data_6YOM # _model_server_result.job_id '_UzStooawx3AEHmxbGDUsA' _model_server_result.datetime_utc '2024-11-17 12:35:20' _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":"J","auth_seq_id":701}' # _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 . . . J 7 8.7 14.648 -21.186 1 71.66 ? PG DTP 701 B 1 HETATM 2 O O1G DTP . . . J 7 9.606 13.958 -22.196 1 66.82 ? O1G DTP 701 B 1 HETATM 3 O O2G DTP . . . J 7 7.626 15.461 -21.909 1 68.11 ? O2G DTP 701 B 1 HETATM 4 O O3G DTP . . . J 7 9.398 15.246 -19.979 1 65.65 ? O3G DTP 701 B 1 HETATM 5 P PB DTP . . . J 7 8.034 11.867 -20.563 1 66.86 ? PB DTP 701 B 1 HETATM 6 O O1B DTP . . . J 7 6.994 11.325 -21.535 1 64.53 ? O1B DTP 701 B 1 HETATM 7 O O2B DTP . . . J 7 9.516 11.635 -20.786 1 71.84 ? O2B DTP 701 B 1 HETATM 8 O O3B DTP . . . J 7 7.922 13.484 -20.35 1 70.06 ? O3B DTP 701 B 1 HETATM 9 P PA DTP . . . J 7 6.226 11.273 -18.397 1 56.96 ? PA DTP 701 B 1 HETATM 10 O O1A DTP . . . J 7 6.161 12.342 -17.332 1 54.28 ? O1A DTP 701 B 1 HETATM 11 O O2A DTP . . . J 7 5.029 11.177 -19.314 1 58.56 ? O2A DTP 701 B 1 HETATM 12 O O3A DTP . . . J 7 7.669 11.336 -19.103 1 58.42 ? O3A DTP 701 B 1 HETATM 13 O O5' DTP . . . J 7 6.484 9.832 -17.723 1 55.2 ? O5' DTP 701 B 1 HETATM 14 C C5' DTP . . . J 7 7.67 9.632 -16.939 1 54.2 ? C5' DTP 701 B 1 HETATM 15 C C4' DTP . . . J 7 7.509 8.536 -15.91 1 52.11 ? C4' DTP 701 B 1 HETATM 16 O O4' DTP . . . J 7 6.323 8.708 -15.133 1 50.39 ? O4' DTP 701 B 1 HETATM 17 C C3' DTP . . . J 7 7.416 7.199 -16.635 1 53.1 ? C3' DTP 701 B 1 HETATM 18 O O3' DTP . . . J 7 8.05 6.119 -15.959 1 52.2 ? O3' DTP 701 B 1 HETATM 19 C C2' DTP . . . J 7 5.951 6.866 -16.626 1 54.25 ? C2' DTP 701 B 1 HETATM 20 C C1' DTP . . . J 7 5.367 7.675 -15.479 1 53.48 ? C1' DTP 701 B 1 HETATM 21 N N9 DTP . . . J 7 4.094 8.387 -15.763 1 55.09 ? N9 DTP 701 B 1 HETATM 22 C C8 DTP . . . J 7 3.652 9.053 -16.863 1 53.73 ? C8 DTP 701 B 1 HETATM 23 N N7 DTP . . . J 7 2.435 9.603 -16.641 1 53.84 ? N7 DTP 701 B 1 HETATM 24 C C5 DTP . . . J 7 2.121 9.308 -15.391 1 56.58 ? C5 DTP 701 B 1 HETATM 25 C C6 DTP . . . J 7 1.003 9.611 -14.502 1 60.48 ? C6 DTP 701 B 1 HETATM 26 N N6 DTP . . . J 7 0.018 10.329 -15.026 1 64.66 ? N6 DTP 701 B 1 HETATM 27 N N1 DTP . . . J 7 0.989 9.147 -13.218 1 62.52 ? N1 DTP 701 B 1 HETATM 28 C C2 DTP . . . J 7 2.041 8.404 -12.757 1 63.05 ? C2 DTP 701 B 1 HETATM 29 N N3 DTP . . . J 7 3.133 8.074 -13.513 1 58.72 ? N3 DTP 701 B 1 HETATM 30 C C4 DTP . . . J 7 3.202 8.503 -14.806 1 57.12 ? C4 DTP 701 B 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 393 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 30 #