data_7N7I # _model_server_result.job_id t4JAMG0fgi_uCsVyqHL30g _model_server_result.datetime_utc '2025-02-22 15:17:34' _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 7n7i # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":403}' # _entry.id 7N7I # _exptl.entry_id 7N7I _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 484.141 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE 5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 3 _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 120 _cell.entry_id 7N7I _cell.length_a 85.943 _cell.length_b 85.943 _cell.length_c 111.718 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7N7I _symmetry.cell_setting ? _symmetry.Int_Tables_number 144 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,F 1 1 B,G,H,I 2 1 C,J,K,L 3 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 ? 4 F N N ? 4 I N N ? 4 L 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 D N SAM . A SAM 401 1_555 E FE2 SF4 . A SF4 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.653 ? metalc ? metalc2 D OXT SAM . A SAM 401 1_555 E FE2 SF4 . A SF4 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.555 ? metalc ? metalc3 G N SAM . B SAM 401 1_555 H FE2 SF4 . B SF4 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.679 ? metalc ? metalc4 G OXT SAM . B SAM 401 1_555 H FE2 SF4 . B SF4 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.589 ? metalc ? metalc5 J OXT SAM . C SAM 401 1_555 K FE2 SF4 . C SF4 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.616 ? # _chem_comp.formula 'C9 H15 N2 O15 P3' _chem_comp.formula_weight 484.141 _chem_comp.id UTP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE 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 PA O1A UTP doub 419 n n PA O2A UTP sing 420 n n PA O3A UTP sing 421 n n PA O5' UTP sing 422 n n O2A H2A UTP sing 423 n n O3A PB UTP sing 424 n n O5' C5' UTP sing 425 n n PB O1B UTP sing 426 n n PB O2B UTP doub 427 n n PB O3B UTP sing 428 n n O1B H1B UTP sing 429 n n O3B PG UTP sing 430 n n PG O1G UTP sing 431 n n PG O2G UTP doub 432 n n PG O3G UTP sing 433 n n O1G H1G UTP sing 434 n n O3G H3G UTP sing 435 n n C5' C4' UTP sing 436 n n C5' "H5'1" UTP sing 437 n n C5' "H5'2" UTP sing 438 n n C4' O4' UTP sing 439 n n C4' C3' UTP sing 440 n n C4' H4' UTP sing 441 n n O4' C1' UTP sing 442 n n C1' C2' UTP sing 443 n n C1' N1 UTP sing 444 n n C1' H1' UTP sing 445 n n C2' O2' UTP sing 446 n n C2' C3' UTP sing 447 n n C2' H2' UTP sing 448 n n O2' HA UTP sing 449 n n C3' O3' UTP sing 450 n n C3' H3' UTP sing 451 n n O3' HB UTP sing 452 n n N1 C6 UTP sing 453 n y N1 C2 UTP sing 454 n y C6 C5 UTP doub 455 n y C6 H6 UTP sing 456 n n C2 O2 UTP doub 457 n n C2 N3 UTP sing 458 n y N3 C4 UTP sing 459 n y N3 H3 UTP sing 460 n n C4 O4 UTP doub 461 n n C4 C5 UTP sing 462 n y C5 H5 UTP sing 463 n n # _atom_sites.entry_id 7N7I _atom_sites.fract_transf_matrix[1][1] 0.011636 _atom_sites.fract_transf_matrix[1][2] 0.006718 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013436 _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] 0.008951 _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 D 2 SAM A 1 401 304 SAM SAM . E 3 SF4 A 1 402 305 SF4 SF4 . F 4 UTP A 1 403 306 UTP UTP . G 2 SAM B 1 401 304 SAM SAM . H 3 SF4 B 1 402 305 SF4 SF4 . I 4 UTP B 1 403 306 UTP UTP . J 2 SAM C 1 401 304 SAM SAM . K 3 SF4 C 1 402 305 SF4 SF4 . L 4 UTP C 1 403 306 UTP UTP . # 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 PA UTP . . . I 4 -84.384 -96.768 -10.041 1 33.44 ? PA UTP 403 B 1 HETATM 2 O O1A UTP . . . I 4 -83.87 -96.299 -11.408 1 30.88 ? O1A UTP 403 B 1 HETATM 3 O O2A UTP . . . I 4 -83.515 -97.894 -9.536 1 31.98 -1 O2A UTP 403 B 1 HETATM 4 O O3A UTP . . . I 4 -85.941 -97.284 -10.188 1 33.47 ? O3A UTP 403 B 1 HETATM 5 O O5' UTP . . . I 4 -84.331 -95.504 -8.949 1 30.99 ? O5' UTP 403 B 1 HETATM 6 P PB UTP . . . I 4 -86.418 -98.662 -10.962 1 31.31 ? PB UTP 403 B 1 HETATM 7 O O1B UTP . . . I 4 -86.419 -99.801 -10.005 1 33.48 -1 O1B UTP 403 B 1 HETATM 8 O O2B UTP . . . I 4 -87.745 -98.473 -11.513 1 29.12 ? O2B UTP 403 B 1 HETATM 9 O O3B UTP . . . I 4 -85.345 -99.017 -12.187 1 28.26 ? O3B UTP 403 B 1 HETATM 10 P PG UTP . . . I 4 -85.428 -100.441 -13.058 1 27.48 ? PG UTP 403 B 1 HETATM 11 O O1G UTP . . . I 4 -85.174 -101.589 -12.14 1 29.57 ? O1G UTP 403 B 1 HETATM 12 O O2G UTP . . . I 4 -84.408 -100.434 -14.124 1 26.37 ? O2G UTP 403 B 1 HETATM 13 O O3G UTP . . . I 4 -86.804 -100.578 -13.686 1 28.03 ? O3G UTP 403 B 1 HETATM 14 C C5' UTP . . . I 4 -84.704 -94.205 -9.364 1 29.75 ? C5' UTP 403 B 1 HETATM 15 C C4' UTP . . . I 4 -85.545 -93.608 -8.395 1 27.87 ? C4' UTP 403 B 1 HETATM 16 O O4' UTP . . . I 4 -85.579 -92.061 -8.585 1 25.79 ? O4' UTP 403 B 1 HETATM 17 C C1' UTP . . . I 4 -86.837 -91.756 -8.276 1 25.07 ? C1' UTP 403 B 1 HETATM 18 C C2' UTP . . . I 4 -87.703 -92.963 -8.933 1 26.36 ? C2' UTP 403 B 1 HETATM 19 O O2' UTP . . . I 4 -89.024 -92.984 -8.388 1 26.8 ? O2' UTP 403 B 1 HETATM 20 C C3' UTP . . . I 4 -87.027 -94.07 -8.59 1 27.61 ? C3' UTP 403 B 1 HETATM 21 O O3' UTP . . . I 4 -87.55 -94.622 -7.353 1 28.1 ? O3' UTP 403 B 1 HETATM 22 N N1 UTP . . . I 4 -87.211 -90.478 -8.819 1 25.17 ? N1 UTP 403 B 1 HETATM 23 C C6 UTP . . . I 4 -86.895 -90.158 -10.055 1 27.13 ? C6 UTP 403 B 1 HETATM 24 C C2 UTP . . . I 4 -87.888 -89.602 -8.043 1 26.31 ? C2 UTP 403 B 1 HETATM 25 O O2 UTP . . . I 4 -88.169 -89.901 -6.913 1 29.67 ? O2 UTP 403 B 1 HETATM 26 N N3 UTP . . . I 4 -88.236 -88.402 -8.532 1 26.75 ? N3 UTP 403 B 1 HETATM 27 C C4 UTP . . . I 4 -87.922 -88.08 -9.776 1 27.33 ? C4 UTP 403 B 1 HETATM 28 O O4 UTP . . . I 4 -88.231 -87.035 -10.202 1 27.17 ? O4 UTP 403 B 1 HETATM 29 C C5 UTP . . . I 4 -87.251 -88.95 -10.549 1 27.89 ? C5 UTP 403 B 1 # _model_server_stats.io_time_ms 73 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 29 #