5dtm

Crystal structure of Dot1L in complex with inhibitor CPD1 [4-(2,6-dichlorobenzoyl)-N-methyl-1H-pyrrole-2-carboxamide]

Method: X-RAY DIFFRACTION D_max: 101.4 Å Quality: GOOD

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1. 蛋白身份与相关结构 Protein Identity & Related Structures

Histone-lysine N-methyltransferase, H3 lysine-79 specific

Homo sapiens

当前结构中的状态

Assembly	聚集状态	构建体	突变与修饰	配体、离子与共同组分	实验方法与环境	结构质量
1	蛋白单体单体蛋白 × 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 A； UniProt 2–332	未记录	5F4 4-(2,6-dichlorobenzoyl)-N-methyl-1H-pyrrole-2-carboxamide × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION；293 K；1.0M K/Na tartrate 0.1M Hepes pH6.8	分辨率 2.20 Å R-free 0.199
2	蛋白单体单体蛋白 × 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 B； UniProt 2–332	未记录	5F4 4-(2,6-dichlorobenzoyl)-N-methyl-1H-pyrrole-2-carboxamide × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION；293 K；1.0M K/Na tartrate 0.1M Hepes pH6.8	分辨率 2.20 Å R-free 0.199

数据库中的同蛋白其他状态

以下每一行都是同一 UniProt 蛋白在另一个 PDB 条目中的 biological assembly， “相对当前条目”直接指出证据层面的不同；没有差异标签表示当前已读取字段一致。

