data_5MIL # _model_server_result.job_id '_QrH9wHmCw9bnRD-ov5kFQ' _model_server_result.datetime_utc '2024-12-25 16:27:10' _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 5mil # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":201}' # _entry.id 5MIL # _exptl.entry_id 5MIL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 467.157 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-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 91.68 _cell.angle_gamma 90 _cell.entry_id 5MIL _cell.length_a 33.47 _cell.length_b 88.84 _cell.length_c 54.15 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5MIL _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 F 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 OE1 GLU 73 A GLU 39 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? metalc ? metalc2 A OE2 GLU 73 A GLU 39 1_555 E MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc3 A OE1 GLU 76 A GLU 42 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc4 A OE2 GLU 76 A GLU 42 1_555 E MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc5 A OE1 GLU 101 A GLU 67 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? metalc ? metalc6 A OD2 ASP 104 A ASP 70 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? metalc ? metalc7 C O1B DUP . A DUP 201 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? metalc ? metalc8 C O1A DUP . A DUP 201 1_555 E MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc9 C O1B DUP . A DUP 201 1_555 E MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? metalc ? metalc10 C O1G DUP . A DUP 201 1_555 E MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.963 ? metalc ? metalc11 D MG MG . A MG 202 1_555 I O HOH . A HOH 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc12 E MG MG . A MG 203 1_555 J O HOH . B HOH 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc13 I O HOH . A HOH 306 1_555 H MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc14 B OE1 GLU 73 B GLU 39 1_555 G MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc15 B OE2 GLU 73 B GLU 39 1_555 H MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? metalc ? metalc16 B OE1 GLU 76 B GLU 42 1_555 G MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc17 B OE2 GLU 76 B GLU 42 1_555 H MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc18 B OE1 GLU 101 B GLU 67 1_555 G MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc19 B OD2 ASP 104 B ASP 70 1_555 G MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc20 F O2B DUP . B DUP 201 1_555 G MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? metalc ? metalc21 F O2A DUP . B DUP 201 1_555 H MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc22 F O2B DUP . B DUP 201 1_555 H MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc23 F O2G DUP . B DUP 201 1_555 H MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc24 G MG MG . B MG 202 1_555 J O HOH . B HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? # _chem_comp.formula 'C9 H16 N3 O13 P3' _chem_comp.formula_weight 467.157 _chem_comp.id