data_5MQT # _model_server_result.job_id fgfJPTIT0KvRe8rf8UdcBQ _model_server_result.datetime_utc '2024-11-22 13:50:22' _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 5mqt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":301}' # _entry.id 5MQT # _exptl.entry_id 5MQT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 2 _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 90 _cell.entry_id 5MQT _cell.length_a 93.3 _cell.length_b 93.3 _cell.length_c 342.715 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5MQT _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,I,N,O 1 1 C,D,J,K,L,M,P,Q 2 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 E N N ? 2 H N N ? 2 J N N ? 2 L N N # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id G _struct_conn.ptnr1_label_atom_id MG _struct_conn.ptnr1_label_comp_id MG _struct_conn.ptnr1_label_seq_id . _struct_conn.ptnr1_auth_asym_id B _struct_conn.ptnr1_auth_comp_id MG _struct_conn.ptnr1_auth_seq_id 301 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id I _struct_conn.ptnr2_label_atom_id O1P _struct_conn.ptnr2_label_comp_id DCM _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id B _struct_conn.ptnr2_auth_comp_id DCM _struct_conn.ptnr2_auth_seq_id 303 _struct_conn.ptnr2_symmetry 1_555 _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 2.398 _struct_conn.pdbx_value_order ? # _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 465 n n N1 C6 UDP sing 466 n n N1 C1' UDP sing 467 n n C2 N3 UDP sing 468 n n C2 O2 UDP doub 469 n n N3 C4 UDP sing 470 n n N3 HN3 UDP sing 471 n n C4 C5 UDP sing 472 n n C4 O4 UDP doub 473 n n C5 C6 UDP doub 474 n n C5 H5 UDP sing 475 n n C6 H6 UDP sing 476 n n C1' C2' UDP sing 477 n n C1' O4' UDP sing 478 n n C1' H1' UDP sing 479 n n C2' O2' UDP sing 480 n n C2' C3' UDP sing 481 n n C2' H2' UDP sing 482 n n O2' HO2' UDP sing 483 n n C3' C4' UDP sing 484 n n C3' O3' UDP sing 485 n n C3' H3' UDP sing 486 n n C4' O4' UDP sing 487 n n C4' C5' UDP sing 488 n n C4' H4' UDP sing 489 n n O3' HO3' UDP sing 490 n n C5' O5' UDP sing 491 n n C5' "H5'1" UDP sing 492 n n C5' "H5'2" UDP sing 493 n n O5' PA UDP sing 494 n n PA O1A UDP doub 495 n n PA O2A UDP sing 496 n n PA O3A UDP sing 497 n n O2A HOA2 UDP sing 498 n n O3A PB UDP sing 499 n n PB O1B UDP doub 500 n n PB O2B UDP sing 501 n n PB O3B UDP sing 502 n n O2B HOB2 UDP sing 503 n n O3B HOB3 UDP sing 504 n n # _atom_sites.entry_id 5MQT _atom_sites.fract_transf_matrix[1][1] 0.010718 _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] 0.010718 _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] 0.002918 _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 E 2 UDP A 1 301 500 UDP UDP . F 3 STI A 1 302 600 STI STI . G 4 MG B 1 301 450 MG MG . H 2 UDP B 1 302 500 UDP UDP . I 5 DCM B 1 303 550 DCM DCM . J 2 UDP C 1 301 500 UDP UDP . K 3 STI C 1 302 600 STI STI . L 2 UDP D 1 301 500 UDP UDP . M 5 DCM D 1 302 550 DCM DCM . N 6 HOH A 1 401 8 HOH HOH . N 6 HOH A 2 402 12 HOH HOH . N 6 HOH A 3 403 9 HOH HOH . N 6 HOH A 4 404 14 HOH HOH . N 6 HOH A 5 405 2 HOH HOH . O 6 HOH B 1 401 3 HOH HOH . O 6 HOH B 2 402 4 HOH HOH . P 6 HOH C 1 401 10 HOH HOH . P 6 HOH C 2 402 6 HOH HOH . P 6 HOH C 3 403 7 HOH HOH . P 6 HOH C 4 404 5 HOH HOH . Q 6 HOH D 1 401 15 HOH HOH . Q 6 HOH D 2 402 11 HOH HOH . Q 6 HOH D 3 403 1 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 . . . L 2 35.861 151.642 67.465 1 89.28 ? N1 UDP 301 D 1 HETATM 2 C C2 UDP . . . L 2 37.179 151.373 67.142 1 88.86 ? C2 UDP 301 D 1 HETATM 3 N N3 UDP . . . L 2 37.722 152.196 66.182 1 89.21 ? N3 UDP 301 D 1 HETATM 4 C C4 UDP . . . L 2 37.091 153.229 65.511 1 88.83 ? C4 UDP 301 D 1 HETATM 5 C C5 UDP . . . L 2 35.72 153.433 65.877 1 88.17 ? C5 UDP 301 D 1 HETATM 6 C C6 UDP . . . L 2 35.159 152.659 66.827 1 89.48 ? C6 UDP 301 D 1 HETATM 7 O O2 UDP . . . L 2 37.814 150.448 67.63 1 89.06 ? O2 UDP 301 D 1 HETATM 8 O O4 UDP . . . L 2 37.73 153.91 64.7 1 90.34 ? O4 UDP 301 D 1 HETATM 9 C C1' UDP . . . L 2 35.197 150.768 68.467 1 89.38 ? C1' UDP 301 D 1 HETATM 10 C C2' UDP . . . L 2 34.78 151.453 69.775 1 93.65 ? C2' UDP 301 D 1 HETATM 11 O O2' UDP . . . L 2 35.807 151.467 70.767 1 98.63 ? O2' UDP 301 D 1 HETATM 12 C C3' UDP . . . L 2 33.56 150.618 70.192 1 90.76 ? C3' UDP 301 D 1 HETATM 13 C C4' UDP . . . L 2 32.954 150.2 68.859 1 85.36 ? C4' UDP 301 D 1 HETATM 14 O O4' UDP . . . L 2 34.015 150.26 67.886 1 85.58 ? O4' UDP 301 D 1 HETATM 15 O O3' UDP . . . L 2 33.857 149.443 70.938 1 92.04 ? O3' UDP 301 D 1 HETATM 16 C C5' UDP . . . L 2 31.761 150.982 68.375 1 83.99 ? C5' UDP 301 D 1 HETATM 17 O O5' UDP . . . L 2 32.063 152.38 68.197 1 83.49 ? O5' UDP 301 D 1 HETATM 18 P PA UDP . . . L 2 30.952 153.482 68.499 1 83.83 ? PA UDP 301 D 1 HETATM 19 O O1A UDP . . . L 2 31.342 154.854 68.091 1 84.71 ? O1A UDP 301 D 1 HETATM 20 O O2A UDP . . . L 2 30.579 153.395 69.99 1 82.4 ? O2A UDP 301 D 1 HETATM 21 O O3A UDP . . . L 2 29.638 153.039 67.718 1 81.75 ? O3A UDP 301 D 1 HETATM 22 P PB UDP . . . L 2 28.417 153.898 67.175 1 81.23 ? PB UDP 301 D 1 HETATM 23 O O1B UDP . . . L 2 28.788 154.273 65.78 1 80.8 ? O1B UDP 301 D 1 HETATM 24 O O2B UDP . . . L 2 28.225 155.069 68.109 1 83.52 ? O2B UDP 301 D 1 HETATM 25 O O3B UDP . . . L 2 27.184 152.996 67.04 1 79.38 ? O3B UDP 301 D 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 25 #