data_2QRN # _model_server_result.job_id 54lPPPD5g3OU-pK1ALCScQ _model_server_result.datetime_utc '2024-10-18 15:31:09' _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 2qrn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":402}' # _entry.id 2QRN # _exptl.entry_id 2QRN _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 90 _cell.entry_id 2QRN _cell.length_a 94.565 _cell.length_b 94.565 _cell.length_c 335.334 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2QRN _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,J 1 1 C,D,K,L,M,N,O,P 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 ? 3 F N N ? 3 I N N ? 3 L N N ? 3 O 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 OG SER 55 A SER 35 1_555 E MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc2 A OE1 GLU 147 A GLU 127 1_555 E MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? metalc ? metalc3 B OG SER 55 B SER 35 1_555 H MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? metalc ? metalc4 C OG SER 55 C SER 35 1_555 K MG MG . C MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? metalc ? metalc5 K MG MG . C MG 401 1_555 L O1B UDP . C UDP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? metalc ? metalc6 D OG SER 55 D SER 35 1_555 N MG MG . D MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? # _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 391 n n N1 C6 UDP sing 392 n n N1 C1' UDP sing 393 n n C2 N3 UDP sing 394 n n C2 O2 UDP doub 395 n n N3 C4 UDP sing 396 n n N3 HN3 UDP sing 397 n n C4 C5 UDP sing 398 n n C4 O4 UDP doub 399 n n C5 C6 UDP doub 400 n n C5 H5 UDP sing 401 n n C6 H6 UDP sing 402 n n C1' C2' UDP sing 403 n n C1' O4' UDP sing 404 n n C1' H1' UDP sing 405 n n C2' O2' UDP sing 406 n n C2' C3' UDP sing 407 n n C2' H2' UDP sing 408 n n O2' HO2' UDP sing 409 n n C3' C4' UDP sing 410 n n C3' O3' UDP sing 411 n n C3' H3' UDP sing 412 n n C4' O4' UDP sing 413 n n C4' C5' UDP sing 414 n n C4' H4' UDP sing 415 n n O3' HO3' UDP sing 416 n n C5' O5' UDP sing 417 n n C5' "H5'1" UDP sing 418 n n C5' "H5'2" UDP sing 419 n n O5' PA UDP sing 420 n n PA O1A UDP doub 421 n n PA O2A UDP sing 422 n n PA O3A UDP sing 423 n n O2A HOA2 UDP sing 424 n n O3A PB UDP sing 425 n n PB O1B UDP doub 426 n n PB O2B UDP sing 427 n n PB O3B UDP sing 428 n n O2B HOB2 UDP sing 429 n n O3B HOB3 UDP sing 430 n n # _atom_sites.entry_id 2QRN _atom_sites.fract_transf_matrix[1][1] 0.010575 _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] 0.010575 _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] 0.002982 _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 MG A 1 401 401 MG MG . F 3 UDP A 1 402 402 UDP UDP . G 4 DCM A 1 403 403 DCM DCM . H 2 MG B 1 401 401 MG MG . I 3 UDP B 1 402 402 UDP UDP . J 4 DCM B 1 403 403 DCM DCM . K 2 MG C 1 401 401 MG MG . L 3 UDP C 1 402 402 UDP UDP . M 4 DCM C 1 403 403 DCM DCM . N 2 MG D 1 401 401 MG MG . O 3 UDP D 1 402 402 UDP UDP . P 4 DCM D 1 403 403 DCM DCM . # 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 . . . O 3 -19.813 20.066 27.286 1 82.33 ? N1 UDP 402 D 1 HETATM 2 C C2 UDP . . . O 3 -21.128 19.841 27.029 1 82.01 ? C2 UDP 402 D 1 HETATM 3 N N3 UDP . . . O 3 -21.514 18.798 26.274 1 78.28 ? N3 UDP 402 D 1 HETATM 4 C C4 UDP . . . O 3 -20.58 17.943 25.747 1 81.9 ? C4 UDP 402 D 1 HETATM 5 C C5 UDP . . . O 3 -19.197 18.169 26.008 1 82.51 ? C5 UDP 402 D 1 HETATM 6 C C6 UDP . . . O 3 -18.836 19.22 26.768 1 83.18 ? C6 UDP 402 D 1 HETATM 7 O O2 UDP . . . O 3 -21.961 20.587 27.481 1 77.31 ? O2 UDP 402 D 1 HETATM 8 O O4 UDP . . . O 3 -20.927 17.006 25.069 1 84.66 ? O4 UDP 402 D 1 HETATM 9 C C1' UDP . . . O 3 -19.41 21.227 28.114 1 85.19 ? C1' UDP 402 D 1 HETATM 10 C C2' UDP . . . O 3 -19.429 20.853 29.604 1 81.73 ? C2' UDP 402 D 1 HETATM 11 O O2' UDP . . . O 3 -20.617 21.343 30.232 1 66.54 ? O2' UDP 402 D 1 HETATM 12 C C3' UDP . . . O 3 -18.215 21.523 30.176 1 83.73 ? C3' UDP 402 D 1 HETATM 13 C C4' UDP . . . O 3 -17.587 22.237 29.003 1 86.55 ? C4' UDP 402 D 1 HETATM 14 O O4' UDP . . . O 3 -18.084 21.571 27.837 1 87.86 ? O4' UDP 402 D 1 HETATM 15 O O3' UDP . . . O 3 -18.591 22.461 31.188 1 88.93 ? O3' UDP 402 D 1 HETATM 16 C C5' UDP . . . O 3 -16.146 22.118 29.052 1 86.97 ? C5' UDP 402 D 1 HETATM 17 O O5' UDP . . . O 3 -15.625 22.711 27.968 1 83.88 ? O5' UDP 402 D 1 HETATM 18 P PA UDP . . . O 3 -14.091 22.443 27.987 1 87.37 ? PA UDP 402 D 1 HETATM 19 O O1A UDP . . . O 3 -13.503 22.99 29.245 1 85.13 ? O1A UDP 402 D 1 HETATM 20 O O2A UDP . . . O 3 -13.821 20.848 27.912 1 77.61 ? O2A UDP 402 D 1 HETATM 21 O O3A UDP . . . O 3 -13.405 23.186 26.685 1 79.91 ? O3A UDP 402 D 1 HETATM 22 P PB UDP . . . O 3 -11.8 22.913 26.759 1 72.98 ? PB UDP 402 D 1 HETATM 23 O O1B UDP . . . O 3 -11.254 23.415 28.132 1 73.21 ? O1B UDP 402 D 1 HETATM 24 O O2B UDP . . . O 3 -11.107 23.565 25.642 1 69.37 ? O2B UDP 402 D 1 HETATM 25 O O3B UDP . . . O 3 -11.548 21.33 26.657 1 76.22 ? O3B UDP 402 D 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #