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- PDB-6hpw: Crystal structure of ENL (MLLT1) in complex with compound 20 -

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Basic information

Entry
Database: PDB / ID: 6hpw
TitleCrystal structure of ENL (MLLT1) in complex with compound 20
ComponentsProtein ENL
KeywordsTRANSCRIPTION / YEATS domain / inhibitor complex / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / : / RNA Polymerase II Pre-transcription Events / transcription elongation factor complex / fibrillar center / chromatin binding / positive regulation of DNA-templated transcription / nucleoplasm / cytosol
Similarity search - Function
YEATS domain / AF-9, ANC1 homology domain / : / ANC1 homology domain (AHD) / : / YEATS superfamily / YEATS family / YEATS domain profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-GKT / Protein ENL
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHeidenreich, D. / Chaikuad, A. / Moustakim, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Brennan, P.E. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: J.Med.Chem. / Year: 2018
Title: Structure-Based Approach toward Identification of Inhibitory Fragments for Eleven-Nineteen-Leukemia Protein (ENL).
Authors: Heidenreich, D. / Moustakim, M. / Schmidt, J. / Merk, D. / Brennan, P.E. / Fedorov, O. / Chaikuad, A. / Knapp, S.
History
DepositionSep 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Apr 24, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein ENL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,28310
Polymers18,3121
Non-polymers9719
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint21 kcal/mol
Surface area8640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.738, 48.738, 131.623
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Protein ENL / YEATS domain-containing protein 1


Mass: 18312.080 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLLT1, ENL, LTG19, YEATS1 / Plasmid: pNIC-CH / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q03111
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GKT / 3-iodanyl-4-methyl-~{N}-[2-(piperidin-1-ylmethyl)-3~{H}-benzimidazol-5-yl]benzamide


Mass: 474.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C21H23IN4O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

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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: 2.13 Å3/Da / Density % sol: 42.37 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3350, 0.2M ammonium acetate, 0.1M bis-tris, pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→48.74 Å / Num. obs: 13292 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 30.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.034 / Net I/σ(I): 10.8
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.855 / Num. unique obs: 846 / CC1/2: 0.953 / Rpim(I) all: 0.257 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5j9s

5j9s


Resolution: 1.9→45.71 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.916 / SU B: 10.139 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28102 641 4.8 %RANDOM
Rwork0.21339 ---
obs0.21657 12580 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.073 Å2
Baniso -1Baniso -2Baniso -3
1--1.51 Å20 Å20 Å2
2---1.51 Å20 Å2
3---3.02 Å2
Refinement stepCycle: 1 / Resolution: 1.9→45.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1174 0 59 59 1292
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131270
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171182
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.6691704
X-RAY DIFFRACTIONr_angle_other_deg1.2421.6022740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0655143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.29421.12771
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.67715210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9811510
X-RAY DIFFRACTIONr_chiral_restr0.0780.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021473
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02285
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_it1.5552.126572
X-RAY DIFFRACTIONr_mcbond_other1.5522.12571
X-RAY DIFFRACTIONr_mcangle_it2.3823.179716
X-RAY DIFFRACTIONr_mcangle_other2.383.183716
X-RAY DIFFRACTIONr_scbond_it2.5272.586698
X-RAY DIFFRACTIONr_scbond_other2.5262.59699
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6093.689989
X-RAY DIFFRACTIONr_long_range_B_refined7.2125.7131306
X-RAY DIFFRACTIONr_long_range_B_other7.20925.6971306
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 41 -
Rwork0.292 929 -
obs--99.79 %
Refinement TLS params.Method: refined / Origin x: -1.138 Å / Origin y: -3.862 Å / Origin z: 12.73 Å
111213212223313233
T0.0088 Å2-0.0073 Å20.0029 Å2-0.0123 Å2-0.0037 Å2--0.2994 Å2
L2.7902 °2-1.17 °20.2686 °2-7.4027 °2-1.2013 °2--1.815 °2
S0.0893 Å °-0.1029 Å °-0.1182 Å °-0.1105 Å °-0.0191 Å °0.2782 Å °-0.0283 Å °-0.0204 Å °-0.0702 Å °

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