其他 PDB	相对当前条目 5DTM	Assembly / 聚集状态	构建体	突变与修饰	配体、离子与非聚合物	实验方法与环境	结构质量
1NW3 Structure of the Catalytic domain of human DOT1L, a non-SET domain nucleosomal histone methyltransferase 提交 2003-02-05	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–416（416 aa）	未记录	ACT ACETATE ION × 1 SO4 SULFATE ION × 2 SAM S-ADENOSYLMETHIONINE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 4.6；290 K；Ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K	分辨率 2.50 Å R-free 0.246
2MV7 Solution NMR structure of DOT1L in complex with AF9 (DOT1L-AF9) 提交 2014-09-24	构建体不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 B 877–900（24 aa）片段：UNP RESIDUES 877-900	未记录	未记录非水小分子	SOLUTION NMR NMR测量条件 pH 6；298 K；离子强度（mmCIF原始值）100；压力 AMBIENT NMR样品组成 750 uM [U-100% 13C; U-100% 15N] PROTEIN AF, 750 uM [U-100% 13C; U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC, 9.3 mM BIS-TRIS, 15.8 mM MES, 100 mM SODIUM CHLORIDE, 1 mM DTT, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR样品组成 750 mM [U-100% 13C; U-100% 15N] PROTEIN AF, 750 mM [U-100% 13C; U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC, 9.3 mM BIS-TRIS, 15.8 mM MES, 100 mM SODIUM CHLORIDE, 1 mM DTT, 3.5 % (3-ACRYLAMIDOPROPYL)-TRIMETHYLAMMONIUM CHLORIDE, 3.5 % ACRYLIC ACID, 750 mM [U-100% 13C; U-100% 15N] PROTEIN AF, 750 mM [U-100% 13C; U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC, 9.3 mM BIS-TRIS, 15.8 mM MES, 100 mM SODIUM CHLORIDE, 1 mM DTT, 3.5 % (3-ACRYLAMIDOPROPYL)-TRIMETHYLAMMONIUM CHLORIDE, 3.5 % ACRYLAMIDE, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR样品组成 750 mM [U-100% 13C; U-100% 15N] PROTEIN AF, 750 mM [U-100% 13C; U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC, 9.3 mM BIS-TRIS, 15.8 mM MES, 100 mM SODIUM CHLORIDE, 1 mM DTT, 3.5 % (3-ACRYLAMIDOPROPYL)-TRIMETHYLAMMONIUM CHLORIDE, 3.5 % ACRYLIC ACID, 750 mM [U-100% 13C; U-100% 15N] PROTEIN AF, 750 mM [U-100% 13C; U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC, 9.3 mM BIS-TRIS, 15.8 mM MES, 100 mM SODIUM CHLORIDE, 1 mM DTT, 3.5 % (3-ACRYLAMIDOPROPYL)-TRIMETHYLAMMONIUM CHLORIDE, 3.5 % ACRYLAMIDE, 95% H2O/5% D2O \| 95% H2O/5% D2O	分辨率未提供
3QOW DOT1L Structure in complex with SAM 提交 2011-02-11	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–416（416 aa）片段：UNP residues 1-416	未记录	SAM S-ADENOSYLMETHIONINE × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；2 M Ammonium Sulfate, 0.1 M Sodium Acetate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 2.10 Å R-free 0.192
3QOX DOT1L structure in complex with SAH 提交 2011-02-11	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–416（416 aa）片段：UNP residues 1-416	未记录	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 5.3；291 K；2 M Ammonium Sulfate, 2 mM TCEP, 0.1 M Sodium Acetate, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 2.30 Å R-free 0.252
3SR4 Crystal Structure of Human DOT1L in Complex with a Selective Inhibitor 提交 2011-07-06	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–351（351 aa）片段：CATALYTIC DOMAIN OF HDOT1L (UNP residues 1-351)	未记录	TT8 (2S)-2-azanyl-4-[[(2S,3S,4R,5R)-5-[6-(methylamino)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl]butanoic acid × 1 GOL GLYCEROL × 1 ACT ACETATE ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 5.3；295 K；PROTEIN SOLUTION: 20 mM Tris, pH 8.0, 200 mM NaCl, 1 mM EDTA, 10% glycerol, 3 mM inhibitor, 3 mM TCEP. RESERVOIR SOLUTION: 0.1 M HAC, pH 5.3, 1.25-1.7 M (NH4)2SO4. , VAPOR DIFFUSION, HANGING DROP, temperature 295K	分辨率 2.50 Å R-free 0.274
3SX0 Crystal structure of Dot1l in complex with a brominated SAH analog 提交 2011-07-14	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–420（420 aa）片段：sequence database residues 1-420	未记录	SX0 (2S)-2-amino-4-({[(2S,3S,4R,5R)-5-(4-amino-5-bromo-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}sulfanyl)butanoic acid (non-preferred name) × 1 SO4 SULFATE ION × 1 UNX UNKNOWN LIGAND × 20	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；pH 4.6；291 K；1.5 M ammonium sulfate, 0.1 M sodium acetate, 0.0015 M ligand, pH 4.6, vapor diffusion, temperature 291K, VAPOR DIFFUSION	分辨率 2.28 Å R-free 0.228
3UWP Crystal structure of Dot1l in complex with 5-iodotubercidin 提交 2011-12-02	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–420（420 aa）片段：UNP Residues 1-420	未记录	5ID (2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL × 1 IOD IODIDE ION × 2 NA SODIUM ION × 1 UNX UNKNOWN LIGAND × 6	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；pH 4.6；291 K；3.5M sodium formate, 0.1M sodium acetate, pH 4.6, vapor diffusion, temperature 291K	分辨率 2.05 Å R-free 0.223
4EK9 Crystal structure of DOT1L in complex with EPZ000004 提交 2012-04-09	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–416（416 aa）片段：UNP residues 1-416	未记录	EP4 5'-deoxy-5'-(dimethylamino)adenosine × 1 SO4 SULFATE ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；100 mM Sodium Acetate, 1.8-2.0 M Ammonium Sulfate, 5 mM TCEP, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 2.50 Å R-free 0.263
4EKG Crystal Structure of DOT1L in Complex with EPZ003696 提交 2012-04-09	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–416（416 aa）片段：UNP residues 1-416	未记录	0QJ 5'-[(3-{[(4-tert-butylphenyl)carbamoyl]amino}propyl)(methyl)amino]-5'-deoxyadenosine × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；100 mM Sodium Acetate, 1.8-2.0 M Ammonium Sulfate, 5 mM TCEP, pH 5.2, soaking the compound into cross-linked DOT1L-SAM crystal, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 2.80 Å R-free 0.261
4EKI Crystal Structure of DOT1L in complex with EPZ004777 提交 2012-04-09	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–416（416 aa）片段：UNP residues 1-416	未记录	0QK 7-{5-[(3-{[(4-tert-butylphenyl)carbamoyl]amino}propyl)(propan-2-yl)amino]-5-deoxy-beta-D-ribofuranosyl}-7H-pyrrolo[2,3-d]pyrimidin-4-amine × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；100 mM Sodium Acetate, 1.8-2.0 M Ammonium Sulfate, 5 mM TCEP, pH 5.2, compound soaked into cross-linked DOT1L-SAM crystal, temperature 293K, VAPOR DIFFUSION, HANGING DROP	分辨率 2.85 Å R-free 0.262
4EQZ Crystal structure of human DOT1L in complex with inhibitor FED2 提交 2012-04-19	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–420（420 aa）	未记录	AW0 5'-deoxy-5'-[(3-{[(4-methylphenyl)carbamoyl]amino}propyl)(propan-2-yl)amino]adenosine × 1 UNX UNKNOWN LIGAND × 6	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；3.5 M NaFormate, 0.1 M NaAcet, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 2.15 Å R-free 0.221
4ER0 Crystal Structure of human DOT1L in complex with inhibitor FED1 提交 2012-04-19	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–420（420 aa）	未记录	AW1 5'-[(3-{[(4-tert-butylphenyl)carbamoyl]amino}propyl)(propan-2-yl)amino]-5'-deoxyadenosine × 1 UNX UNKNOWN LIGAND × 3	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；3.5 M NaFormate, 0.1 M NaAcet, 0.5 mM inhibitor in H2O, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 2.50 Å R-free 0.272
4ER3 Crystal Structure of Human DOT1L in complex with inhibitor EPZ004777 提交 2012-04-19	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–351（351 aa）	未记录	0QK 7-{5-[(3-{[(4-tert-butylphenyl)carbamoyl]amino}propyl)(propan-2-yl)amino]-5-deoxy-beta-D-ribofuranosyl}-7H-pyrrolo[2,3-d]pyrimidin-4-amine × 1 SO4 SULFATE ION × 5 EDO 1,2-ETHANEDIOL × 2 UNX UNKNOWN LIGAND × 6	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；1.6M (NH4)2SO4, 0.01M MgCl2, 0.1M NaCaCo, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 2.40 Å R-free 0.282
4ER5 Crystal structure of human DOT1L in complex with 2 molecules of EPZ004777 提交 2012-04-19	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–412（412 aa）	未记录	0QK 7-{5-[(3-{[(4-tert-butylphenyl)carbamoyl]amino}propyl)(propan-2-yl)amino]-5-deoxy-beta-D-ribofuranosyl}-7H-pyrrolo[2,3-d]pyrimidin-4-amine × 2 UNX UNKNOWN LIGAND × 5	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；3.5 M NaFormate, 0.1 M NaAcet, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 2.57 Å R-free 0.218
4ER6 Crystal structure of human DOT1L in complex with inhibitor SGC0946 提交 2012-04-19	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–412（412 aa）	未记录	BR BROMIDE ION × 1 AW2 5-bromo-7-{5-[(3-{[(4-tert-butylphenyl)carbamoyl]amino}propyl)(propan-2-yl)amino]-5-deoxy-beta-D-ribofuranosyl}-7H-pyrrolo[2,3-d]pyrimidin-4-amine × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；3.5 M NaFormate, 0.1 M NaAcet, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 2.30 Å R-free 0.230
4ER7 Crystal Structure of human DOT1L in complex with inhibitor SGC0947 提交 2012-04-19	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–420（420 aa）	未记录	AW3 5-bromo-7-{5-[(3-{[(4-tert-butylphenyl)carbamoyl]amino}propyl)amino]-5-deoxy-beta-D-ribofuranosyl}-7H-pyrrolo[2,3-d]pyrimidin-4-amine × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；3.5 M NaFormate, 0.1 M NaAcet, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 2.20 Å R-free 0.242
4HRA Crystal Structure of DOT1L in Complex with EPZ-5676 提交 2012-10-26	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–416（416 aa）片段：UNP residues 1-416	未记录	EP6 5'-[{cis-3-[2-(5-tert-butyl-1H-benzimidazol-2-yl)ethyl]cyclobutyl}(propan-2-yl)amino]-5'-deoxyadenosine × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；100 MM SODIUM ACETATE, 1.8-2.0 M AMMONIUM SULFATE, 5 MM TCEP, SOAKING THE COMPOUND INTO CROSS-LINKED DOT1L-SAM CRYSTAL, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 3.15 Å R-free 0.256
4WVL Structure-Guided DOT1L Probe Optimization by Label-Free Ligand Displacement 提交 2014-11-06	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–347（347 aa）	未记录	3US N-[4-(acetylamino)butyl]-5'-[(3-{[(4-tert-butylphenyl)carbamoyl]amino}propyl)(propan-2-yl)amino]-5'-deoxyadenosine × 1 SO4 SULFATE ION × 3 GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 4.9；293 K；A 5-fold excess of 50 mM 5-iodotubercidin (in DMSO) was mixed with protein and crystallized by using the hanging-drop vapor diffusion method at 20 degree in conditions containing 1.8 M (NH4)2SO4, 0.1 M NaAc-pH4.9. Crystals were transferred into stabilization buffer (2.5 M (NH4)2SO4, 0.1 M NaAc-pH4.9, 0.5 M NaCl), incubated with 100 uM inhibitor.	分辨率 2.41 Å R-free 0.197
5DRT Crystal structure of Dot1L in complex with inhibitor CPD2 [2-(2-(5-((2-chlorophenoxy)methyl)-1H-tetrazol-1-yl)acetyl)-N-(4-chlorophenyl)hydrazinecarboxamide] 提交 2015-09-16	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 2–333（332 aa）片段：UNP residues 2-333	未记录	5EG 2-({5-[(2-chlorophenoxy)methyl]-1H-tetrazol-1-yl}acetyl)-N-(4-chlorophenyl)hydrazinecarboxamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；293 K；1.3M K/Na tartrate 0.1M Hepes pH7.2	分辨率 2.69 Å R-free 0.197
5DRT Crystal structure of Dot1L in complex with inhibitor CPD2 [2-(2-(5-((2-chlorophenoxy)methyl)-1H-tetrazol-1-yl)acetyl)-N-(4-chlorophenyl)hydrazinecarboxamide] 提交 2015-09-16	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 2–333（332 aa）片段：UNP residues 2-333	未记录	5EG 2-({5-[(2-chlorophenoxy)methyl]-1H-tetrazol-1-yl}acetyl)-N-(4-chlorophenyl)hydrazinecarboxamide × 1 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；293 K；1.3M K/Na tartrate 0.1M Hepes pH7.2	分辨率 2.69 Å R-free 0.197
5DRY Crystal structure of Dot1L in complex with inhibitor CPD3 [N-(1-(2-chlorophenyl)-1H-indol-6-yl)-2-(2-(5-(2-chlorophenyl)-1H-tetrazol-1-yl)acetyl)hydrazinecarboxamide] 提交 2015-09-16	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 2–333（332 aa）片段：UNP residues 2-333	未记录	K POTASSIUM ION × 1 5EK N-[1-(2-chlorophenyl)-1H-indol-6-yl]-2-{[5-(2-chlorophenyl)-1H-tetrazol-1-yl]acetyl}hydrazinecarboxamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；293 K；1.2M K/Na tartrate 0.1M Hepes pH7.2	分辨率 2.41 Å R-free 0.199
5DRY Crystal structure of Dot1L in complex with inhibitor CPD3 [N-(1-(2-chlorophenyl)-1H-indol-6-yl)-2-(2-(5-(2-chlorophenyl)-1H-tetrazol-1-yl)acetyl)hydrazinecarboxamide] 提交 2015-09-16	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 2–333（332 aa）片段：UNP residues 2-333	未记录	K POTASSIUM ION × 1 5EK N-[1-(2-chlorophenyl)-1H-indol-6-yl]-2-{[5-(2-chlorophenyl)-1H-tetrazol-1-yl]acetyl}hydrazinecarboxamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；293 K；1.2M K/Na tartrate 0.1M Hepes pH7.2	分辨率 2.41 Å R-free 0.199
5DSX Crystal structure of Dot1L in complex with inhibitor CPD10 [6'-chloro-1,4-dimethyl-5'-(2-methyl-6-((4-(methylamino)pyrimidin-2-yl)amino)-1H-indol-1-yl)-[3,3'-bipyridin]-2(1H)-one] 提交 2015-09-17	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 2–332（331 aa）片段：UNP residues 2-332	未记录	K POTASSIUM ION × 1 5EW 6'-chloro-1,4-dimethyl-5'-(2-methyl-6-{[4-(methylamino)pyrimidin-2-yl]amino}-1H-indol-1-yl)-3,3'-bipyridin-2(1H)-one × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；293 K；1.4M K/Na tartrate tetrahydrate, 0.1M Hepes pH6.8	分辨率 2.41 Å R-free 0.202
5DSX Crystal structure of Dot1L in complex with inhibitor CPD10 [6'-chloro-1,4-dimethyl-5'-(2-methyl-6-((4-(methylamino)pyrimidin-2-yl)amino)-1H-indol-1-yl)-[3,3'-bipyridin]-2(1H)-one] 提交 2015-09-17	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 2–332（331 aa）片段：UNP residues 2-332	未记录	K POTASSIUM ION × 1 5EW 6'-chloro-1,4-dimethyl-5'-(2-methyl-6-{[4-(methylamino)pyrimidin-2-yl]amino}-1H-indol-1-yl)-3,3'-bipyridin-2(1H)-one × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；293 K；1.4M K/Na tartrate tetrahydrate, 0.1M Hepes pH6.8	分辨率 2.41 Å R-free 0.202
5DT2 Crystal structure of Dot1L in complex with inhibitor CPD11 [N4-methyl-N2-(2-methyl-1-(2-phenoxyphenyl)-1H-indol-6-yl)pyrimidine-2,4-diamine] 提交 2015-09-17	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 2–332（331 aa）片段：UNP residues 2-332	未记录	5EV N~4~-methyl-N~2~-[2-methyl-1-(2-phenoxyphenyl)-1H-indol-6-yl]pyrimidine-2,4-diamine × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；293 K；1.4M lithium sulfate 0.1M sodium citrate tribasic dihydrate 0.3M ammonium sulfate	分辨率 2.30 Å R-free 0.213
5DT2 Crystal structure of Dot1L in complex with inhibitor CPD11 [N4-methyl-N2-(2-methyl-1-(2-phenoxyphenyl)-1H-indol-6-yl)pyrimidine-2,4-diamine] 提交 2015-09-17	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 2–332（331 aa）片段：UNP residues 2-332	未记录	5EV N~4~-methyl-N~2~-[2-methyl-1-(2-phenoxyphenyl)-1H-indol-6-yl]pyrimidine-2,4-diamine × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；293 K；1.4M lithium sulfate 0.1M sodium citrate tribasic dihydrate 0.3M ammonium sulfate	分辨率 2.30 Å R-free 0.213
5DTQ Crystal structure of Dot1L in complex with inhibitor CPD3 [(2,6-dichlorophenyl)(quinolin-6-yl)methanone] 提交 2015-09-18	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 2–332（331 aa）	未记录	5F6 (2,6-dichlorophenyl)(quinolin-6-yl)methanone × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；293 K；1.6M K/Na tartrate, 0.1M Hepes pH6.6	分辨率 2.61 Å R-free 0.208
5DTQ Crystal structure of Dot1L in complex with inhibitor CPD3 [(2,6-dichlorophenyl)(quinolin-6-yl)methanone] 提交 2015-09-18	配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 2–332（331 aa）	未记录	5F6 (2,6-dichlorophenyl)(quinolin-6-yl)methanone × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；293 K；1.6M K/Na tartrate, 0.1M Hepes pH6.6	分辨率 2.61 Å R-free 0.208
5DTR Crystal structure of Dot1L in complex with inhibitor CPD5 [N-(2,6-dichlorophenyl)-4-methoxy-N-methylquinolin-6-amine] 提交 2015-09-18	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 2–332（331 aa）	未记录	5F7 N-(2,6-dichlorophenyl)-4-methoxy-N-methylquinolin-6-amine × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；293 K；1.2M K/Na tartrate, 0.1M Hepes pH6.6	分辨率 2.34 Å R-free 0.210
5DTR Crystal structure of Dot1L in complex with inhibitor CPD5 [N-(2,6-dichlorophenyl)-4-methoxy-N-methylquinolin-6-amine] 提交 2015-09-18	配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 2–332（331 aa）	未记录	5F7 N-(2,6-dichlorophenyl)-4-methoxy-N-methylquinolin-6-amine × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；293 K；1.2M K/Na tartrate, 0.1M Hepes pH6.6	分辨率 2.34 Å R-free 0.210
5JUW complex of Dot1l with SS148 提交 2016-05-10	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–420（420 aa）片段：UNP residues 1-420	未记录	UNX UNKNOWN LIGAND × 22 6NR (2~{S})-2-azanyl-4-[[(2~{S},3~{S},4~{R},5~{R})-5-(4-azanyl-5-cyano-pyrrolo[2,3-d]pyrimidin-7-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl]butanoic acid × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；1.5 M ammonium sulfate, 0.1 M ammonium acetate	分辨率 2.28 Å R-free 0.215
5MVS Crystal structure of Dot1L in complex with adenosine and inhibitor CPD1 [N6-(2,6-dichlorophenyl)-N6-(pent-2-yn-1-yl)quinoline-4,6-diamine] 提交 2017-01-17	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 2–332（331 aa）链 B 2–332（331 aa）	未记录	ADN ADENOSINE × 2 5JJ N~6~-(2,6-dichlorophenyl)-N~6~-(pent-2-yn-1-yl)quinoline-4,6-diamine × 2 TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；293 K；1.4M K/Na tartrate, 0.1M Hepes pH6.8	分辨率 2.18 Å R-free 0.187
5MW3 Crystal structure of Dot1L in complex with inhibitor CPD1 [N6-(2,6-dichlorophenyl)-N6-(pent-2-yn-1-yl)quinoline-4,6-diamine] and inhibitor CPD2 [(R)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-3-amine] 提交 2017-01-18	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 2–332（331 aa）	未记录	5JJ N~6~-(2,6-dichlorophenyl)-N~6~-(pent-2-yn-1-yl)quinoline-4,6-diamine × 1 5JT (3R)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-3-amine × 1 TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；293 K；1.4M K/Na tartrate, 0.1M Hepes pH6.6	分辨率 2.09 Å R-free 0.193
5MW3 Crystal structure of Dot1L in complex with inhibitor CPD1 [N6-(2,6-dichlorophenyl)-N6-(pent-2-yn-1-yl)quinoline-4,6-diamine] and inhibitor CPD2 [(R)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-3-amine] 提交 2017-01-18	配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 2–332（331 aa）	未记录	5JJ N~6~-(2,6-dichlorophenyl)-N~6~-(pent-2-yn-1-yl)quinoline-4,6-diamine × 1 5JT (3R)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-3-amine × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；293 K；1.4M K/Na tartrate, 0.1M Hepes pH6.6	分辨率 2.09 Å R-free 0.193
5MW4 Crystal structure of Dot1L in complex with inhibitor CPD7 [N-(3-(((R)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-3-yl)(methyl)amino)propyl)-2-(3-(2-chloro-3-(2-methylpyridin-3-yl)benzo[b]thiophen-5-yl)ureido)acetamide] 提交 2017-01-18	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 2–332（331 aa）	未记录	5JU N~2~-{[2-chloro-3-(2-methylpyridin-3-yl)-1-benzothiophen-5-yl]carbamoyl}-N-(3-{methyl[(3R)-1-(5H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-3-yl]amino}propyl)glycinamide × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；293 K；0.92M Lithium sulfate monohydrate, 0.1M Ammonium sulfate, 0.1M Sodium citrate tribasic dihydrate	分辨率 2.19 Å R-free 0.202
5MW4 Crystal structure of Dot1L in complex with inhibitor CPD7 [N-(3-(((R)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-3-yl)(methyl)amino)propyl)-2-(3-(2-chloro-3-(2-methylpyridin-3-yl)benzo[b]thiophen-5-yl)ureido)acetamide] 提交 2017-01-18	配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 2–332（331 aa）	未记录	5JU N~2~-{[2-chloro-3-(2-methylpyridin-3-yl)-1-benzothiophen-5-yl]carbamoyl}-N-(3-{methyl[(3R)-1-(5H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-3-yl]amino}propyl)glycinamide × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；293 K；0.92M Lithium sulfate monohydrate, 0.1M Ammonium sulfate, 0.1M Sodium citrate tribasic dihydrate	分辨率 2.19 Å R-free 0.202
6IN3 Crystal structure of DOT1L in complex with 18-Crown-6 提交 2018-10-24	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 4–330（327 aa）	未记录	O4B 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；293 K；1.8 M ammonium sulfate, 22 mM acetic acid, 78 mM sodium acetate	分辨率 2.30 Å R-free 0.213
6J99 Cryo-EM structure of human DOT1L in complex with an H2B-monoubiquitinated nucleosome 提交 2019-01-22	构建体不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 异源复合物；蛋白 × 10 PDB 声明：dodecameric	链 K 1–416（416 aa）	未记录	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 7.5 cryo-EM玻璃化条件冷冻剂 ETHANE	分辨率 4.10 Å
6JM9 cryo-EM structure of DOT1L bound to unmodified nucleosome 提交 2019-03-07	构建体不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 异源复合物；蛋白 × 9 PDB 声明：undecameric	链 X 5–332（328 aa）	未记录	SAM S-ADENOSYLMETHIONINE × 1	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 7.5 cryo-EM玻璃化条件冷冻剂 ETHANE	分辨率 7.30 Å
6JMA cryo-EM structure of DOT1L bound to H2B ubiquitinated nucleosome 提交 2019-03-07	构建体不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 异源复合物；蛋白 × 10 PDB 声明：dodecameric	链 X 5–332（328 aa）	未记录	SAM S-ADENOSYLMETHIONINE × 1	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 7.5 cryo-EM玻璃化条件冷冻剂 ETHANE	分辨率 6.80 Å
6JN2 Crystal structure of the coiled-coil domains of human DOT1L in complex with AF10 提交 2019-03-13	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 8 PDB 声明：octameric	链 B 470–550（81 aa）	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 4.8；289 K；0.1 M SODIUM ACETATE PH 4.8, 0.3 M KSCN, 8% V/V PENTAERYTHRITOL ETHOXYLATE (3/4 EO/OH),	分辨率 3.60 Å R-free 0.381
6NJ9 Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 2-to-1 complex 提交 2019-01-02	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 异源复合物；蛋白 × 12 PDB 声明：tetradecameric	链 K 2–416（415 aa）链 M 2–416（415 aa）	未记录	SAM S-ADENOSYLMETHIONINE × 2	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 7.5；Solutions were prepared on the day of freezing and filtered though a 0.2 um filter prior to use. cryo-EM玻璃化条件冷冻剂 ETHANE；Blot once for 3.5 seconds before freezing.	分辨率 2.96 Å
6NN6 Structure of Dot1L-H2BK120ub nucleosome complex 提交 2019-01-14	构建体不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 异源复合物；蛋白 × 10 PDB 声明：dodecameric	链 K 3–416（414 aa）	未记录	未记录非水小分子	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 7.5 cryo-EM玻璃化条件冷冻剂 ETHANE	分辨率 3.90 Å
6NOG Poised-state Dot1L bound to the H2B-Ubiquitinated nucleosome 提交 2019-01-16	构建体不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 异源复合物；蛋白 × 10 PDB 声明：dodecameric	链 K 2–416（415 aa）	未记录	未记录非水小分子	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 7.5；Solutions were prepared on the day of freezing and filtered though a 0.2 um filter prior to use. cryo-EM玻璃化条件冷冻剂 ETHANE；Blot once for 3.5 seconds before freezing	分辨率 3.90 Å
6NQA Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 1-to-1 complex 提交 2019-01-19	构建体不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 异源复合物；蛋白 × 10 PDB 声明：dodecameric	链 K 2–416（415 aa）	未记录	SAM S-ADENOSYLMETHIONINE × 1	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 7.5；Solutions were prepared on the day of freezing and filtered though a 0.2 um filter prior to use. cryo-EM玻璃化条件冷冻剂 ETHANE；Blot once for 3.5 seconds before freezing.	分辨率 3.54 Å
6O96 Dot1L bound to the H2BK120 Ubiquitinated nucleosome 提交 2019-03-13	聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 异源复合物；蛋白 × 10 PDB 声明：dodecameric	链 K 2–332（331 aa）	未记录	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 7 cryo-EM玻璃化条件冷冻剂 PROPANE；blotted for 3s before plunging	分辨率 3.50 Å
6TE6 Crystal structure of Dot1L in complex with an inhibitor (compound 3). 提交 2019-11-11	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 2–332（331 aa）	未记录	N4W ~{N}1-[(~{S})-(3-chlorophenyl)-pyridin-2-yl-methyl]-4-methylsulfonyl-~{N}2-pyrimidin-2-yl-benzene-1,2-diamine × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；293 K；1.28 M Na/K-tartrate 0.1 M Hepes pH 6.6	分辨率 1.98 Å R-free 0.201
6TE6 Crystal structure of Dot1L in complex with an inhibitor (compound 3). 提交 2019-11-11	配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 2–332（331 aa）	未记录	N4W ~{N}1-[(~{S})-(3-chlorophenyl)-pyridin-2-yl-methyl]-4-methylsulfonyl-~{N}2-pyrimidin-2-yl-benzene-1,2-diamine × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；293 K；1.28 M Na/K-tartrate 0.1 M Hepes pH 6.6	分辨率 1.98 Å R-free 0.201
6TEL Crystal structure of Dot1L in complex with an inhibitor (compound 10). 提交 2019-11-12	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 2–332（331 aa）	未记录	N4Z ~{N}1-[(~{S})-[2,2-bis(fluoranyl)-1,3-benzodioxol-4-yl]-(3-chloranylpyridin-2-yl)methyl]-~{N}2-(4-methoxy-6-piperazin-1-yl-1,3,5-triazin-2-yl)-4-methylsulfonyl-benzene-1,2-diamine × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；293 K；1.28 M K/Na tartrate 0.1 M Hepes pH 7.0	分辨率 2.19 Å R-free 0.212
6TEL Crystal structure of Dot1L in complex with an inhibitor (compound 10). 提交 2019-11-12	配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 2–332（331 aa）	未记录	N4Z ~{N}1-[(~{S})-[2,2-bis(fluoranyl)-1,3-benzodioxol-4-yl]-(3-chloranylpyridin-2-yl)methyl]-~{N}2-(4-methoxy-6-piperazin-1-yl-1,3,5-triazin-2-yl)-4-methylsulfonyl-benzene-1,2-diamine × 1 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；293 K；1.28 M K/Na tartrate 0.1 M Hepes pH 7.0	分辨率 2.19 Å R-free 0.212
6TEN Crystal structure of Dot1L in complex with an inhibitor (compound 11). 提交 2019-11-12	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 2–332（331 aa）	未记录	N5K 3-[(4-azanyl-6-methoxy-1,3,5-triazin-2-yl)amino]-4-[[(~{S})-[2,2-bis(fluoranyl)-1,3-benzodioxol-4-yl]-(3-chloranylpyridin-2-yl)methyl]amino]benzenesulfonamide × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；293 K；1.5 M Li sulfate 0.1 M Hepes pH 7.0	分辨率 2.21 Å R-free 0.201
6TEN Crystal structure of Dot1L in complex with an inhibitor (compound 11). 提交 2019-11-12	配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 2–332（331 aa）	未记录	N5K 3-[(4-azanyl-6-methoxy-1,3,5-triazin-2-yl)amino]-4-[[(~{S})-[2,2-bis(fluoranyl)-1,3-benzodioxol-4-yl]-(3-chloranylpyridin-2-yl)methyl]amino]benzenesulfonamide × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；293 K；1.5 M Li sulfate 0.1 M Hepes pH 7.0	分辨率 2.21 Å R-free 0.201
7BWD Structure of Dot1L-H2BK34ub Nucleosome Complex 提交 2020-04-14	构建体不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 异源复合物；蛋白 × 11 PDB 声明：tridecameric	链 K 1–416（416 aa）	未记录	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 8 cryo-EM玻璃化条件冷冻剂 ETHANE-PROPANE	分辨率 4.32 Å
7EDP Crystal structure of AF10-DOT1L complex 提交 2021-03-16	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 B 610–649（40 aa）	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；293 K；25% Ethylene glycol	分辨率 2.20 Å R-free 0.268
7S7E STRUCTURE OF HLA-B*07:02 IN COMPLEX WITH DOT1L(998-1006) PEPTIDE 提交 2021-09-15	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合异源复合物；蛋白 × 3 PDB 声明：trimeric	链 C 998–1006（9 aa）片段：DOT1L(998-1006) PEPTIDE	未记录	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；290 K；18-24% PEG4000, 0.1 SODIUM CITRATE, 20% ISOPROPANOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE	分辨率 2.04 Å R-free 0.235
7S7F STRUCTURE OF HLA-B*07:02 IN COMPLEX WITH DOT1L(998-1006) PHOSPHOPEPTIDE 提交 2021-09-15	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合异源复合物；蛋白 × 3 PDB 声明：trimeric	链 C 998–1006（9 aa）片段：DOT1L(998-1006) PHOSPHOPEPTIDE	非标准单体：是（mmCIF未提供具体位点）	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；290 K；18-24% PEG4000, 0.1 SODIUM CITRATE, 20% ISOPROPANOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE	分辨率 1.88 Å R-free 0.217
7XCR Cryo-EM structure of Dot1L and H2BK34ub-H3K79Nle nucleosome 1:1 complex 提交 2022-03-25	构建体不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 异源复合物；蛋白 × 10 PDB 声明：dodecameric	链 K 5–332（328 aa）	未记录	SAM S-ADENOSYLMETHIONINE × 1	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 7.5 cryo-EM玻璃化条件冷冻剂 ETHANE	分辨率 2.57 Å
7XCT Cryo-EM structure of Dot1L and H2BK34ub-H3K79Nle nucleosome 2:1 complex 提交 2022-03-25	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 异源复合物；蛋白 × 12 PDB 声明：tetradecameric	链 K 5–332（328 aa）链 M 5–332（328 aa）	未记录	SAM S-ADENOSYLMETHIONINE × 2	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 7.5 cryo-EM玻璃化条件冷冻剂 ETHANE	分辨率 2.72 Å

共 47 个其他 PDB 条目、58 个 assembly。打开独立比较页并筛选聚集状态

查看构建体与数据证据

UniProt名称	DOT1L_HUMAN
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 3–333； UniProt 2–332 作者链 B； PDB构建体 3–333； UniProt 2–332

页面优先展示蛋白身份、当前 assembly、共同组分、聚集状态和跨 PDB 结构链接。链映射与序列区间收在“数据证据”中；数据库内部编号、导入时间和 assembly 操作表达式仅用于维护，因此不在读者页面展示。

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

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

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2. 结构基本信息 2. Structure Basics

条目编号 entry_id	5dtm
沉积日期 deposition_date	2015-09-18
结构标题 title	Crystal structure of Dot1L in complex with inhibitor CPD1 [4-(2,6-dichlorobenzoyl)-N-methyl-1H-pyrrole-2-carboxamide]
关键词 keywords	Inhibitor, Complex, Methyltransferase, transferase; TRANSFERASE
实验方法 method	X-RAY DIFFRACTION

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3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	28.64 Å
回转半径 Rg (电子) rg_electron	27.75 Å
零角强度 I(0) i0	85403800.00
分子量 molecular_weight	73144.0 kDa
排除体积 excluded_volume	91661 Å³
包络体积 envelope_volume	113960 Å³
水化壳体积 shell_volume	34320 Å³
包络直径 envelope_diameter	107.2 Å
壳层 Rg shell_rg	34.65 Å
包络 Rg envelope_rg	28.10 Å
形状 Rg shape_rg	27.73 Å
总 Rg total_rg	28.51 Å
总原子数 total_atoms	5163
残基数 n_residues	638
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	101.4 Å
Rg (实空间) rg_real	28.63 Å
Rg 误差 (实空间) rg_real_error	0.83 Å
I(0) (实空间) i0_real	8.5400e+07
I(0) 误差 (实空间) i0_real_error	1.1770e+06
Rg (倒空间) rg_reciprocal	28.64 Å
I(0) (倒空间) i0_reciprocal	85400000.0000
解质量估计 total_estimate	0.8571
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	33.2 Å
偏度 Skewness skewness	0.379
峰度 Kurtosis kurtosis	-0.174
角度范围 angular_range	— – 0.2750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	26520000.0000
实空间数据点数 n_real_points	56
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.750; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.928; Smooth: 0.961

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5. 晶体学与实验 5. Crystallography & Experiment

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6. 实体与聚合物信息 Entities & Polymers (3)

实体 1 Entity 1 polymer

描述 description	Histone-lysine N-methyltransferase, H3 lysine-79 specific
分子量 formula_weight	38456.6 kDa
EC 编号 ec_number	2.1.1.43
来源方法 src_method	man
拷贝数 entity_count	2

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	5626

GPGEKLELRLKSPVGAEPAVYPWPLPVYDKHHDAAHEIIETIRWVCEEIPDLKLAMENYVLIDYDTKSFESMQRLCDKYNRAIDSIHQLWKGTTQPMKLNTRPSTGLLRHILQQVYNHSVTDPEKLNNYEPFSPEVYGETSFDLVAQMIDEIKMTDDDLFVDLGSGVGQVVLQVAAATNCKHHYGVEKADIPAKYAETMDREFRKWMKWYGKKHAEYTLERGDFLSEEWRERIANTSVIFVNNFAFGPEVDHQLKERFANMKEGGRIVSSKPFAPLNFRINSRNLSDIGTIMRVVELSPLKGSVSWTGKPVSYYLHTIDRTILENYFSSLKNPG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

实体 2 Entity 2 non-polymer

描述 description	4-(2,6-dichlorobenzoyl)-N-methyl-1H-pyrrole-2-carboxamide
分子量 formula_weight	297.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

实体 3 Entity 3 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	463

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7. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d5dtma_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family family	c.66.1.31 — Catalytic, N-terminal domain of histone methyltransferase Dot1l

结构域编号 domain_id	d5dtmb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family family	c.66.1.31 — Catalytic, N-terminal domain of histone methyltransferase Dot1l

CATH v4.4 (4 domains)

结构域编号 domain_id	5dtmA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	260 — 434 Repressor (Amino-terminal Domain)
同源超家族 H-superfamily homologous superfamily	60 —

结构域编号 domain_id	5dtmA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

结构域编号 domain_id	5dtmB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	260 — 434 Repressor (Amino-terminal Domain)
同源超家族 H-superfamily homologous superfamily	60 —

结构域编号 domain_id	5dtmB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

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8. 引用文献 (1)

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晶胞边长 a length_a	158.559 Å
晶胞边长 b length_b	158.559 Å
晶胞边长 c length_c	73.396 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	120.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	P 63
空间群编号 int_tables_number	173
晶系 crystal_system	—

分辨率 resolution	2.200 Å
最低分辨率 resolution_low	44.000 Å
R 因子 r_factor	0.1757
R_work r_work	0.1744
R_free r_free	0.1991

fit	/app/data/saxs_computation/dt/5dtm/5dtm.fit
pddf	/app/data/pr_computation/dt/5dtm/5dtm.pr.out
profile	/app/data/saxs_computation/dt/5dtm/5dtm.dat