4dfk

large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with 5-(N-(10-hydroxydecanoyl)-aminopentinyl)-2-dUTP

Method: X-RAY DIFFRACTION D_max: 81.1 Å Quality: GOOD

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

DNA polymerase I, thermostable

Thermus aquaticus

UniProt P19821

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–DNA 单体蛋白 × 1 DNA 2 PDB 声明：trimeric（3）与全部聚合物数一致	链 A； UniProt 293–832	片段：Klenow Fragment	;5'-d(GACCACGGCGC DOC)-3' ; × 1 5'-d(AAAAGGCGCCGTGGTC)-3' × 1 0L5 2'-deoxy-5-{5-[(10-hydroxydecanoyl)amino]pent-1-yn-1-yl}uridine 5'-(tetrahydrogen triphosphate) × 1 MG MAGNESIUM ION × 6 EDO 1,2-ETHANEDIOL × 3 FMT FORMIC ACID × 5	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；18% PEG 8000, 200mM Mg-Formate, 100 mMTris pH 8.0 , VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 1.65 Å R-free 0.195

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 4DFK	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
1BGX TAQ POLYMERASE IN COMPLEX WITH TP7, AN INHIBITORY FAB 提交 1998-06-02	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 × 3 PDB 声明：trimeric	链 T 1–832（832 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 7.4；277 K；PROTEIN WAS CRYSTALLIZED FROM 22% PEG 3350, 200 MM TRIS/HCL, PH 7.4. COMPLEX WAS MADE AT A PROTEIN CONCENTRATION OF 0.5 MG/ML, LEFT FOR 2-3 DAYS AT 4 DEGREES CELSIUS, CONCENTRATED TO 5MG/ML PROTEIN AND CRYSTALLIZATION CARRIED OUT IN HANGING DROPS., vapor diffusion - hanging drop, temperature 277K	分辨率 2.30 Å R-free 0.253
1JXE STOFFEL FRAGMENT OF TAQ DNA POLYMERASE I 提交 1996-10-09	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 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 293–832（540 aa）片段：STOFFEL FRAGMENT, RESIDUES 290 - 832	未记录	未记录非水小分子	X-RAY DIFFRACTION mmCIF 未提供已读取条件	分辨率 2.85 Å
1KTQ DNA POLYMERASE 提交 1995-08-16	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 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 290–832（543 aa）	未记录	未记录非水小分子	X-RAY DIFFRACTION mmCIF 未提供已读取条件	分辨率 2.50 Å R-free 0.262
1QSS DDGTP-TRAPPED CLOSED TERNARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS 提交 1999-06-23	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–831（539 aa）片段：KLENOW FRAGMENT	突变：A348E	MG MAGNESIUM ION × 2 DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；HEPES, SODIUM ACETATE, PEG 4000, MANGANESE CHLORIDE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	分辨率 2.30 Å R-free 0.285
1QSY DDATP-Trapped closed ternary complex of the large fragment of DNA Polymerase I from thermus aquaticus 提交 1999-06-24	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–831（539 aa）片段：KLENOW FRAGMENT	突变：A348E	MG MAGNESIUM ION × 2 DDS 2',3'-dideoxyadenosine triphosphate × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；HEPES, SODIUM ACETATE, PEG 4000, MANGANESE CHLORIDE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	分辨率 2.30 Å R-free 0.276
1QTM DDTTP-TRAPPED CLOSED TERNARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS 提交 1999-06-28	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–831（539 aa）片段：KLENOW FRAGMENT, RESIDUES 293-831	未记录	MG MAGNESIUM ION × 2 TTP THYMIDINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；HEPES, SODIUM ACETATE, PEG 4000, MNCL2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	分辨率 2.30 Å R-free 0.280
1TAQ STRUCTURE OF TAQ DNA POLYMERASE 提交 1996-06-04	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 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–832（832 aa）	突变：S575C, S576C, S577C	BGL 2-O-octyl-beta-D-glucopyranose × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION mmCIF 未提供已读取条件	分辨率 2.40 Å R-free 0.323
1TAU TAQ POLYMERASE (E.C.2.7.7.7)/DNA/B-OCTYLGLUCOSIDE COMPLEX 提交 1996-06-17	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 1–832（832 aa）	未记录	BGL 2-O-octyl-beta-D-glucopyranose × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 295.00K	分辨率 3.00 Å R-free 0.305
2KTQ OPEN TERNARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS 提交 1998-07-30	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 295–832（538 aa）	未记录	MG MAGNESIUM ION × 1 DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray结晶条件 pH 8；pH 8.0	分辨率 2.30 Å R-free 0.288
3KTQ CRYSTAL STRUCTURE OF AN ACTIVE TERNARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS 提交 1998-07-28	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）	未记录	MG MAGNESIUM ION × 2 DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray结晶条件 pH 8；pH 8.0	分辨率 2.30 Å R-free 0.275
3LWL Structure of Klenow fragment of Taq polymerase in complex with an abasic site 提交 2010-02-24	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：KLENOW FRAGMENT, UNP residues 293-832	未记录	DDS 2',3'-dideoxyadenosine triphosphate × 1 MG MAGNESIUM ION × 1 ACT ACETATE ION × 5 GOL GLYCEROL × 7 NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.05M sodium cacodylate, 0.2M ammonium acetate, 0.01M magnesium acetate, 30% PEG 8000, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 2.25 Å R-free 0.234
3LWM Structure of the large fragment of thermus aquaticus DNA polymerase I in complex with a blunt-ended DNA and ddATP 提交 2010-02-24	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：KLENOW FRAGMENT, UNP residues 293-832	未记录	DDS 2',3'-dideoxyadenosine triphosphate × 1 ACT ACETATE ION × 4 GOL GLYCEROL × 5 MG MAGNESIUM ION × 1 NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；0.05M TRIS HCl, pH 8, 0.2M ammonium chloride, 0.01M calcium chloride and 35% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 291K	分辨率 2.19 Å R-free 0.228
3M8R Crystal structure of the large fragment of DNA polymerase I from Thermus aquaticus in a closed ternary complex with trapped 4'-ethylated dTTP 提交 2010-03-19	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：Klenow Fragment	未记录	HXZ 4'-ethylthymidine 5'-(tetrahydrogen triphosphate) × 1 MG MAGNESIUM ION × 2 15P POLYETHYLENE GLYCOL (N=34) × 2 GOL GLYCEROL × 4 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；30% (w/v) PEG 8000, 0.2M ammonium acetate, 0.02M magnesium acetate, 0.05M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K	分辨率 2.00 Å R-free 0.221
3M8S Crystal structure of the large fragment of DNA polymerase I from Thermus aquaticus in a closed ternary complex with trapped 4'-methylated dTTP 提交 2010-03-19	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：KLENOW FRAGMENT	未记录	HXB 4'-methylthymidine 5'-(tetrahydrogen triphosphate) × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 3 PEG DI(HYDROXYETHYL)ETHER × 1 15P POLYETHYLENE GLYCOL (N=34) × 1 ACT ACETATE ION × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；30% (w/v) PEG 8000, 0.2M ammonium acetate, 0.02M magnesium acetate, 0.05M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K	分辨率 2.20 Å R-free 0.224
3OJS Snapshots of the large fragment of DNA polymerase I from Thermus Aquaticus processing C5 modified thymidines 提交 2010-08-23	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：unp residues 292-832	未记录	XJS 2'-deoxy-5-[9-(3-{[4-(diethylamino)-4-oxobutanoyl]amino}propyl)-18-ethyl-5,8,14,17-tetraoxo-4,9,13,18-tetraazaicos-1-yn-1-yl]uridine 5'-(tetrahydrogen triphosphate) × 1 GOL GLYCEROL × 8 MG MAGNESIUM ION × 2 PGE TRIETHYLENE GLYCOL × 4 ACT ACETATE ION × 3	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.05M Na cacodylate ph 6.5, 0.2M NH4OAc, 0.01M Mg(OAc)2, 26% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 1.90 Å R-free 0.212
3OJU Snapshot of the large fragment of DNA polymerase I from Thermus Aquaticus processing c5 modified thymidies 提交 2010-08-23	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：unp residues 292-832	未记录	SSJ 2'-deoxy-5-[(1-hydroxy-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)ethynyl]uridine 5'-(tetrahydrogen triphosphate) × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 6 PGE TRIETHYLENE GLYCOL × 11	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 9；291 K；0.05M Tris HCl ph 9, 0.2M NH4Cl, 0.01M CaCl2, 26% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 2.00 Å R-free 0.219
3PO4 Structure of a mutant of the large fragment of DNA polymerase I from Thermus aquaticus in complex with a blunt-ended DNA and ddATP 提交 2010-11-22	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：KLENOW FRAGMENT	突变：I614K, M747K	MG MAGNESIUM ION × 3 NA SODIUM ION × 1 GOL GLYCEROL × 1 DDS 2',3'-dideoxyadenosine triphosphate × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.05M sodium cacodylate, 0.2M KCl, 0.1M Mg(OAc)2, 20% PEG 8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 1.80 Å R-free 0.194
3PO5 Structure of a mutant of the large fragment of DNA polymerase I from Thermus Auqaticus in complex with an abasic site and ddATP 提交 2010-11-22	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：Klenow Fragment	突变：I614K, M747K	MG MAGNESIUM ION × 1 PGE TRIETHYLENE GLYCOL × 2 DDS 2',3'-dideoxyadenosine triphosphate × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 8.8；291 K；0.05M Tris HCl, 0.2M NH4Cl, 0.01M CaCl2, 28% PEG 4000, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 2.39 Å R-free 0.266
3PY8 Crystal structure of a mutant of the large fragment of DNA polymerase I from thermus aquaticus in a closed ternary complex with DNA and ddCTP 提交 2010-12-12	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：DNA polymerase I large fragment	突变：I614K, M747K	DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 2 MN MANGANESE (II) ION × 5 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.1；291 K；0.1M Hepes, 20mM MnCl2, 0.1M Na-acetate, 12 % PEG 4000, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 1.74 Å R-free 0.199
3RR7 Binary Structure of the large fragment of Taq DNA polymerase bound to an abasic site 提交 2011-04-29	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：klenow fragment	未记录	FMT FORMIC ACID × 1 GOL GLYCEROL × 3 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1 M TRIS HCl pH 7.5, 0.2 M Magnesium Formate, 12% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 1.95 Å R-free 0.232
3RR8 Ternary Structure of the large fragment of Taq DNA polymerase bound to an abasic site and a ddGTP 提交 2011-04-29	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：klenow fragment	未记录	DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.05 M Na cacodylate pH 6.5, 0.2 M NH4OAc, 0.01 M Mg(OAc)2, 25% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 2.40 Å R-free 0.256
3RRG Ternary Structure of the large fragment of Taq DNA polymerase bound to an abasic site and a ddGTP 提交 2011-04-29	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：klenow fragment	未记录	DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 NA SODIUM ION × 1 GOL GLYCEROL × 2 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.05 M Na cacodylate pH 6.5, 0.2 M NH4OAc, 0.01 M Mg(OAc)2, 28% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 2.30 Å R-free 0.250
3RRH Ternary Structure of the large fragment of Taq DNA polymerase bound to an abasic site and a ddTTP 提交 2011-04-29	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：klenow fragment	未记录	TTP THYMIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 4 PGE TRIETHYLENE GLYCOL × 2 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.05 M Na cacodylate pH 6.5, 0.2 M NH4OAc, 0.01 M Mg(OAc)2, 28% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 1.80 Å R-free 0.201
3RTV Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a closed ternary complex with natural primer/template DNA 提交 2011-05-04	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：Klenow Fragment	未记录	DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 3 GOL GLYCEROL × 6 ACT ACETATE ION × 3	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.05M sodium cacodylate, 0.2M ammonium acetate, 0.01M magnesium acetate, 30% PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 1.90 Å R-free 0.202
3SV3 Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a closed ternary complex with the artificial base pair dNaM-d5SICSTP 提交 2011-07-12	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：Klenow Fragment, UNP residues 293-832	未记录	5SI 2-{2-deoxy-5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-6-methylisoquinoline-1(2H)-thione × 2 MG MAGNESIUM ION × 5 GOL GLYCEROL × 4 FMT FORMIC ACID × 16	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；13% PEG 8000, 100mM NH4Cl, 0.1M MgFormate, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 2.10 Å R-free 0.215
3SV4 Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with dT as templating nucleobase 提交 2011-07-12	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：Klenow Fragment, UNP residues 293-832	未记录	FMT FORMIC ACID × 9 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；18% PEG 8000, 0.2M MgFormate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 1.99 Å R-free 0.216
3SYZ Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with dNaM as templating nucleobase 提交 2011-07-18	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：Klenow Fragment, UNP residues 293-832	未记录	FMT FORMIC ACID × 6 GOL GLYCEROL × 10 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；11% PEG 8000, 0.2M MgFormate, 0.1M Tris, 20mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 1.95 Å R-free 0.201
3SZ2 Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with dG as templating nucleobase 提交 2011-07-18	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：Klenow Fragment, UNP residues 293-832	未记录	FMT FORMIC ACID × 6 MG MAGNESIUM ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；15% PEG 8000, 0.2M MgFormate, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 2.15 Å R-free 0.237
3T3F Ternary Structure of the large fragment of Taq DNA polymerase bound to an abasic site and dNITP 提交 2011-07-25	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：klenow fragment (UNP residues 293-832)	未记录	GOL GLYCEROL × 13 MG MAGNESIUM ION × 4 NA SODIUM ION × 1 N5P 1-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO-PENTOFURANOSYL}-5-NITRO -1H-INDOLE × 1 FMT FORMIC ACID × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.1 M TRIS HCl, 0.2 M MgFormate, 18% PEG 8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 1.90 Å R-free 0.206
4BWJ KlenTaq mutant in complex with DNA and ddCTP 提交 2013-07-03	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：KLENOW FRAGMENT, RESIDUES 293-832	突变：YES	DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 5	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP. 100MM TRIS PH 7.5, 200MM MG-FORMATE, 15% PEG 8K	分辨率 1.55 Å R-free 0.201
4BWM KlenTaq mutant in complex with a RNA/DNA hybrid 提交 2013-07-03	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 其他组合单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：KLENOW FRAGMENT, RESIDUES 293-832	突变：YES	DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE × 1 CL CHLORIDE ION × 2 MG MAGNESIUM ION × 3 FMT FORMIC ACID × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 8.5；HANGING DROP. 100MM TRIS PH8.5, 200MM MG-FORMATE, 20% PEG 8K MICROSEEDED	分辨率 1.75 Å R-free 0.208
4C8K Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a partially closed complex with the artificial base pair d5SICS-dNaMTP 提交 2013-10-01	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：KLENOW FRAGMENT, RESIDUES 293-832	未记录	GOL GLYCEROL × 2 BMR ((2R,3S,5R)-3-hydroxy-5-(3-methoxynaphthalen-2-yl)methyl-tetrahydrogen-triphosphate × 1 MG MAGNESIUM ION × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray结晶条件 pH 7；15% W/V PEG 8000, 100MM TRIS PH 7.0, 200MM MAGNESIUM FORMIAT	分辨率 2.17 Å R-free 0.221
4C8L Binary complex of the large fragment of DNA polymerase I from Thermus Aquaticus with the artificial base pair dNaM-d5SICS at the postinsertion site (sequence context 1) 提交 2013-10-01	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：KLENOW FRAGMENT, RESIDUES 293-832	未记录	GOL GLYCEROL × 5 SO4 SULFATE ION × 4 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 pH 6.5；0.2M AMMONIUM SULFATE, 0.1M MES PH 6.5, 28% W/V PEG 5000MME	分辨率 1.70 Å R-free 0.214
4C8M Binary complex of the large fragment of DNA polymerase I from Thermus Aquaticus with the aritificial base pair d5SICS-dNaM at the postinsertion site (sequence context 2) 提交 2013-10-01	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：KLENOW FRAGMENT, RESIDUES 293-832	未记录	SO4 SULFATE ION × 3 GOL GLYCEROL × 5 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 pH 6.5；0.2M AMMONIUM SULFATE, 0.1M MES PH 6.5, 30% (W/V) PEG 5000MME	分辨率 1.57 Å R-free 0.207
4C8N Binary complex of the large fragment of DNA polymerase I from Thermus Aquaticus with the aritificial base pair dNaM-d5SICS at the postinsertion site (sequence context 3) 提交 2013-10-01	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：KLENOW FRAGMENT, RESIDUES 293-832	未记录	SO4 SULFATE ION × 5 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray结晶条件 pH 7.5；1.2M LITHIUM SULFATE, 2% W/V PEG 1000, 50MM HEPES PH 7.5	分辨率 1.88 Å R-free 0.232
4C8O Binary complex of the large fragment of DNA polymerase I from Thermus Aquaticus with the aritificial base pair dNaM-d5SICS at the postinsertion site (sequence context 2) 提交 2013-10-01	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：KLENOW FRAGMENT, RESIDUES 293-832	未记录	SO4 SULFATE ION × 7 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray结晶条件 pH 6.5；0.2M AMMONIUM SULFATE, 0.1M MES PH 6.5, 30% W/V PEG 5000MME	分辨率 1.75 Å R-free 0.212
4CCH Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with d5SICS as templating nucleotide 提交 2013-10-23	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：KLENOW FRAGMENT, RESIDUES 293-832	未记录	FMT FORMIC ACID × 4 MG MAGNESIUM ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray结晶条件 pH 8；20% W/V PEG 8000, 0.1M TRIS PH 8.0, 0.2M MAGNESIUM FORMATE, 20% GLYCEROL	分辨率 2.55 Å R-free 0.261
4DF4 Crystal structure of the large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with 7-(N-(10-hydroxydecanoyl)-aminopentinyl)-7-deaza-2 -dATP 提交 2012-01-23	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：Klenow Fragment	未记录	MG MAGNESIUM ION × 5 0L3 7-{2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-5-{5-[(10-hydroxydecanoyl)amino]pent-1-yn-1-yl}-7H-pyrrolo[2,3-d]pyrimidin-4-amine × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；18% PEG 8000, 200mM Mg-Formate, 100 mMTris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 2.20 Å R-free 0.227
4DF8 Crystal structure of the large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with aminopentinyl-7-deaza-2-dATP 提交 2012-01-23	配体/离子不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：Klenow Fragment	未记录	0L4 5-(5-aminopent-1-yn-1-yl)-7-{2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-7H-pyrrolo[2,3-d]pyrimidin-4-amine × 1 MG MAGNESIUM ION × 3 EDO 1,2-ETHANEDIOL × 4 FMT FORMIC ACID × 4 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；18% PEG 8000, 200mM Mg-Formate, 100 mMTris pH 8.0 , VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 2.00 Å R-free 0.234
4DFJ Crystal structure of the large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with 5-(aminopentinyl)-dTTP 提交 2012-01-23	配体/离子不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：Klenow Fragment	未记录	MG MAGNESIUM ION × 8 0KL 5-(5-aminopent-1-yn-1-yl)-2'-deoxyuridine 5'-(tetrahydrogen triphosphate) × 1 FMT FORMIC ACID × 6 EDO 1,2-ETHANEDIOL × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；18% PEG 8000, 200mM Mg-Formate, 100 mMTris pH 8.0 , VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 1.90 Å R-free 0.204
4DFM Crystal structure of the large fragment of DNA polymerase I from Thermus aquaticus in ternary complex with 5-(aminopentinyl)-2-dCTP 提交 2012-01-24	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：Klenow Fragment	未记录	0L6 5-(5-aminopent-1-yn-1-yl)-2'-deoxycytidine 5'-(tetrahydrogen triphosphate) × 1 MG MAGNESIUM ION × 4 FMT FORMIC ACID × 1 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；18% PEG 8000, 200mM Mg-Formate, 100 mM Tris pH 8.0 , VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 1.89 Å R-free 0.216
4DFP Crystal structure of the large fragment of DNA Polymerase I from Thermus aqauticus in a ternary complex with 7-(aminopentinyl)-7-deaza-dGTP 提交 2012-01-24	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：Klenow Fragment, UNP residues 293-831	未记录	MG MAGNESIUM ION × 5 EDO 1,2-ETHANEDIOL × 5 FMT FORMIC ACID × 7 0L7 2-amino-5-(5-aminopent-1-yn-1-yl)-7-{2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；18% PEG 8000, 200mM Mg-Formate, 100 mM Tris pH 8.0 , VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 2.00 Å R-free 0.224
4DLE Ternary Structure of the large Fragment of Taq DNA Polymerase: 4-Fluoroproline Variant 提交 2012-02-06	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：UNP RESIDUES 293-832	非标准单体：是（mmCIF未提供具体位点）	MG MAGNESIUM ION × 1 GOL GLYCEROL × 2 DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE × 1 MN MANGANESE (II) ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.1 M HEPES, 20 mM MnCl2, 0.1 M NH4(OAc), 15% PEG 4000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K	分辨率 2.44 Å R-free 0.282
4DLG Ternary Structure of the large Fragment of Taq DNA polymerase 提交 2012-02-06	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：UNP residues 293-832	未记录	DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 ACT ACETATE ION × 3 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；50 mM Na cacodylate, 0.2 M NH4(OAc), 10 mM Mg(OAc)2, 15% PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K	分辨率 1.89 Å R-free 0.252
4ELT Snapshot of the large fragment of DNA polymerase I from Thermus Aquaticus processing modified pyrimidines 提交 2012-04-11	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）	未记录	0R5 2'-deoxy-5-[(4-ethynylphenyl)ethynyl]uridine 5'-(tetrahydrogen triphosphate) × 1 MG MAGNESIUM ION × 3 GOL GLYCEROL × 9 ACT ACETATE ION × 3 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；50 mM Na cacodylate pH=6.5, 0.2 M NH4(OAc), 10 mM Mg(OAc)2, 28% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 2.20 Å R-free 0.209
4ELU Snapshot of the large fragment of DNA polymerase I from Thermus Aquaticus processing modified pyrimidines 提交 2012-04-11	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：UNP RESIDUES 293-832	未记录	0R6 2'-deoxy-5-[(4-ethynylphenyl)ethynyl]cytidine 5'-(tetrahydrogen triphosphate) × 1 MG MAGNESIUM ION × 3 GOL GLYCEROL × 11 PGE TRIETHYLENE GLYCOL × 2 ACT ACETATE ION × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；50 mM Na cacodylate pH=6.5, 0.2 M NH4(OAc), 10 mM Mg(OAc)2, 28% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 1.80 Å R-free 0.182
4ELV Snapshot of the large fragment of DNA polymerase I from Thermus Aquaticus processing modified pyrimidines 提交 2012-04-11	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：UNP RESIDUES 293-832	未记录	MG MAGNESIUM ION × 3 0R7 [[(2S,5R)-5-[4-azanyl-5-[2-(4-ethynylphenyl)ethynyl]-2-oxidanylidene-pyrimidin-1-yl]oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 GOL GLYCEROL × 4 PGE TRIETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 2 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 8.4；291 K；50 mM Tris HCl pH=8.4, 0.2 M NH4Cl, 10 mM CaCl2, 34% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 1.90 Å R-free 0.216
4KTQ BINARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM T. AQUATICUS BOUND TO A PRIMER/TEMPLATE DNA 提交 1998-09-09	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 294–832（539 aa）	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 pH 7.5；pH 7.5	分辨率 2.50 Å R-free 0.298
4N56 Binary complex structure of Klenow fragment of Taq DNA polymerase I707L mutant (Cs3C KlenTaq) with DNA 提交 2013-10-09	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 281–832（552 aa）片段：Klenow fragment (UNP residues 281-832)	突变：I707L	MN MANGANESE (II) ION × 1 GOL GLYCEROL × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M HEPES, pH 7.5, 20 mM manganese chloride, 0.1 M sodium acetate, 10% w/v PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 289K	分辨率 2.20 Å R-free 0.273
4N5S Ternary complex structure of Klenow fragment of Taq DNA polymerase I707L mutant (Cs3C KlenTaq) with DNA and ddCTP 提交 2013-10-10	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 281–832（552 aa）片段：Klenow fragment (UNP residues 281-832)	突变：I707L	MN MANGANESE (II) ION × 6 MG MAGNESIUM ION × 1 DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 ACT ACETATE ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M HEPES, pH 7.5, 20 mM manganese chloride, 0.1 M sodium acetate, 10% w/v PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 289K	分辨率 1.67 Å R-free 0.192
4XIU Binary complex structure of Klenow fragment of Taq DNA polymerase I707L mutant with DNA containing TTT overhang 提交 2015-01-07	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 294–832（539 aa）片段：Klenow fragment of DNA polymerase I from Thermus aquatics	突变：I707L	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；PEG4000	分辨率 2.50 Å R-free 0.286
5E41 Crystal structure of the large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with 5-(N-(10-hydroxydecanoyl)-aminopentenyl)-2'-deoxyuridine-triphosphate 提交 2015-10-05	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）	未记录	MG MAGNESIUM ION × 2 AUL 2'-deoxy-5-{(1E)-5-[(10-hydroxydecanoyl)amino]pent-1-en-1-yl}uridine 5'-(tetrahydrogen triphosphate) × 1 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；291 K；0.05M Sodium cacodylate pH 6.5, 0.01M Magnesium acetate, 0.2M Ammonium acetate, 30% PEG 4000	分辨率 1.80 Å R-free 0.236
5KTQ LARGE FRAGMENT OF TAQ DNA POLYMERASE BOUND TO DCTP 提交 1998-09-22	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 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 290–832（543 aa）	未记录	DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray结晶条件 pH 9；pH 9.0	分辨率 2.50 Å R-free 0.280
5NKL Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a closed ternary complex with the artificial base pair dDs-dPxTP 提交 2017-03-31	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）	未记录	MG MAGNESIUM ION × 2 ACT ACETATE ION × 1 91T [[(2~{R},3~{S},5~{R})-5-[4-[(4~{R})-4,5-bis(oxidanyl)pent-1-ynyl]-2-nitro-pyrrol-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 91R [[(2~{R},3~{S},5~{R})-5-[4-[(4~{S})-4,5-bis(oxidanyl)pent-1-ynyl]-2-nitro-pyrrol-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；291 K；100mM TRIS pH 8.5, 0.2M Sodium acetate, 30% PEG 4000	分辨率 1.70 Å R-free 0.237
5O7T Crystal structure of KlenTaq mutant M747K in a closed ternary complex with a dG:dCTP base pair 提交 2017-06-09	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）	突变：M747K	MG MAGNESIUM ION × 3 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；291 K；20% PEG 3350, 0 .1M Magnesiumacetate	分辨率 1.80 Å R-free 0.235
5OXJ Crystal structure of KlenTaq mutant M747K in a closed ternary complex with a O6-MeG:BenziTP base pair 提交 2017-09-06	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）	突变：M747K	MN MANGANESE (II) ION × 2 NZI [(2~{R},3~{S},5~{R})-3-oxidanyl-5-(2-oxidanylidene-3~{H}-benzimidazol-1-yl)oxolan-2-yl]methyl [oxidanyl(phosphonooxy)phosphoryl] hydrogen phosphate × 1 ACT ACETATE ION × 3 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；22% PEG3350 + 0.1M Mg(OAc)2 + 0.1M HEPES pH 7.5	分辨率 2.00 Å R-free 0.257
5SZT Crystal structure of the large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with 7-(N-(10-hydroxydecanoyl)-aminopentenyl)-7-deaza-2'-dATP 提交 2016-08-15	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）	未记录	MG MAGNESIUM ION × 3 GOL GLYCEROL × 2 ACT ACETATE ION × 4 72J 7-(N-(10-hydroxydecanoyl)-aminopentenyl)-7-deaza-2'-dATP × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；291 K；0.05 M sodium cacodylate pH 6.5, 0.01 M magnesium acetate, 0.2 M ammonium acetate, 30% PEG 4000	分辨率 1.80 Å R-free 0.230
5W6K Structure of mutant Taq Polymerase incorporating unnatural base pairs Z:P 提交 2017-06-16	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）片段：UNP residues 293-831	未记录	A5J (1R)-1-[6-amino-5-(dihydroxyamino)-2-hydroxypyridin-3-yl]-1,4-anhydro-2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-D-erythro-pentitol × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.16 K；19 % PEG 4000, 0.2 M ammonium acetate, 0.01 M magnesium acetate, 0.05 M sodium cacodylate pH 6.5	分辨率 2.34 Å R-free 0.275
5W6Q Structural basis for recognition of artificial DNA by an evolved KlenTaq variant 提交 2017-06-16	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 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 6；277.15 K；14 % PEG 8000, 0.2 M Mg formate, 0.1 M MES pH 6.0	分辨率 2.66 Å R-free 0.247
5W6Q Structural basis for recognition of artificial DNA by an evolved KlenTaq variant 提交 2017-06-16	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 293–832（540 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 6；277.15 K；14 % PEG 8000, 0.2 M Mg formate, 0.1 M MES pH 6.0	分辨率 2.66 Å R-free 0.247
5W6Q Structural basis for recognition of artificial DNA by an evolved KlenTaq variant 提交 2017-06-16	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 3 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 G 293–832（540 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 6；277.15 K；14 % PEG 8000, 0.2 M Mg formate, 0.1 M MES pH 6.0	分辨率 2.66 Å R-free 0.247
5YTC Large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with the unnatural base M-fC pair with dATP in the active site 提交 2017-11-17	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 294–832（539 aa）片段：large fragment	未记录	DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 EVAPORATION；pH 8.5；293.15 K；0.2 M Mg(HCOO)2, 0.1 M Tris HCl (pH 8.5), 18% PEG 8000	分辨率 2.28 Å R-free 0.258
5YTD large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with the natural base pair 5fC:dGTP 提交 2017-11-17	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 294–832（539 aa）	未记录	DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 EVAPORATION；pH 7；293.15 K；0.05 M sodium cacodylate (pH 7.0), 0.2 M ammonium acetate, 0.01 M magnesium acetate, 30% PEG 8000	分辨率 2.00 Å R-free 0.239
5YTE Large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with with natural dT:dATP base pair 提交 2017-11-17	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 294–832（539 aa）	未记录	DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray结晶条件 EVAPORATION；pH 7；293.15 K；0.05 M sodium cacodylate (pH 7.0), 0.2 M ammonium acetate, 0.01 M magnesium acetate, 30% PEG 8000	分辨率 2.21 Å R-free 0.238
5YTF Structure of large fragment of DNA Polymerase I from Thermus aquaticus Host-Guest complex with the unnatural base M-fC pair with dA 提交 2017-11-17	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 294–832（539 aa）片段：large fragment	未记录	MG MAGNESIUM ION × 3 DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray结晶条件 EVAPORATION；pH 7；293.15 K；0.05 M sodium cacodylate (pH 7.0), 0.2 M ammonium acetate, 0.01 M magnesium acetate, 30% PEG 8000	分辨率 1.98 Å R-free 0.233
5YTG Structure of large fragment of DNA Polymerase I from Thermus aquaticus Host-Guest complex with the unnatural base I-fC pair with dA 提交 2017-11-17	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 294–832（539 aa）	未记录	DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray结晶条件 EVAPORATION；pH 7；293.15 K；0.05 M sodium cacodylate (pH 7.0), 0.2 M ammonium acetate, 0.01 M magnesium acetate, 30% PEG 8000	分辨率 2.07 Å R-free 0.252
5YTH Structure of large fragment of DNA Polymerase I from Thermus aquaticus Host-Guest complex with the unnatural base M-fC pair with dG 提交 2017-11-17	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 294–832（539 aa）片段：large fragment	未记录	DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray结晶条件 EVAPORATION；pH 7；293.15 K；0.05 M sodium cacodylate (pH 7.0), 0.2 M ammonium acetate, 0.01 M magnesium acetate, 30% PEG 8000	分辨率 2.53 Å R-free 0.275
5Z3N Structure of large fragment of DNA Polymerase I from Thermus aquaticus Host-Guest complex with the unnatural base 5fC pair with dA 提交 2018-01-08	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 294–832（539 aa）	未记录	MG MAGNESIUM ION × 3 DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray结晶条件 EVAPORATION；pH 7；293.15 K；0.05 M sodium cacodylate (pH 7.0), 0.2 M ammonium acetate, 0.01 M magnesium acetate, 24% PEG 8000	分辨率 1.91 Å R-free 0.229
6FBC KlenTaq DNA polymerase processing a modified primer - bearing the modification at the 3'-terminus of the primer. 提交 2017-12-19	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）	未记录	XG4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine × 1 EDO 1,2-ETHANEDIOL × 2 MN MANGANESE (II) ION × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；pH 7；291 K；14 % PEG 4000, 0.1 M HEPES, 20 mM manganese(II) chloride, 0.1 M sodium actetate	分辨率 1.54 Å R-free 0.208
6FBD KlenTaq DNA polymerase processing a modified primer - bearing the modification upstream at the second primer nucleotide. 提交 2017-12-19	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）	未记录	MN MANGANESE (II) ION × 2 XG4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；pH 7；291 K；16 % PEG 4000, 0.1 M HEPES, 25 mM manganese(II) chloride, 0.1 M sodium acetate	分辨率 2.10 Å R-free 0.233
6FBE KlenTaq DNA polymerase processing a modified primer - bearing the modification upstream at the third primer nucleotide. 提交 2017-12-19	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）	未记录	MN MANGANESE (II) ION × 2 EDO 1,2-ETHANEDIOL × 2 XG4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；pH 7；291 K；20 % PEG 4000, 0.1 M HEPES, 20 mM manganese(II) chloride, 0.1 M sodium acetate	分辨率 1.59 Å R-free 0.203
6FBF KlenTaq DNA polymerase processing a modified primer - bearing the modification upstream at the fourth primer nucleotide. 提交 2017-12-19	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）	未记录	MN MANGANESE (II) ION × 2 XG4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；pH 6；291 K；16 % PEG 4000, 20 mM manganese(II) chloride, 0.1 M TRIS, 0.1 M sodium acetate	分辨率 2.00 Å R-free 0.226
6FBG KlenTaq DNA polymerase processing a modified primer - bearing the modification upstream at the fifth primer nucleotide. 提交 2017-12-19	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）	未记录	MN MANGANESE (II) ION × 2 EDO 1,2-ETHANEDIOL × 6 XG4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；pH 7；291 K；15 % PEG 4000, 0.1 M HEPES, 20 mM manganese(II) chloride, 0.1 M sodium acetate	分辨率 1.70 Å R-free 0.217
6FBH KlenTaq DNA polymerase processing a modified primer - bearing the modification upstream at the sixth primer nucleotide. 提交 2017-12-19	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）	未记录	MN MANGANESE (II) ION × 2 EDO 1,2-ETHANEDIOL × 1 XG4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；pH 7；291 K；29 % PEG 4000, 0.05 M TRIS, 20 mM manganese(II) chloride, 0.2 M ammonium chloride	分辨率 1.80 Å R-free 0.223
6FBI KlenTaq DNA polymerase in a closed, ternary complex with dGpNHpp bound in the active site 提交 2017-12-19	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）	未记录	XG4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine × 1 MN MANGANESE (II) ION × 2 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；291 K；(A) 16 % PEG 4000, 0.1 M sodium acetate, 20 mM manganese(II) chloride, 0.1 M MES (B) 17 % PEG 4000, 0.1 M ammonium acetate, 0.1 M HEPES, 20 mM manganese(II) chloride (C) 15 % PEG 4000, 0.1 M sodium acetate, 20 mM manganese(II) chloride, 0.1 M MES	分辨率 1.90 Å R-free 0.235
6Q4U KlenTaq DNA pol in a closed ternary complex with 7-deaza-7-(2-(2-hydroxyethoxy)-N-(prop-2-yn-1-yl)acetamide)-2-dATP 提交 2018-12-06	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）	未记录	MG MAGNESIUM ION × 2 MN MANGANESE (II) ION × 1 HHZ [[(2~{R},3~{S},5~{R})-5-[4-azanyl-5-[3-[2-(2-hydroxyethyloxy)ethanoylamino]prop-1-ynyl]pyrrolo[2,3-d]pyrimidin-7-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；14 % PEG 8000, 0.1 M Tris pH 8.0, 0.2 M magnesium formate, 10 % glycerol	分辨率 2.00 Å R-free 0.220
6Q4V KlenTaq DNA polymerase in complex with dATP 提交 2018-12-06	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）	未记录	DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；291 K；27 % PEG 4000, 0.2 M ammonium acetate, 0.01 M magnesium (II) acetate, 0.1 M MES pH 6.5	分辨率 2.01 Å R-free 0.219
7OWF KlenTaq DNA polymerase in a ternary complex with primer/template and the fluorescent nucleotide analog BFdUTP 提交 2021-06-18	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）	未记录	MG MAGNESIUM ION × 3 2IU [[(2R,3S,5R)-5-[5-(1-benzofuran-2-yl)-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 8；291.15 K；16% PEG 6000, 0.1M Tris pH 8.0, 0.2M magnesium formate	分辨率 1.91 Å R-free 0.241
8XJR Apo form of DNA polymerase SFM4-3 recognizing C2 methyoxy nucleotide 提交 2023-12-22	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 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 290–832（543 aa）	未记录	SO4 SULFATE ION × 10	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；289 K；0.1M HEPES pH7.5, 1.5M Lithium sulfate	分辨率 1.97 Å R-free 0.242
8XK7 binary complex of DNA polymerase SFM4-3 recognizing C2 methyoxy nucleotide 提交 2023-12-22	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 294–832（539 aa）	未记录	PO4 PHOSPHATE ION × 2 SO4 SULFATE ION × 3 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；289 K；0.2 M lithium sulfate monohydrate, 0.1 M HEPES pH 7.5, and 28% PEG 3350	分辨率 2.00 Å R-free 0.231
8XK9 ternary complex of DNA polymerase SFM4-3 recognizing C2 methyoxy nucleotide 提交 2023-12-22	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–DNA 同源多聚体；蛋白 × 2 PDB 声明：hexameric	链 A 294–832（539 aa）链 D 294–832（539 aa）	未记录	MG MAGNESIUM ION × 6 A1LWE [[(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 2 PEG DI(HYDROXYETHYL)ETHER × 2 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；289 K；0.1 M HEPES pH 7.5, 10% propanol, and 20% PEG 4000	分辨率 2.40 Å R-free 0.218
9FM3 KlenTaq DNA polymerase in a ternary complex with primer/template and a selenophene-modified dUTP (SedUTP) 提交 2024-06-05	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）	未记录	A1IDZ [[(2~{R},3~{S},5~{R})-5-[2,4-bis(oxidanylidene)-5-selenophen-2-yl-pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 MG MAGNESIUM ION × 1 DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；291.15 K；JBScreen Nuc-Pro HTS condition F12: 1M di-Sodium tartrate, 50 mM TRIS pH 7.5, 30 mM Magnesium chloride	分辨率 2.59 Å R-free 0.245
9FMF KlenTaq DNA polymerase in a ternary complex with primer/template and a fluorobenzofuran-modified dUTP (FBFdUTP) 提交 2024-06-06	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–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 293–832（540 aa）	未记录	MG MAGNESIUM ION × 1 A1IDW [[(2~{R},3~{S},5~{R})-5-[5-(5-fluoranyl-1-benzofuran-2-yl)-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；Nextal Nucleix Suite condition D12: 0.2 M Ammonium chloride, 0.01 M Calcium chloride, 0.05 M TRIS HCl pH 8.5, 20% (w/v) PEG 4000	分辨率 2.10 Å R-free 0.233

共 81 个其他 PDB 条目、83 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	DPO1_THEAQ
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–540； UniProt 293–832

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	4dfk
沉积日期 deposition_date	2012-01-24
结构标题 title	large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with 5-(N-(10-hydroxydecanoyl)-aminopentinyl)-2-dUTP
关键词 keywords	DNA Polymerase, TRANSFERASE-DNA complex; TRANSFERASE/DNA
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	25.51 Å
回转半径 Rg (电子) rg_electron	24.92 Å
零角强度 I(0) i0	168231000.00
分子量 molecular_weight	65429.0 kDa
排除体积 excluded_volume	61400 Å³
包络体积 envelope_volume	103520 Å³
水化壳体积 shell_volume	33659 Å³
包络直径 envelope_diameter	84.8 Å
壳层 Rg shell_rg	33.00 Å
包络 Rg envelope_rg	24.95 Å
形状 Rg shape_rg	24.97 Å
总 Rg total_rg	25.41 Å
总原子数 total_atoms	4908
残基数 n_residues	566
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	81.1 Å
Rg (实空间) rg_real	25.38 Å
Rg 误差 (实空间) rg_real_error	0.45 Å
I(0) (实空间) i0_real	1.6820e+08
I(0) 误差 (实空间) i0_real_error	2.2840e+06
Rg (倒空间) rg_reciprocal	25.42 Å
I(0) (倒空间) i0_reciprocal	168200000.0000
解质量估计 total_estimate	0.8953
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	79.8 Å
偏度 Skewness skewness	0.189
峰度 Kurtosis kurtosis	-0.390
角度范围 angular_range	— – 0.3100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	18800000.0000
实空间数据点数 n_real_points	63
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.885; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.990

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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 (8)

实体 1 Entity 1 polymer

描述 description	DNA polymerase I, thermostable
分子量 formula_weight	60937.0 kDa
EC 编号 ec_number	2.7.7.7
来源方法 src_method	man
拷贝数 entity_count	1

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	5287

ALEEAPWPPPEGAFVGFVLSRKEPMWADLLALAAARGGRVHRAPEPYKALRDLKEARGLLAKDLSVLALREGLGLPPGDDPMLLAYLLDPSNTTPEGVARRYGGEWTEEAGERAALSERLFANLWGRLEGEERLLWLYREVERPLSAVLAHMEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGHPFNLNSRDQLERVLFDELGLPAIGKTEKTGKRSTSAAVLEALREAHPIVEKILQYRELTKLKSTYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQRIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPREAVDPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWIEKTLEEGRRRGYVETLFGRRRYVPDLEARVKSVREAAERMAFNMPVQGTAADLMKLAMVKLFPRLEEMGARMLLQVHDELVLEAPKERAEAVARLAKEVMEGVYPLAVPLEVEVGIGEDWLSAKE

来源 Source

来源生物 organism	Thermus aquaticus
NCBI 分类编号 ncbi_taxonomy_id	271
宿主生物 host_organism	Escherichia coli

实体 2 Entity 2 polymer

描述 description	;5'-d(GACCACGGCGC DOC)-3' ;
分子量 formula_weight	3617.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合物 Polymer

聚合物类型 type	polydeoxyribonucleotide
链编号 strand_id	B

GACCACGGCGCC

实体 3 Entity 3 polymer

描述 description	5'-d(AAAAGGCGCCGTGGTC)-3'
分子量 formula_weight	4948.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合物 Polymer

聚合物类型 type	polydeoxyribonucleotide
链编号 strand_id	C

AAAAGGCGCCGTGGTC

实体 4 Entity 4 non-polymer

描述 description	;2'-deoxy-5-{5-[(10-hydroxydecanoyl)amino]pent-1-yn-1-yl}uridine 5'-(tetrahydrogen triphosphate) ;
分子量 formula_weight	719.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

实体 5 Entity 5 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

实体 6 Entity 6 non-polymer

描述 description	1,2-ETHANEDIOL
分子量 formula_weight	62.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

实体 7 Entity 7 non-polymer

描述 description	FORMIC ACID
分子量 formula_weight	46.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

实体 8 Entity 8 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	367

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7. 折叠分类 (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

结构域编号 domain_id	4dfkA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

结构域编号 domain_id	4dfkA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1060 — Taq DNA Polymerase; Chain T, domain 4
同源超家族 H-superfamily homologous superfamily	10 — Taq DNA Polymerase; Chain T, domain 4

结构域编号 domain_id	4dfkA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	370 —

结构域编号 domain_id	4dfkA04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	150 — DNA polymerase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

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8. 引用文献 (1)

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晶胞边长 a length_a	108.211 Å
晶胞边长 b length_b	108.211 Å
晶胞边长 c length_c	90.115 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	6

空间群 space_group	P 31 2 1
空间群编号 int_tables_number	152
晶系 crystal_system	—

分辨率 resolution	1.647 Å
最低分辨率 resolution_low	46.857 Å
R 因子 r_factor	0.1715
R_work r_work	0.1703
R_free r_free	0.1946

fit	/app/data/saxs_computation/df/4dfk/4dfk.fit
pddf	/app/data/pr_computation/df/4dfk/4dfk.pr.out
profile	/app/data/saxs_computation/df/4dfk/4dfk.dat

large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with 5-(N-(10-hydroxydecanoyl)-aminopentinyl)-2-dUTP

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

DNA polymerase I, thermostable

当前结构中的状态

数据库中的同蛋白其他状态

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

2. 结构基本信息 2. Structure Basics

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

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

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

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

6. 实体与聚合物信息 Entities & Polymers (8)

实体 1 Entity 1 polymer

聚合物 Polymer

来源 Source

实体 2 Entity 2 polymer

聚合物 Polymer

实体 3 Entity 3 polymer

聚合物 Polymer

实体 4 Entity 4 non-polymer

实体 5 Entity 5 non-polymer

实体 6 Entity 6 non-polymer

实体 7 Entity 7 non-polymer

实体 8 Entity 8 water

7. 折叠分类 (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. 引用文献 (1)

9. 文件与曲线 (10)

Files (7)

Curves (3)