data_5A2Y # _model_server_result.job_id OqnwdPdukR3PxYSk8i0KTg _model_server_result.datetime_utc '2024-10-19 08:22:22' _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 5a2y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1528}' # _entry.id 5A2Y # _exptl.entry_id 5A2Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 484.141 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE 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 5A2Y _cell.length_a 59.71 _cell.length_b 93.83 _cell.length_c 192.436 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5A2Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _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 _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 E 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 OD2 ASP 226 A ASP 239 1_555 D MG MG . A MG 1529 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.831 ? metalc ? metalc2 C O2A UTP . A UTP 1528 1_555 D MG MG . A MG 1529 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? metalc ? metalc3 C O1G UTP . A UTP 1528 1_555 D MG MG . A MG 1529 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.691 ? metalc ? metalc4 B OD2 ASP 226 B ASP 239 1_555 F MG MG . B MG 1529 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.625 ? metalc ? metalc5 E O1B UTP . B UTP 1528 1_555 F MG MG . B MG 1529 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.401 ? # _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 358 n n PA O2A UTP sing 359 n n PA O3A UTP sing 360 n n PA O5' UTP sing 361 n n O2A H2A UTP sing 362 n n O3A PB UTP sing 363 n n O5' C5' UTP sing 364 n n PB O1B UTP sing 365 n n PB O2B UTP doub 366 n n PB O3B UTP sing 367 n n O1B H1B UTP sing 368 n n O3B PG UTP sing 369 n n PG O1G UTP sing 370 n n PG O2G UTP doub 371 n n PG O3G UTP sing 372 n n O1G H1G UTP sing 373 n n O3G H3G UTP sing 374 n n C5' C4' UTP sing 375 n n C5' "H5'1" UTP sing 376 n n C5' "H5'2" UTP sing 377 n n C4' O4' UTP sing 378 n n C4' C3' UTP sing 379 n n C4' H4' UTP sing 380 n n O4' C1' UTP sing 381 n n C1' C2' UTP sing 382 n n C1' N1 UTP sing 383 n n C1' H1' UTP sing 384 n n C2' O2' UTP sing 385 n n C2' C3' UTP sing 386 n n C2' H2' UTP sing 387 n n O2' HA UTP sing 388 n n C3' O3' UTP sing 389 n n C3' H3' UTP sing 390 n n O3' HB UTP sing 391 n n N1 C6 UTP sing 392 n y N1 C2 UTP sing 393 n y C6 C5 UTP doub 394 n y C6 H6 UTP sing 395 n n C2 O2 UTP doub 396 n n C2 N3 UTP sing 397 n y N3 C4 UTP sing 398 n y N3 H3 UTP sing 399 n n C4 O4 UTP doub 400 n n C4 C5 UTP sing 401 n y C5 H5 UTP sing 402 n n # _atom_sites.entry_id 5A2Y _atom_sites.fract_transf_matrix[1][1] 0.016748 _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] 0.010658 _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] 0.005197 _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 UTP A 1 1528 1528 UTP UTP . D 3 MG A 1 1529 1529 MG MG . E 2 UTP B 1 1528 1528 UTP UTP . F 3 MG B 1 1529 1529 MG MG . G 4 HOH A 1 2001 2001 HOH HOH . G 4 HOH A 2 2002 2002 HOH HOH . G 4 HOH A 3 2003 2003 HOH HOH . H 4 HOH B 1 2001 2001 HOH HOH . H 4 HOH B 2 2002 2002 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 P PA UTP . . . E 2 -25.276 3.244 -1.188 1 135.03 ? PA UTP 1528 B 1 HETATM 2 O O1A UTP . . . E 2 -24.301 4.344 -0.837 1 137.69 ? O1A UTP 1528 B 1 HETATM 3 O O2A UTP . . . E 2 -26.309 3.465 -2.269 1 133.67 ? O2A UTP 1528 B 1 HETATM 4 O O3A UTP . . . E 2 -25.992 2.774 0.179 1 133.84 ? O3A UTP 1528 B 1 HETATM 5 O O5' UTP . . . E 2 -24.412 1.946 -1.588 1 134.11 ? O5' UTP 1528 B 1 HETATM 6 P PB UTP . . . E 2 -27.579 2.866 0.452 1 130.54 ? PB UTP 1528 B 1 HETATM 7 O O1B UTP . . . E 2 -28.315 2.431 -0.794 1 130.8 ? O1B UTP 1528 B 1 HETATM 8 O O2B UTP . . . E 2 -27.835 2.12 1.741 1 130.87 ? O2B UTP 1528 B 1 HETATM 9 O O3B UTP . . . E 2 -27.793 4.447 0.747 1 129.85 ? O3B UTP 1528 B 1 HETATM 10 P PG UTP . . . E 2 -28.772 5.47 -0.045 1 123.81 ? PG UTP 1528 B 1 HETATM 11 O O1G UTP . . . E 2 -28.67 5.087 -1.502 1 125.91 ? O1G UTP 1528 B 1 HETATM 12 O O2G UTP . . . E 2 -30.146 5.255 0.544 1 119 ? O2G UTP 1528 B 1 HETATM 13 O O3G UTP . . . E 2 -28.174 6.821 0.28 1 121.81 ? O3G UTP 1528 B 1 HETATM 14 C C5' UTP . . . E 2 -24.984 0.64 -1.55 1 130.7 ? C5' UTP 1528 B 1 HETATM 15 C C4' UTP . . . E 2 -24.13 -0.274 -0.68 1 130.98 ? C4' UTP 1528 B 1 HETATM 16 O O4' UTP . . . E 2 -22.752 -0.233 -1.068 1 130.62 ? O4' UTP 1528 B 1 HETATM 17 C C1' UTP . . . E 2 -21.931 -0.547 0.066 1 131.96 ? C1' UTP 1528 B 1 HETATM 18 C C2' UTP . . . E 2 -22.838 -0.489 1.293 1 131.21 ? C2' UTP 1528 B 1 HETATM 19 O O2' UTP . . . E 2 -23.047 -1.804 1.819 1 126.9 ? O2' UTP 1528 B 1 HETATM 20 C C3' UTP . . . E 2 -24.15 0.078 0.797 1 130.24 ? C3' UTP 1528 B 1 HETATM 21 O O3' UTP . . . E 2 -25.273 -0.511 1.463 1 125.35 ? O3' UTP 1528 B 1 HETATM 22 N N1 UTP . . . E 2 -20.796 0.386 0.206 1 133.06 ? N1 UTP 1528 B 1 HETATM 23 C C6 UTP . . . E 2 -20.906 1.673 -0.176 1 131.13 ? C6 UTP 1528 B 1 HETATM 24 C C2 UTP . . . E 2 -19.565 -0.071 0.753 1 131.55 ? C2 UTP 1528 B 1 HETATM 25 O O2 UTP . . . E 2 -19.43 -1.264 1.118 1 124.29 ? O2 UTP 1528 B 1 HETATM 26 N N3 UTP . . . E 2 -18.525 0.775 0.883 1 129.48 ? N3 UTP 1528 B 1 HETATM 27 C C4 UTP . . . E 2 -18.627 2.06 0.504 1 129.71 ? C4 UTP 1528 B 1 HETATM 28 O O4 UTP . . . E 2 -17.648 2.831 0.634 1 126.6 ? O4 UTP 1528 B 1 HETATM 29 C C5 UTP . . . E 2 -19.821 2.536 -0.034 1 130.43 ? C5 UTP 1528 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 29 #