.31450.692-0.2359-1.01590.15420.2355-0.01030.00690.7486-0.13450.36353.2822-22.774-12.0902
25.0546-2.48622.27194.7837-1.8831.1947-0.48650.5405-0.303-0.7617-0.29560.08950.2028-0.26380.15090.507-0.06070.11360.4393-0.24540.534519.136-31.0165-23.7657
32.29030.95010.18730.4902-0.4052.6211-0.5904-0.2533-1.1479-0.3222-0.1342-0.43631.32810.94490.39360.71020.18960.21690.5737-0.03760.710428.1014-36.3665-13.5198
43.78180.896-0.76391.1026-0.12124.1702-0.3205-0.8135-0.28570.1664-0.01490.02580.2738-0.19810.27010.29150.020.02530.5076-0.04930.296819.1532-25.9531-8.652
52.9852-0.563-0.67390.11360.11382.0851-0.18460.0755-0.066-0.0087-0.00780.1385-0.0849-0.03940.24120.2578-0.0417-0.00720.3293-0.11180.33321.5799-21.7022-22.2066
60.8770.3663-1.66720.9710.30393.9803-0.0886-0.3931.0660.07450.3650.1369-1.2628-0.5131-0.01710.51160.251-0.06030.8352-0.45520.67695.6402-9.4373-6.3237
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 327 through 349 )
2X-RAY DIFFRACTION2chain 'A' and (resid 350 through 355 )
3X-RAY DIFFRACTION3chain 'A' and (resid 356 through 369 )
4X-RAY DIFFRACTION4chain 'A' and (resid 370 through 412 )
5X-RAY DIFFRACTION5chain 'A' and (resid 413 through 436 )
6X-RAY DIFFRACTION6chain 'A' and (resid 437 through 456 )

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