data_7S0Y # _model_server_result.job_id raQI0I4q2LzLwJOsJqolgA _model_server_result.datetime_utc '2024-11-24 17:03:06' _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 7s0y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":602}' # _entry.id 7S0Y # _exptl.entry_id 7S0Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _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 7S0Y _cell.length_a 122.354 _cell.length_b 140.948 _cell.length_c 111.803 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7S0Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 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,I,J,K,L,M,N,O,P,Q,R,S _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 290 A ASP 288 1_555 C MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc2 A OE1 GLU 517 A GLU 515 1_555 C MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc3 C MN MN . A MN 601 1_555 D O1A UDP . A UDP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? metalc ? metalc4 C MN MN . A MN 601 1_555 D O1B UDP . A UDP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc5 C MN MN . A MN 601 1_555 R O HOH . A HOH 710 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc6 C MN MN . A MN 601 1_555 R O HOH . A HOH 711 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? metalc ? metalc7 B OG1 THR 18 B THR 17 1_555 O MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? metalc ? metalc8 N O2B GDP . B GDP 201 1_555 O MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? metalc ? metalc9 O MG MG . B MG 202 1_555 S O HOH . B HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.86 ? metalc ? metalc10 O MG MG . B MG 202 1_555 S O HOH . B HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? metalc ? metalc11 O MG MG . B MG 202 1_555 S O HOH . B HOH 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.77 ? metalc ? metalc12 O MG MG . B MG 202 1_555 S O HOH . B HOH 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.438 ? # _chem_comp.formula 'C9 H14 N2 O12 P2' _chem_comp.formula_weight 404.161 _chem_comp.id UDP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 N1 C2 UDP sing 407 n n N1 C6 UDP sing 408 n n N1 C1' UDP sing 409 n n C2 N3 UDP sing 410 n n C2 O2 UDP doub 411 n n N3 C4 UDP sing 412 n n N3 HN3 UDP sing 413 n n C4 C5 UDP sing 414 n n C4 O4 UDP doub 415 n n C5 C6 UDP doub 416 n n C5 H5 UDP sing 417 n n C6 H6 UDP sing 418 n n C1' C2' UDP sing 419 n n C1' O4' UDP sing 420 n n C1' H1' UDP sing 421 n n C2' O2' UDP sing 422 n n C2' C3' UDP sing 423 n n C2' H2' UDP sing 424 n n O2' HO2' UDP sing 425 n n C3' C4' UDP sing 426 n n C3' O3' UDP sing 427 n n C3' H3' UDP sing 428 n n C4' O4' UDP sing 429 n n C4' C5' UDP sing 430 n n C4' H4' UDP sing 431 n n O3' HO3' UDP sing 432 n n C5' O5' UDP sing 433 n n C5' "H5'1" UDP sing 434 n n C5' "H5'2" UDP sing 435 n n O5' PA UDP sing 436 n n PA O1A UDP doub 437 n n PA O2A UDP sing 438 n n PA O3A UDP sing 439 n n O2A HOA2 UDP sing 440 n n O3A PB UDP sing 441 n n PB O1B UDP doub 442 n n PB O2B UDP sing 443 n n PB O3B UDP sing 444 n n O2B HOB2 UDP sing 445 n n O3B HOB3 UDP sing 446 n n # _atom_sites.entry_id 7S0Y _atom_sites.fract_transf_matrix[1][1] 0.008173 _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] 0.007095 _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] 0.008944 _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 3 MN A 1 601 1542 MN MN . D 4 UDP A 1 602 1543 UDP UDP . E 5 SO4 A 1 603 1 SO4 SO4 . F 5 SO4 A 1 604 2 SO4 SO4 . G 5 SO4 A 1 605 3 SO4 SO4 . H 5 SO4 A 1 606 4 SO4 SO4 . I 5 SO4 A 1 607 5 SO4 SO4 . J 5 SO4 A 1 608 8 SO4 SO4 . K 5 SO4 A 1 609 22 SO4 SO4 . L 5 SO4 A 1 610 23 SO4 SO4 . M 5 SO4 A 1 611 24 SO4 SO4 . N 6 GDP B 1 201 200 GDP GDP . O 7 MG B 1 202 201 MG MG . P 5 SO4 B 1 203 6 SO4 SO4 . Q 5 SO4 B 1 204 7 SO4 SO4 . R 8 HOH A 1 701 23 HOH HOH . R 8 HOH A 2 702 21 HOH HOH . R 8 HOH A 3 703 35 HOH HOH . R 8 HOH A 4 704 7 HOH HOH . R 8 HOH A 5 705 1 HOH HOH . R 8 HOH A 6 706 2 HOH HOH . R 8 HOH A 7 707 9 HOH HOH . R 8 HOH A 8 708 11 HOH HOH . R 8 HOH A 9 709 22 HOH HOH . R 8 HOH A 10 710 39 HOH HOH . R 8 HOH A 11 711 38 HOH HOH . R 8 HOH A 12 712 18 HOH HOH . R 8 HOH A 13 713 28 HOH HOH . R 8 HOH A 14 714 14 HOH HOH . R 8 HOH A 15 715 27 HOH HOH . R 8 HOH A 16 716 24 HOH HOH . S 8 HOH B 1 301 15 HOH HOH . S 8 HOH B 2 302 32 HOH HOH . S 8 HOH B 3 303 17 HOH HOH . S 8 HOH B 4 304 4 HOH HOH . S 8 HOH B 5 305 16 HOH HOH . S 8 HOH B 6 306 37 HOH HOH . S 8 HOH B 7 307 5 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 N N1 UDP . . . D 4 -32.133 -31.232 -9.678 1 56.45 ? N1 UDP 602 A 1 HETATM 2 C C2 UDP . . . D 4 -33.24 -31.672 -10.437 1 55.1 ? C2 UDP 602 A 1 HETATM 3 N N3 UDP . . . D 4 -34.341 -30.899 -10.525 1 55.69 ? N3 UDP 602 A 1 HETATM 4 C C4 UDP . . . D 4 -34.403 -29.695 -9.916 1 56.52 ? C4 UDP 602 A 1 HETATM 5 C C5 UDP . . . D 4 -33.324 -29.245 -9.162 1 52.04 ? C5 UDP 602 A 1 HETATM 6 C C6 UDP . . . D 4 -32.193 -30.043 -9.055 1 56.33 ? C6 UDP 602 A 1 HETATM 7 O O2 UDP . . . D 4 -33.193 -32.784 -11.005 1 51.95 ? O2 UDP 602 A 1 HETATM 8 O O4 UDP . . . D 4 -35.42 -28.957 -10.023 1 59.33 ? O4 UDP 602 A 1 HETATM 9 C C1' UDP . . . D 4 -30.942 -32.086 -9.562 1 57.22 ? C1' UDP 602 A 1 HETATM 10 C C2' UDP . . . D 4 -30.049 -31.956 -10.768 1 57.72 ? C2' UDP 602 A 1 HETATM 11 O O2' UDP . . . D 4 -29.462 -33.239 -11.01 1 62.55 ? O2' UDP 602 A 1 HETATM 12 C C3' UDP . . . D 4 -29.011 -30.955 -10.325 1 55.2 ? C3' UDP 602 A 1 HETATM 13 C C4' UDP . . . D 4 -28.801 -31.369 -8.878 1 51.06 ? C4' UDP 602 A 1 HETATM 14 O O4' UDP . . . D 4 -30.107 -31.728 -8.454 1 55.81 ? O4' UDP 602 A 1 HETATM 15 O O3' UDP . . . D 4 -27.842 -31.037 -11.149 1 54.76 ? O3' UDP 602 A 1 HETATM 16 C C5' UDP . . . D 4 -28.301 -30.326 -7.897 1 52.91 ? C5' UDP 602 A 1 HETATM 17 O O5' UDP . . . D 4 -28.077 -29.109 -8.558 1 57.13 ? O5' UDP 602 A 1 HETATM 18 P PA UDP . . . D 4 -27.516 -27.847 -7.799 1 57.65 ? PA UDP 602 A 1 HETATM 19 O O1A UDP . . . D 4 -26.322 -27.395 -8.589 1 63.98 ? O1A UDP 602 A 1 HETATM 20 O O2A UDP . . . D 4 -28.694 -26.929 -7.656 1 59.44 ? O2A UDP 602 A 1 HETATM 21 O O3A UDP . . . D 4 -27.058 -28.427 -6.36 1 58.28 ? O3A UDP 602 A 1 HETATM 22 P PB UDP . . . D 4 -25.893 -27.72 -5.486 1 56.97 ? PB UDP 602 A 1 HETATM 23 O O1B UDP . . . D 4 -24.69 -27.708 -6.386 1 59.87 ? O1B UDP 602 A 1 HETATM 24 O O2B UDP . . . D 4 -26.37 -26.329 -5.172 1 56.73 ? O2B UDP 602 A 1 HETATM 25 O O3B UDP . . . D 4 -25.816 -28.654 -4.318 1 54.55 ? O3B UDP 602 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 348 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #