data_6YOM # _model_server_result.job_id GkmZeiENSua4gu0ujF4Acw _model_server_result.datetime_utc '2025-06-21 00:57:44' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 6yom # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":707}' # _entry.id 6YOM # _exptl.entry_id 6YOM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 491.182 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYADENOSINE 5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 6YOM _cell.length_a 105.298 _cell.length_b 105.298 _cell.length_c 195.629 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YOM _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 7 I N N ? 7 J N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A NE2 HIS 61 A HIS 167 1_555 C FE FE . A FE 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc2 A NE2 HIS 100 A HIS 206 1_555 C FE FE . A FE 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? metalc ? metalc3 A OD2 ASP 101 A ASP 207 1_555 C FE FE . A FE 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc4 A OD1 ASP 101 A ASP 207 1_555 D MN MN . A MN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? metalc ? metalc5 A NE2 HIS 127 A HIS 233 1_555 D MN MN . A MN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc6 A OD1 ASP 205 A ASP 311 1_555 C FE FE . A FE 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? metalc ? metalc7 C FE FE . A FE 701 1_555 G O2A 0KX . A 0KX 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? metalc ? metalc8 D MN MN . A MN 702 1_555 G O1A 0KX . A 0KX 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc9 E MG MG . A MG 703 1_555 G O3G 0KX . A 0KX 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc10 E MG MG . A MG 703 1_555 G O1B 0KX . A 0KX 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.489 ? metalc ? metalc11 F MG MG . A MG 704 1_555 H O9 CZF . A CZF 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc12 F MG MG . A MG 704 1_555 H O12 CZF . A CZF 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? metalc ? metalc13 F MG MG . A MG 704 1_555 H O14 CZF . A CZF 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? metalc ? metalc14 F MG MG . A MG 704 1_555 J O2B DTP . B DTP 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? metalc ? metalc15 F MG MG . A MG 704 1_555 J O1G DTP . B DTP 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? metalc ? metalc16 I O3G DTP . A DTP 707 1_555 N MG MG . B MG 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? metalc ? metalc17 I O1B DTP . A DTP 707 1_555 N MG MG . B MG 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? metalc ? metalc18 B NE2 HIS 61 B HIS 167 1_555 K FE FE . B FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc19 B NE2 HIS 100 B HIS 206 1_555 K FE FE . B FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc20 B OD2 ASP 101 B ASP 207 1_555 K FE FE . B FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc21 B OD1 ASP 101 B ASP 207 1_555 L MN MN . B MN 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? metalc ? metalc22 B NE2 HIS 127 B HIS 233 1_555 L MN MN . B MN 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc23 B OD1 ASP 205 B ASP 311 1_555 K FE FE . B FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc24 K FE FE . B FE 702 1_555 O O2A 0KX . B 0KX 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc25 L MN MN . B MN 703 1_555 O O1A 0KX . B 0KX 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? metalc ? metalc26 M MG MG . B MG 704 1_555 O O1B 0KX . B 0KX 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? metalc ? metalc27 M MG MG . B MG 704 1_555 O O3G 0KX . B 0KX 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc28 N MG MG . B MG 705 1_555 P O9 CZF . B CZF 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? metalc ? metalc29 N MG MG . B MG 705 1_555 P O14 CZF . B CZF 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc30 N MG MG . B MG 705 1_555 P O12 CZF . B CZF 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? # _chem_comp.formula 'C10 H16 N5 O12 P3' _chem_comp.formula_weight 491.182 _chem_comp.id DTP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYADENOSINE 5'-TRIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag PG O1G DTP doub 178 n n PG O2G DTP sing 179 n n PG O3G DTP sing 180 n n PG O3B DTP sing 181 n n O2G HOG2 DTP sing 182 n n O3G HOG3 DTP sing 183 n n PB O1B DTP doub 184 n n PB O2B DTP sing 185 n n PB O3B DTP sing 186 n n PB O3A DTP sing 187 n n O2B HOB2 DTP sing 188 n n PA O1A DTP doub 189 n n PA O2A DTP sing 190 n n PA O3A DTP sing 191 n n PA O5' DTP sing 192 n n O2A HOA2 DTP sing 193 n n O5' C5' DTP sing 194 n n C5' C4' DTP sing 195 n n C5' "H5'1" DTP sing 196 n n C5' "H5'2" DTP sing 197 n n C4' O4' DTP sing 198 n n C4' C3' DTP sing 199 n n C4' H4' DTP sing 200 n n O4' C1' DTP sing 201 n n C3' O3' DTP sing 202 n n C3' C2' DTP sing 203 n n C3' H3' DTP sing 204 n n O3' HO3' DTP sing 205 n n C2' C1' DTP sing 206 n n C2' "H2'1" DTP sing 207 n n C2' "H2'2" DTP sing 208 n n C1' N9 DTP sing 209 n n C1' H1' DTP sing 210 n n N9 C8 DTP sing 211 n y N9 C4 DTP sing 212 n y C8 N7 DTP doub 213 n y C8 H8 DTP sing 214 n n N7 C5 DTP sing 215 n y C5 C6 DTP sing 216 n y C5 C4 DTP doub 217 n y C6 N6 DTP sing 218 n n C6 N1 DTP doub 219 n y N6 HN61 DTP sing 220 n n N6 HN62 DTP sing 221 n n N1 C2 DTP sing 222 n y C2 N3 DTP doub 223 n y C2 H2 DTP sing 224 n n N3 C4 DTP sing 225 n y # _atom_sites.entry_id 6YOM _atom_sites.fract_transf_matrix[1][1] 0.009497 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009497 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.005112 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 FE A 1 701 701 FE FE . D 3 MN A 1 702 702 MN MN . E 4 MG A 1 703 703 MG MG . F 4 MG A 1 704 704 MG MG . G 5 0KX A 1 705 801 0KX dCN . H 6 CZF A 1 706 802 CZF XTP . I 7 DTP A 1 707 803 DTP DTP . J 7 DTP B 1 701 803 DTP DTP . K 2 FE B 1 702 701 FE FE . L 3 MN B 1 703 702 MN MN . M 4 MG B 1 704 703 MG MG . N 4 MG B 1 705 704 MG MG . O 5 0KX B 1 706 801 0KX dCN . P 6 CZF B 1 707 802 CZF XTP . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 P PG DTP . . . I 7 1.513 -28.81 -1.912 1 66.88 ? PG DTP 707 A 1 HETATM 2 O O1G DTP . . . I 7 2.65 -29.596 -1.319 1 69.07 ? O1G DTP 707 A 1 HETATM 3 O O2G DTP . . . I 7 0.303 -28.611 -1.084 1 63.14 ? O2G DTP 707 A 1 HETATM 4 O O3G DTP . . . I 7 1.262 -29.272 -3.309 1 69.64 ? O3G DTP 707 A 1 HETATM 5 P PB DTP . . . I 7 2.518 -26.438 -3.307 1 70.28 ? PB DTP 707 A 1 HETATM 6 O O1B DTP . . . I 7 1.716 -26.953 -4.489 1 73.71 ? O1B DTP 707 A 1 HETATM 7 O O2B DTP . . . I 7 4.023 -26.284 -3.498 1 66.31 ? O2B DTP 707 A 1 HETATM 8 O O3B DTP . . . I 7 2.06 -27.288 -1.99 1 68.92 ? O3B DTP 707 A 1 HETATM 9 P PA DTP . . . I 7 2.509 -23.922 -1.926 1 63.93 ? PA DTP 707 A 1 HETATM 10 O O1A DTP . . . I 7 1.712 -23.738 -0.68 1 63.86 ? O1A DTP 707 A 1 HETATM 11 O O2A DTP . . . I 7 3.991 -23.98 -1.844 1 65.07 ? O2A DTP 707 A 1 HETATM 12 O O3A DTP . . . I 7 1.825 -25.06 -2.826 1 65.64 ? O3A DTP 707 A 1 HETATM 13 O O5' DTP . . . I 7 2.348 -22.625 -2.856 1 65.9 ? O5' DTP 707 A 1 HETATM 14 C C5' DTP . . . I 7 1.095 -22.251 -3.421 1 65.64 ? C5' DTP 707 A 1 HETATM 15 C C4' DTP . . . I 7 1.124 -20.802 -3.886 1 63.93 ? C4' DTP 707 A 1 HETATM 16 O O4' DTP . . . I 7 1.377 -19.993 -2.752 1 64.67 ? O4' DTP 707 A 1 HETATM 17 C C3' DTP . . . I 7 2.226 -20.517 -4.873 1 63.86 ? C3' DTP 707 A 1 HETATM 18 O O3' DTP . . . I 7 1.749 -19.57 -5.831 1 62.76 ? O3' DTP 707 A 1 HETATM 19 C C2' DTP . . . I 7 3.354 -19.984 -4.002 1 64.39 ? C2' DTP 707 A 1 HETATM 20 C C1' DTP . . . I 7 2.65 -19.383 -2.777 1 63.6 ? C1' DTP 707 A 1 HETATM 21 N N9 DTP . . . I 7 3.23 -19.544 -1.404 1 62.52 ? N9 DTP 707 A 1 HETATM 22 C C8 DTP . . . I 7 3.982 -20.535 -0.924 1 62.64 ? C8 DTP 707 A 1 HETATM 23 N N7 DTP . . . I 7 4.307 -20.304 0.364 1 62.77 ? N7 DTP 707 A 1 HETATM 24 C C5 DTP . . . I 7 3.739 -19.156 0.72 1 62.09 ? C5 DTP 707 A 1 HETATM 25 C C6 DTP . . . I 7 3.697 -18.335 1.934 1 62.66 ? C6 DTP 707 A 1 HETATM 26 N N6 DTP . . . I 7 4.333 -18.769 3.024 1 65.02 ? N6 DTP 707 A 1 HETATM 27 N N1 DTP . . . I 7 3.037 -17.17 1.936 1 62.13 ? N1 DTP 707 A 1 HETATM 28 C C2 DTP . . . I 7 2.385 -16.758 0.828 1 63.35 ? C2 DTP 707 A 1 HETATM 29 N N3 DTP . . . I 7 2.387 -17.449 -0.332 1 62.73 ? N3 DTP 707 A 1 HETATM 30 C C4 DTP . . . I 7 3.031 -18.648 -0.437 1 62.63 ? C4 DTP 707 A 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 30 #