DUP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-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 O4 C4 DUP doub 70 n n C4 C5 DUP sing 71 n y C4 N3 DUP sing 72 n y C5 C6 DUP doub 73 n y C5 H5 DUP sing 74 n n C6 N1 DUP sing 75 n y C6 H6 DUP sing 76 n n N3 C2 DUP sing 77 n y N3 HN3 DUP sing 78 n n C2 O2 DUP doub 79 n n C2 N1 DUP sing 80 n y N1 C1' DUP sing 81 n n C1' C2' DUP sing 82 n n C1' O4' DUP sing 83 n n C1' H1' DUP sing 84 n n C2' C3' DUP sing 85 n n C2' "H2'1" DUP sing 86 n n C2' "H2'2" DUP sing 87 n n C3' O3' DUP sing 88 n n C3' C4' DUP sing 89 n n C3' H1 DUP sing 90 n n O3' H3' DUP sing 91 n n O4' C4' DUP sing 92 n n C4' C5' DUP sing 93 n n C4' H4' DUP sing 94 n n C5' O5' DUP sing 95 n n C5' "H5'1" DUP sing 96 n n C5' "H5'2" DUP sing 97 n n O5' PA DUP sing 98 n n PA O1A DUP doub 99 n n PA O2A DUP sing 100 n n PA N3A DUP sing 101 n n O2A H2A DUP sing 102 n n N3A PB DUP sing 103 n n N3A H3A DUP sing 104 n n PB O1B DUP doub 105 n n PB O2B DUP sing 106 n n PB O3B DUP sing 107 n n O2B H2B DUP sing 108 n n O3B PG DUP sing 109 n n PG O2G DUP doub 110 n n PG O1G DUP sing 111 n n PG O3G DUP sing 112 n n O1G H1G DUP sing 113 n n O3G H3G DUP sing 114 n n # _atom_sites.entry_id 5MIL _atom_sites.fract_transf_matrix[1][1] 0.029878 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000876 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011256 _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] 0.018475 _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 DUP A 1 201 1265 DUP DUP . D 3 MG A 1 202 1 MG MG . E 3 MG A 1 203 3 MG MG . F 2 DUP B 1 201 1265 DUP DUP . G 3 MG B 1 202 2 MG MG . H 3 MG B 1 203 4 MG MG . I 4 HOH A 1 301 66 HOH HOH . I 4 HOH A 2 302 91 HOH HOH . I 4 HOH A 3 303 99 HOH HOH . I 4 HOH A 4 304 83 HOH HOH . I 4 HOH A 5 305 86 HOH HOH . I 4 HOH A 6 306 18 HOH HOH . I 4 HOH A 7 307 3 HOH HOH . I 4 HOH A 8 308 33 HOH HOH . I 4 HOH A 9 309 37 HOH HOH . I 4 HOH A 10 310 23 HOH HOH . I 4 HOH A 11 311 12 HOH HOH . I 4 HOH A 12 312 26 HOH HOH . I 4 HOH A 13 313 80 HOH HOH . I 4 HOH A 14 314 88 HOH HOH . I 4 HOH A 15 315 77 HOH HOH . I 4 HOH A 16 316 4 HOH HOH . I 4 HOH A 17 317 11 HOH HOH . I 4 HOH A 18 318 74 HOH HOH . I 4 HOH A 19 319 75 HOH HOH . I 4 HOH A 20 320 79 HOH HOH . I 4 HOH A 21 321 100 HOH HOH . I 4 HOH A 22 322 50 HOH HOH . I 4 HOH A 23 323 9 HOH HOH . I 4 HOH A 24 324 22 HOH HOH . I 4 HOH A 25 325 58 HOH HOH . I 4 HOH A 26 326 93 HOH HOH . I 4 HOH A 27 327 63 HOH HOH . I 4 HOH A 28 328 14 HOH HOH . I 4 HOH A 29 329 64 HOH HOH . I 4 HOH A 30 330 72 HOH HOH . I 4 HOH A 31 331 31 HOH HOH . I 4 HOH A 32 332 29 HOH HOH . I 4 HOH A 33 333 19 HOH HOH . I 4 HOH A 34 334 95 HOH HOH . I 4 HOH A 35 335 40 HOH HOH . I 4 HOH A 36 336 82 HOH HOH . I 4 HOH A 37 337 89 HOH HOH . I 4 HOH A 38 338 96 HOH HOH . I 4 HOH A 39 339 98 HOH HOH . I 4 HOH A 40 340 97 HOH HOH . J 4 HOH B 1 301 68 HOH HOH . J 4 HOH B 2 302 1 HOH HOH . J 4 HOH B 3 303 48 HOH HOH . J 4 HOH B 4 304 2 HOH HOH . J 4 HOH B 5 305 45 HOH HOH . J 4 HOH B 6 306 94 HOH HOH . J 4 HOH B 7 307 27 HOH HOH . J 4 HOH B 8 308 54 HOH HOH . J 4 HOH B 9 309 10 HOH HOH . J 4 HOH B 10 310 56 HOH HOH . J 4 HOH B 11 311 8 HOH HOH . J 4 HOH B 12 312 17 HOH HOH . J 4 HOH B 13 313 30 HOH HOH . J 4 HOH B 14 314 65 HOH HOH . J 4 HOH B 15 315 92 HOH HOH . J 4 HOH B 16 316 44 HOH HOH . J 4 HOH B 17 317 60 HOH HOH . J 4 HOH B 18 318 67 HOH HOH . J 4 HOH B 19 319 46 HOH HOH . J 4 HOH B 20 320 43 HOH HOH . J 4 HOH B 21 321 7 HOH HOH . J 4 HOH B 22 322 69 HOH HOH . J 4 HOH B 23 323 70 HOH HOH . J 4 HOH B 24 324 32 HOH HOH . J 4 HOH B 25 325 15 HOH HOH . J 4 HOH B 26 326 85 HOH HOH . J 4 HOH B 27 327 6 HOH HOH . J 4 HOH B 28 328 76 HOH HOH . J 4 HOH B 29 329 28 HOH HOH . J 4 HOH B 30 330 47 HOH HOH . J 4 HOH B 31 331 5 HOH HOH . J 4 HOH B 32 332 71 HOH HOH . J 4 HOH B 33 333 20 HOH HOH . J 4 HOH B 34 334 41 HOH HOH . # 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 O O4 DUP . . . F 2 22.83 14.515 23.961 1 26.55 ? O4 DUP 201 B 1 HETATM 2 C C4 DUP . . . F 2 22.02 14.209 24.787 1 28.68 ? C4 DUP 201 B 1 HETATM 3 C C5 DUP . . . F 2 21.318 15.155 25.465 1 27.99 ? C5 DUP 201 B 1 HETATM 4 C C6 DUP . . . F 2 20.42 14.776 26.417 1 26.08 ? C6 DUP 201 B 1 HETATM 5 N N3 DUP . . . F 2 21.826 12.912 25.064 1 26.86 ? N3 DUP 201 B 1 HETATM 6 C C2 DUP . . . F 2 20.934 12.538 26.006 1 24.61 ? C2 DUP 201 B 1 HETATM 7 O O2 DUP . . . F 2 20.792 11.356 26.208 1 24.8 ? O2 DUP 201 B 1 HETATM 8 N N1 DUP . . . F 2 20.218 13.465 26.697 1 25.02 ? N1 DUP 201 B 1 HETATM 9 C C1' DUP . . . F 2 19.269 13.078 27.701 1 25.82 ? C1' DUP 201 B 1 HETATM 10 C C2' DUP . . . F 2 19.989 12.483 29.034 1 23.45 ? C2' DUP 201 B 1 HETATM 11 C C3' DUP . . . F 2 19.339 12.918 30.064 1 23.95 ? C3' DUP 201 B 1 HETATM 12 O O3' DUP . . . F 2 18.256 11.957 30.511 1 21.23 ? O3' DUP 201 B 1 HETATM 13 O O4' DUP . . . F 2 18.547 14.094 28.095 1 26.8 ? O4' DUP 201 B 1 HETATM 14 C C4' DUP . . . F 2 18.668 14.235 29.62 1 24.84 ? C4' DUP 201 B 1 HETATM 15 C C5' DUP . . . F 2 19.453 15.341 30.015 1 20.32 ? C5' DUP 201 B 1 HETATM 16 O O5' DUP . . . F 2 18.937 16.577 29.483 1 24.41 ? O5' DUP 201 B 1 HETATM 17 P PA DUP . . . F 2 18.344 17.717 30.497 1 23.3 ? PA DUP 201 B 1 HETATM 18 O O1A DUP . . . F 2 17.868 18.922 29.683 1 21.79 ? O1A DUP 201 B 1 HETATM 19 O O2A DUP . . . F 2 19.413 18.159 31.431 1 20.46 ? O2A DUP 201 B 1 HETATM 20 N N3A DUP . . . F 2 17.048 17.001 31.309 1 21.56 ? N3A DUP 201 B 1 HETATM 21 P PB DUP . . . F 2 16.994 16.939 32.98 1 23.1 ? PB DUP 201 B 1 HETATM 22 O O1B DUP . . . F 2 16.073 15.836 33.464 1 20.64 ? O1B DUP 201 B 1 HETATM 23 O O2B DUP . . . F 2 18.36 16.696 33.553 1 20.88 ? O2B DUP 201 B 1 HETATM 24 O O3B DUP . . . F 2 16.416 18.367 33.395 1 24.15 ? O3B DUP 201 B 1 HETATM 25 P PG DUP . . . F 2 17.118 19.454 34.34 1 19.83 ? PG DUP 201 B 1 HETATM 26 O O2G DUP . . . F 2 18.56 19.655 33.957 1 21.59 ? O2G DUP 201 B 1 HETATM 27 O O1G DUP . . . F 2 16.373 20.754 34.111 1 21.12 ? O1G DUP 201 B 1 HETATM 28 O O3G DUP . . . F 2 16.983 19.026 35.761 1 14.99 ? O3G DUP 201 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #