6t1m

Crystal structure of MLLT1 (ENL) YEATS domain in complexed with benzimidazole-amide derivative 4

Method: X-RAY DIFFRACTION D_max: 70.1 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein ENL

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–148	Not recorded	M8K 4-cyano-~{N}-[2-(piperidin-1-ylmethyl)-1~{H}-benzimidazol-5-yl]benzamide × 1 EDO 1,2-ETHANEDIOL × 7	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；25% PEG 3350, 0.2M sodium chloride, 0.1M bis-tris pH 5.5	Resolution 1.85 Å R-free 0.275

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6T1M	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5J9S ENL YEATS in complex with histone H3 acetylation at K27 Deposited 2016-04-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–148（148 aa） Fragment：UNP residues 1-148	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1M K/Na Tartrate, 0.1M Sodium citrate tribasic dihydrate, pH 5.6, 2M (NH4)2SO4	Resolution 2.70 Å R-free 0.210
6HPW Crystal structure of ENL (MLLT1) in complex with compound 20 Deposited 2018-09-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–148（148 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 8 GKT 3-iodanyl-4-methyl-~{N}-[2-(piperidin-1-ylmethyl)-3~{H}-benzimidazol-5-yl]benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；25% PEG 3350, 0.2M ammonium acetate, 0.1M bis-tris, pH 5.5	Resolution 1.90 Å R-free 0.281
6HPX Crystal structure of ENL (MLLT1) in complex with compound 19 Deposited 2018-09-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–148（148 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 4 GKQ ~{N}-[(3-chlorophenyl)methyl]-1-(2-pyrrolidin-1-ylethyl)benzimidazole-5-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；25% medium molecular weight PEG smears, 0.1M citrate, pH 5.5	Resolution 2.30 Å R-free 0.261
6HPY Crystal structure of ENL (MLLT1) in complex with compound 12 Deposited 2018-09-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–148（148 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 3 SO4 SULFATE ION × 1 GKN 3-[4-[(4-~{tert}-butylphenyl)carbonylamino]phenyl]propanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；25% PEG 3350, 0.2M ammonium sulfate, 0.1M bis-tris, pH 5.5	Resolution 2.00 Å R-free 0.260
6HPZ Crystal structure of ENL (MLLT1) in complex with acetyllysine Deposited 2018-09-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–148（148 aa） Fragment：YEATS domain	Not recorded	EDO 1,2-ETHANEDIOL × 2 ALY N(6)-ACETYLLYSINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；25% PEG 1500	Resolution 2.30 Å R-free 0.296
6HQ0 Crystal structure of ENL (MLLT1), apo form Deposited 2018-09-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–148（148 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；30% PEG 2000MME, 0.1M KBr	Resolution 1.81 Å R-free 0.237
6HT0 Crystal structure of MLLT1 (ENL) YEATS domain in complexed with compound 94 Deposited 2018-10-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–148（148 aa）	Not recorded	SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 8 GQ8 1-cyclopropyl-~{N}-[2-[[(2~{S})-2-methylpyrrolidin-1-yl]methyl]-3~{H}-benzimidazol-5-yl]indazole-5-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；25% PEG3350, 0.2M ammonium sulfate, 0.1M bis-tris pH 5.5 or 25% PEG Smear Medi-um, 0.1M citrate pH 5.5	Resolution 1.80 Å R-free 0.230
6HT1 Crystal structure of MLLT1 (ENL) YEATS domain in complexed with SGC-iMLLT (compound 92) Deposited 2018-10-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–148（148 aa）	Not recorded	SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 7 GQ5 1-methyl-~{N}-[2-[[(2~{S})-2-methylpyrrolidin-1-yl]methyl]-3~{H}-benzimidazol-5-yl]indazole-5-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；25% PEG3350, 0.2M ammonium sulfate, 0.1M bis-tris pH 5.5 or 25% PEG Smear Medi-um, 0.1M citrate pH 5.5	Resolution 2.10 Å R-free 0.252
6T1I Crystal structure of MLLT1 (ENL) YEATS domain in complexed with piperazine-urea derivative 1 Deposited 2019-10-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–148（148 aa）	Not recorded	M7W 4-(4-ethanoylphenyl)-~{N}-[(6-methoxypyridin-3-yl)methyl]piperazine-1-carboxamide × 1 EDO 1,2-ETHANEDIOL × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；25% PEG 3350, 0.2 M sodium chloride, 0.1 M bis-tris pH 6.5	Resolution 1.80 Å R-free 0.232
6T1J Crystal structure of MLLT1 (ENL) YEATS domain in complexed with piperazine-urea derivative 2 Deposited 2019-10-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–148（148 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 7 M7T ~{N}-[[4-(pyrrolidin-1-ylmethyl)phenyl]methyl]-4-thiophen-2-ylcarbonyl-piperazine-1-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；25% PEG 3350, 0.2M sodium chloride, 0.1M bis-tris pH 6.5	Resolution 1.97 Å R-free 0.275
6T1L Crystal structure of MLLT1 (ENL) YEATS domain in complexed with piperazine-urea derivative 3 Deposited 2019-10-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–148（148 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 10 M7N ~{N}-[[4-(diethylaminomethyl)phenyl]methyl]-4-pyrimidin-2-yl-piperazine-1-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；25% PEG 3350, 0.2M sodium chloride, 0.1 M bis-tris pH 6.5	Resolution 2.00 Å R-free 0.265
6T1N Crystal structure of MLLT1 (ENL) YEATS domain in complexed with benzimidazole-amide derivative 5 Deposited 2019-10-04	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–148（148 aa）	Not recorded	M7Z 4-chloranyl-~{N}-[2-(piperidin-1-ylmethyl)-3~{H}-benzimidazol-5-yl]benzamide × 1 EDO 1,2-ETHANEDIOL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；25% PEG 3350, 0.2M sodium chloride, 0.1M bis-tris pH 5.5	Resolution 1.95 Å R-free 0.266
6T1O Crystal structure of MLLT1 (ENL) YEATS domain in complexed with benzimidazole-amide derivative 6 Deposited 2019-10-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–148（148 aa）	Not recorded	M82 4-iodanyl-~{N}-[2-(piperidin-1-ylmethyl)-3~{H}-benzimidazol-5-yl]benzamide × 1 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；25% PEG 3350, 0.2M sodium chloride, 0.1M HEPES pH 7.5	Resolution 1.90 Å R-free 0.251
7B0T Crystal structure of MLLT1 YEATS domain T3 mutant in complex with benzimidazole-amide based compound 1 Deposited 2020-11-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomer	Chain A 1–148（148 aa）	Not recorded	GKT 3-iodanyl-4-methyl-~{N}-[2-(piperidin-1-ylmethyl)-3~{H}-benzimidazol-5-yl]benzamide × 1 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；28% PEG 3350, 0.2M NaOAc, 0.1M Bis-Tris, pH6.0	Resolution 2.05 Å R-free 0.276
7B10 Crystal structure of MLLT1 YEATS domain T1 mutant in complex with benzimidazole-amide based compound 1 Deposited 2020-11-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomer	Chain A 1–148（148 aa）	Not recorded	GKT 3-iodanyl-4-methyl-~{N}-[2-(piperidin-1-ylmethyl)-3~{H}-benzimidazol-5-yl]benzamide × 1 IOD IODIDE ION × 1 EDO 1,2-ETHANEDIOL × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；25% w/v PEG 3350, 0.1M Bis-Tris, pH 5.5	Resolution 1.92 Å R-free 0.209
7E74 Crystal structure of ENL YEATS domain T3 mutant in complex with histone H3 acetylation at K27 Deposited 2021-02-25	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–148（148 aa）	Mutation：N111K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2M sodium formate, 0.1M sodium acetate trihydrate pH 4.6	Resolution 2.90 Å R-free 0.248
7E74 Crystal structure of ENL YEATS domain T3 mutant in complex with histone H3 acetylation at K27 Deposited 2021-02-25	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–148（148 aa）	Mutation：N111K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2M sodium formate, 0.1M sodium acetate trihydrate pH 4.6	Resolution 2.90 Å R-free 0.248
7E74 Crystal structure of ENL YEATS domain T3 mutant in complex with histone H3 acetylation at K27 Deposited 2021-02-25	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–148（148 aa）	Mutation：N111K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2M sodium formate, 0.1M sodium acetate trihydrate pH 4.6	Resolution 2.90 Å R-free 0.248
7E74 Crystal structure of ENL YEATS domain T3 mutant in complex with histone H3 acetylation at K27 Deposited 2021-02-25	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–148（148 aa）	Mutation：N111K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2M sodium formate, 0.1M sodium acetate trihydrate pH 4.6	Resolution 2.90 Å R-free 0.248
7E7A Crystal structure of apo ENL YEATS domain T3 mutant Deposited 2021-02-25	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–148（148 aa）	Mutation：N111K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2M sodium formate, 0.1M sodium acetate trihydrate pH 4.6	Resolution 2.64 Å R-free 0.230
7E7A Crystal structure of apo ENL YEATS domain T3 mutant Deposited 2021-02-25	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–148（148 aa）	Mutation：N111K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2M sodium formate, 0.1M sodium acetate trihydrate pH 4.6	Resolution 2.64 Å R-free 0.230
7E7A Crystal structure of apo ENL YEATS domain T3 mutant Deposited 2021-02-25	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–148（148 aa）	Mutation：N111K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2M sodium formate, 0.1M sodium acetate trihydrate pH 4.6	Resolution 2.64 Å R-free 0.230
7E7A Crystal structure of apo ENL YEATS domain T3 mutant Deposited 2021-02-25	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–148（148 aa）	Mutation：N111K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2M sodium formate, 0.1M sodium acetate trihydrate pH 4.6	Resolution 2.64 Å R-free 0.230
7E7C Crystal structure of ENL YEATS domain T1 mutant in complex with histone H3 acetylation at K27 Deposited 2021-02-25	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–148（148 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2 IOD IODIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；25% PEG 4000, 0.1M MES pH 6.5, 0.2M Potassium iodide	Resolution 1.84 Å R-free 0.251
7X88 Crystal structure of ENL YEATS domain T2 mutant in complex with histone H3 acetylation at K27 Deposited 2022-03-11	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–148（148 aa）	Mutation：Deletion 112-113, V114L	CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；291 K；20% (w/v) PE G3350, 0.1M sodium citrate/citric acid pH 4.0, 0.2M sodium citrate tribasic	Resolution 2.25 Å R-free 0.240
7X8B Crystal structure of ENL T1 mutant YEATS domain in complex with histone H3 acetylation at K27 Deposited 2022-03-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–148（148 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20 % (w/v) PEG 4000, 0.1M sodium citrate pH5.6, 20 % (v/v) 2-propanol	Resolution 2.30 Å R-free 0.226
7X8B Crystal structure of ENL T1 mutant YEATS domain in complex with histone H3 acetylation at K27 Deposited 2022-03-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–148（148 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20 % (w/v) PEG 4000, 0.1M sodium citrate pH5.6, 20 % (v/v) 2-propanol	Resolution 2.30 Å R-free 0.226
7X8F Crystal structure of ENL T4 mutant YEATS domain in complex with histone H3 acetylation at K27 Deposited 2022-03-12	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–148（148 aa）	Mutation：insertions	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；291 K；20 % (w/v) PEG 4000, 0.1 M sodium citrate pH 5.6, 20 % (v/v) 2-propanol	Resolution 2.44 Å R-free 0.252
7X8F Crystal structure of ENL T4 mutant YEATS domain in complex with histone H3 acetylation at K27 Deposited 2022-03-12	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–148（148 aa）	Mutation：insertions	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；291 K；20 % (w/v) PEG 4000, 0.1 M sodium citrate pH 5.6, 20 % (v/v) 2-propanol	Resolution 2.44 Å R-free 0.252
7X8G Crystal structure of ENL T1(H116P) mutant YEATS domain in complex with histone H3 acetylation at K27 Deposited 2022-03-12	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–148（148 aa）	Mutation：insertions	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；291 K；20 % (w/v) PEG 4000, 0.1M sodium citrate pH 5.6, 20 % (v/v) 2-propanol	Resolution 1.91 Å R-free 0.230
7X8G Crystal structure of ENL T1(H116P) mutant YEATS domain in complex with histone H3 acetylation at K27 Deposited 2022-03-12	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–148（148 aa）	Mutation：insertions	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；291 K；20 % (w/v) PEG 4000, 0.1M sodium citrate pH 5.6, 20 % (v/v) 2-propanol	Resolution 1.91 Å R-free 0.230
8PJI MLLT1 in complex with compound 10a Deposited 2023-06-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–148（148 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2 DMS DIMETHYL SULFOXIDE × 1 ZJF ~{N}-cyclopentyl-1-(3-hydroxyphenyl)imidazole-4-carboxamide × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Bis-Tris pH=7.0 150 mM AmSO4 Gradient 20-30% PEG3350	Resolution 1.70 Å R-free 0.277
9DUR Cryo-EM Structure of CRBN:dHTC1:ENL YEATS Deposited 2024-10-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–148（148 aa） Fragment：YEATS domain	Not recorded	ZN ZINC ION × 1 A1IQT 2-[3-[2-[4-[[(5~{S})-1,3-bis(oxidanylidene)-2,7-diazaspiro[4.4]nonan-7-yl]sulfonylamino]piperidin-1-yl]ethylcarbamoyl]phenyl]-~{N}-cyclobutyl-imidazo[1,2-a]pyridine-6-carboxamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；30 mM HEPES/NaOH pH7.4, 150 mM NaCl. DMSO concentrations were kept below 2% (v/v) cryo-EM vitrification conditions Cryogen ETHANE；Grids were vitrified using a Leica EM GP plunge freezer operated at 90% humidity and 10 C. Grids were first pre-incubated with 4 uL of 10 uM CRBN-agnostic IKZF1_140-196_Q146A,G151N for 1 minute and then blotted from behind for 4 s. Immediately, 4 uL of mixturewas applied to the grids before blotting for 4 s and plunging into liquid ethane at -181 C	Resolution 2.90 Å
9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–146（145 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0	Resolution 2.60 Å R-free 0.267
9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 10 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 2–146（145 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0	Resolution 2.60 Å R-free 0.267
9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 11 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 2–146（145 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0	Resolution 2.60 Å R-free 0.267
9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 12 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 2–146（145 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0	Resolution 2.60 Å R-free 0.267
9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 13 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 2–146（145 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0	Resolution 2.60 Å R-free 0.267
9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 14 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain N 2–146（145 aa）	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0	Resolution 2.60 Å R-free 0.267
9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 15 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain O 2–146（145 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0	Resolution 2.60 Å R-free 0.267
9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 16 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 2–146（145 aa）	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0	Resolution 2.60 Å R-free 0.267
9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–146（145 aa）	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0	Resolution 2.60 Å R-free 0.267
9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2–146（145 aa）	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0	Resolution 2.60 Å R-free 0.267
9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 2–146（145 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0	Resolution 2.60 Å R-free 0.267
9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 2–146（145 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0	Resolution 2.60 Å R-free 0.267
9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 2–146（145 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0	Resolution 2.60 Å R-free 0.267
9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 2–146（145 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0	Resolution 2.60 Å R-free 0.267
9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 2–146（145 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0	Resolution 2.60 Å R-free 0.267
9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 9 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 2–146（145 aa）	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0	Resolution 2.60 Å R-free 0.267

25 other PDB entries and 49 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ENL_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–148； UniProt 1–148

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6t1m
Deposition date deposition_date	2019-10-04
Structure title title	Crystal structure of MLLT1 (ENL) YEATS domain in complexed with benzimidazole-amide derivative 4
Keywords keywords	TRANSCRIPTION, YEATS domain, ENL, MLLT1, chemical probe, inhibitor, Structural Genomics, Structural Genomics Consortium, SGC; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	18.34 Å
Radius of gyration Rg (electron density) rg_electron	17.35 Å
Forward intensity I(0) i0	5558180.00
Molecular weight molecular_weight	17488.0 kDa
Excluded volume excluded_volume	22039 Å³
Envelope volume envelope_volume	25755 Å³
Hydration-shell volume shell_volume	13368 Å³
Envelope diameter envelope_diameter	69.8 Å
Shell Rg shell_rg	22.43 Å
Envelope Rg envelope_rg	18.04 Å
Shape Rg shape_rg	17.32 Å
Total Rg total_rg	18.33 Å
Total atoms total_atoms	1232
Residues n_residues	142
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	70.1 Å
Rg (real space) rg_real	18.47 Å
Rg uncertainty (real space) rg_real_error	0.63 Å
I(0) (real space) i0_real	5.5580e+06
I(0) uncertainty (real space) i0_real_error	7.6380e+04
Rg (reciprocal space) rg_reciprocal	18.45 Å
I(0) (reciprocal space) i0_reciprocal	5558000.0000
Solution quality estimate total_estimate	0.7853
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.9 Å
Skewness Skewness skewness	0.574
Kurtosis Kurtosis kurtosis	0.011
Angular range angular_range	— – 0.4350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1355000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.507; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.693; Smooth: 0.992

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Protein ENL
Molecular weight formula_weight	18225.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1288

MDNQCTVQVRLELGHRAQLRKKPTTEGFTHDWMVFVRGPEQCDIQHFVEKVVFWLHDSFPKPRRVCKEPPYKVEESGYAGFIMPIEVHFKNKEEPRKVCFTYDLFLNLEGNPPVNHLRCEKLTFNNPTTEFRYKLLRAGGVMVMPEGAHHHHHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	4-cyano-~{N}-[2-(piperidin-1-ylmethyl)-1~{H}-benzimidazol-5-yl]benzamide
Molecular weight formula_weight	359.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	48

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6t1mA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1970 — YEATS domain

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8. Citations (1)

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Unit-cell length a length_a	49.069 Å
Unit-cell length b length_b	49.069 Å
Unit-cell length c length_c	129.992 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	45.910 Å
R factor r_factor	0.2181
R_work r_work	0.2152
R_free r_free	0.2745

fit	/app/data/saxs_computation/t1/6t1m/6t1m.fit
pddf	/app/data/pr_computation/t1/6t1m/6t1m.pr.out
profile	/app/data/saxs_computation/t1/6t1m/6t1m.dat