data_4AY5 # _model_server_result.job_id BgXRD_tZ_t3vzL4slEND0w _model_server_result.datetime_utc '2024-11-23 19:35:06' _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 4ay5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":1201}' # _entry.id 4AY5 # _exptl.entry_id 4AY5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 4 _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 4AY5 _cell.length_a 274.17 _cell.length_b 274.17 _cell.length_c 142.15 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4AY5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 150 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 3 2 1' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 PISA dimeric 2 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,I,M 1 1 B,F,J,N 2 1 C,G,K,O 3 1 D,H,L,P 4 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 ? 3 I N N ? 3 J N N ? 3 K N N ? 3 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 covale ? covale1 E OG SER 7 I SER 7 1_555 M C1 NAG . I NAG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.481 ? covale ? covale2 F OG SER 7 J SER 7 1_555 N C1 NAG . J NAG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.505 ? covale ? covale3 G OG SER 7 K SER 7 1_555 O C1 NAG . K NAG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale4 H OG SER 7 L SER 7 1_555 P C1 NAG . L NAG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? # _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 386 n n N1 C6 UDP sing 387 n n N1 C1' UDP sing 388 n n C2 N3 UDP sing 389 n n C2 O2 UDP doub 390 n n N3 C4 UDP sing 391 n n N3 HN3 UDP sing 392 n n C4 C5 UDP sing 393 n n C4 O4 UDP doub 394 n n C5 C6 UDP doub 395 n n C5 H5 UDP sing 396 n n C6 H6 UDP sing 397 n n C1' C2' UDP sing 398 n n C1' O4' UDP sing 399 n n C1' H1' UDP sing 400 n n C2' O2' UDP sing 401 n n C2' C3' UDP sing 402 n n C2' H2' UDP sing 403 n n O2' HO2' UDP sing 404 n n C3' C4' UDP sing 405 n n C3' O3' UDP sing 406 n n C3' H3' UDP sing 407 n n C4' O4' UDP sing 408 n n C4' C5' UDP sing 409 n n C4' H4' UDP sing 410 n n O3' HO3' UDP sing 411 n n C5' O5' UDP sing 412 n n C5' "H5'1" UDP sing 413 n n C5' "H5'2" UDP sing 414 n n O5' PA UDP sing 415 n n PA O1A UDP doub 416 n n PA O2A UDP sing 417 n n PA O3A UDP sing 418 n n O2A HOA2 UDP sing 419 n n O3A PB UDP sing 420 n n PB O1B UDP doub 421 n n PB O2B UDP sing 422 n n PB O3B UDP sing 423 n n O2B HOB2 UDP sing 424 n n O3B HOB3 UDP sing 425 n n # _atom_sites.entry_id 4AY5 _atom_sites.fract_transf_matrix[1][1] 0.003647 _atom_sites.fract_transf_matrix[1][2] 0.002106 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004212 _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] 0.007035 _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 I 3 UDP A 1 1201 1201 UDP UDP . J 3 UDP B 1 1201 1201 UDP UDP . K 3 UDP C 1 1201 1201 UDP UDP . L 3 UDP D 1 1201 1201 UDP UDP . M 4 NAG I 1 1202 1202 NAG NAG . N 4 NAG J 1 1202 1202 NAG NAG . O 4 NAG K 1 1202 1202 NAG NAG . P 4 NAG L 1 1202 1202 NAG NAG . # 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 . . . J 3 99.163 27.141 24.981 1 65.44 ? N1 UDP 1201 B 1 HETATM 2 C C2 UDP . . . J 3 98.485 28.349 25.315 1 61.6 ? C2 UDP 1201 B 1 HETATM 3 N N3 UDP . . . J 3 97.182 28.486 24.987 1 55.08 ? N3 UDP 1201 B 1 HETATM 4 C C4 UDP . . . J 3 96.505 27.529 24.334 1 56.59 ? C4 UDP 1201 B 1 HETATM 5 C C5 UDP . . . J 3 97.148 26.34 23.998 1 68.65 ? C5 UDP 1201 B 1 HETATM 6 C C6 UDP . . . J 3 98.502 26.155 24.328 1 75.29 ? C6 UDP 1201 B 1 HETATM 7 O O2 UDP . . . J 3 99.083 29.281 25.928 1 62.87 ? O2 UDP 1201 B 1 HETATM 8 O O4 UDP . . . J 3 95.301 27.685 24.034 1 54.64 ? O4 UDP 1201 B 1 HETATM 9 C C1' UDP . . . J 3 100.581 26.992 25.31 1 65.03 ? C1' UDP 1201 B 1 HETATM 10 C C2' UDP . . . J 3 101.022 25.817 26.163 1 65.76 ? C2' UDP 1201 B 1 HETATM 11 O O2' UDP . . . J 3 100.665 25.944 27.538 1 67.15 ? O2' UDP 1201 B 1 HETATM 12 C C3' UDP . . . J 3 102.515 25.922 25.899 1 69.03 ? C3' UDP 1201 B 1 HETATM 13 C C4' UDP . . . J 3 102.482 25.999 24.378 1 64.64 ? C4' UDP 1201 B 1 HETATM 14 O O4' UDP . . . J 3 101.327 26.789 24.106 1 66.54 ? O4' UDP 1201 B 1 HETATM 15 O O3' UDP . . . J 3 103.111 27.147 26.419 1 67.77 ? O3' UDP 1201 B 1 HETATM 16 C C5' UDP . . . J 3 102.377 24.642 23.677 1 56.44 ? C5' UDP 1201 B 1 HETATM 17 O O5' UDP . . . J 3 103.572 24.504 22.882 1 59.5 ? O5' UDP 1201 B 1 HETATM 18 P PA UDP . . . J 3 104.164 23.055 22.449 1 76.02 ? PA UDP 1201 B 1 HETATM 19 O O1A UDP . . . J 3 102.993 22.214 21.849 1 72.87 ? O1A UDP 1201 B 1 HETATM 20 O O2A UDP . . . J 3 105.575 23.288 21.919 1 59.3 ? O2A UDP 1201 B 1 HETATM 21 O O3A UDP . . . J 3 104.446 22.413 23.887 1 69.15 ? O3A UDP 1201 B 1 HETATM 22 P PB UDP . . . J 3 104.529 20.858 24.191 1 50.38 ? PB UDP 1201 B 1 HETATM 23 O O1B UDP . . . J 3 103.128 20.543 24.749 1 35.93 ? O1B UDP 1201 B 1 HETATM 24 O O2B UDP . . . J 3 105.705 21.044 25.139 1 54.53 ? O2B UDP 1201 B 1 HETATM 25 O O3B UDP . . . J 3 104.998 20.27 22.874 1 43.64 ? O3B UDP 1201 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 230 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 25 #