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- PDB-6hpx: Crystal structure of ENL (MLLT1) in complex with compound 19 -

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Basic information

Entry
Database: PDB / ID: 6hpx
TitleCrystal structure of ENL (MLLT1) in complex with compound 19
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-GKQ / Protein ENL
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHeidenreich, D. / Chaikuad, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / 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

Downloads & links

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Assembly

Deposited unit
A: Protein ENL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9436
Polymers18,3121
Non-polymers6315
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint12 kcal/mol
Surface area8740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.350, 48.350, 137.415
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.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GKQ / ~{N}-[(3-chlorophenyl)methyl]-1-(2-pyrrolidin-1-ylethyl)benzimidazole-5-carboxamide


Mass: 382.887 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23ClN4O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.19 Å3/Da / Density % sol: 43.91 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% medium molecular weight PEG smears, 0.1M citrate, 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: Jul 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→45.8 Å / Num. obs: 7846 / % possible obs: 100 % / Redundancy: 5.6 % / Biso Wilson estimate: 35.4 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.029 / Net I/σ(I): 15.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.169 / Num. unique obs: 719 / CC1/2: 0.982 / Rpim(I) all: 0.083 / % 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: 2.3→45.61 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.924 / SU B: 14.878 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.36 / ESU R Free: 0.252 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26086 390 5 %RANDOM
Rwork0.21137 ---
obs0.21372 7398 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.457 Å2
Baniso -1Baniso -2Baniso -3
1--1.42 Å20 Å20 Å2
2---1.42 Å20 Å2
3---2.83 Å2
Refinement stepCycle: 1 / Resolution: 2.3→45.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1178 0 43 29 1250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131262
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171156
X-RAY DIFFRACTIONr_angle_refined_deg1.2611.6581701
X-RAY DIFFRACTIONr_angle_other_deg1.1121.6062683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4655144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.66421.2572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63615208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2911510
X-RAY DIFFRACTIONr_chiral_restr0.0590.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021483
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02287
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_it1.6332.457577
X-RAY DIFFRACTIONr_mcbond_other1.6182.445575
X-RAY DIFFRACTIONr_mcangle_it2.6653.663720
X-RAY DIFFRACTIONr_mcangle_other2.6633.67721
X-RAY DIFFRACTIONr_scbond_it2.0462.827685
X-RAY DIFFRACTIONr_scbond_other2.0442.835686
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2924.133982
X-RAY DIFFRACTIONr_long_range_B_refined5.63829.0391307
X-RAY DIFFRACTIONr_long_range_B_other5.64129.0951308
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 24 -
Rwork0.201 517 -
obs--100 %
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)
11.3956-1.3872-0.40425.7766-0.80681.71630.1551-0.2002-0.1127-0.12940.14740.1667-0.06930.1181-0.30260.024-0.05320.00410.1737-0.05330.1134-2.6613-0.149713.9065
22.9826-3.72621.4376.6306-1.46210.77220.0617-0.23810.0146-0.30840.0261-0.2875-0.0361-0.1042-0.08780.0697-0.05010.08720.1817-0.06240.11092.1662-1.7488.403
36.7142-1.56-1.4823.96770.00673.752-0.0209-0.2491-0.31120.17880.09780.2290.09440.0475-0.07690.04290.0038-0.04150.08360.01750.09462.7218-22.317214.4038
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 91
2X-RAY DIFFRACTION2A92 - 121
3X-RAY DIFFRACTION3A122 - 144

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