data_6TRQ # _model_server_result.job_id ZlmmFN_bTCMpjnMnI1zMJg _model_server_result.datetime_utc '2024-11-05 07:53:18' _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 6trq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":402}' # _entry.id 6TRQ # _exptl.entry_id 6TRQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 324.181 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-MONOPHOSPHATE" _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 6TRQ _cell.length_a 87.761 _cell.length_b 104.103 _cell.length_c 189.223 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6TRQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # 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 1 1 C,D,I,J,K,L,M,N,O 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 # 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 disulf ? disulf1 A SG CYS 67 A CYS 72 1_555 A SG CYS 73 A CYS 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf2 B SG CYS 67 B CYS 72 1_555 B SG CYS 73 B CYS 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf3 C SG CYS 67 C CYS 72 1_555 C SG CYS 73 C CYS 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf4 D SG CYS 67 D CYS 72 1_555 D SG CYS 73 D CYS 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? covale ? covale1 A NZ LYS 121 A LYS 126 1_555 G OP2 0G . A 0G 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.302 ? covale ? covale2 E P 2PO . A 2PO 401 1_555 F O3' U . A U 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.606 ? covale ? covale3 F P U . A U 402 1_555 G O3' 0G . A 0G 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.613 ? covale ? covale4 G P 0G . A 0G 403 1_555 H O3B M7G . A M7G 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.629 ? covale ? covale5 C ND1 HIS 254 C HIS 259 1_555 L O1B M7G . C M7G 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.305 ? covale ? covale6 I O3' U . C U 401 1_555 J P 2PO . C 2PO 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.599 ? covale ? covale7 I P U . C U 401 1_555 K O3' 0G . C 0G 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.63 ? covale ? covale8 K P 0G . C 0G 403 1_555 L O3B M7G . C M7G 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.62 ? # _chem_comp.formula 'C9 H13 N2 O9 P' _chem_comp.formula_weight 324.181 _chem_comp.id U _chem_comp.mon_nstd_flag y _chem_comp.name "URIDINE-5'-MONOPHOSPHATE" _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 OP3 P U sing 455 n n OP3 HOP3 U sing 456 n n P OP1 U doub 457 n n P OP2 U sing 458 n n P O5' U sing 459 n n OP2 HOP2 U sing 460 n n O5' C5' U sing 461 n n C5' C4' U sing 462 n n C5' H5' U sing 463 n n C5' "H5''" U sing 464 n n C4' O4' U sing 465 n n C4' C3' U sing 466 n n C4' H4' U sing 467 n n O4' C1' U sing 468 n n C3' O3' U sing 469 n n C3' C2' U sing 470 n n C3' H3' U sing 471 n n O3' HO3' U sing 472 n n C2' O2' U sing 473 n n C2' C1' U sing 474 n n C2' H2' U sing 475 n n O2' HO2' U sing 476 n n C1' N1 U sing 477 n n C1' H1' U sing 478 n n N1 C2 U sing 479 n n N1 C6 U sing 480 n n C2 O2 U doub 481 n n C2 N3 U sing 482 n n N3 C4 U sing 483 n n N3 H3 U sing 484 n n C4 O4 U doub 485 n n C4 C5 U sing 486 n n C5 C6 U doub 487 n n C5 H5 U sing 488 n n C6 H6 U sing 489 n n # _atom_sites.entry_id 6TRQ _atom_sites.fract_transf_matrix[1][1] 0.011395 _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] 0.009606 _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] 0.005285 _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 2PO A 1 401 1 2PO GGU . F 3 U A 1 402 1 U GGU . G 4 0G A 1 403 1 0G GGU . H 5 M7G A 1 404 1 M7G GGU . I 3 U C 1 401 2 U GGU . J 2 2PO C 1 402 2 2PO GGU . K 4 0G C 1 403 2 0G GGU . L 5 M7G C 1 404 2 M7G GGU . M 6 SO4 D 1 401 1 SO4 SO4 . N 6 SO4 D 1 402 2 SO4 SO4 . O 7 HOH C 1 501 4 HOH HOH . O 7 HOH C 2 502 3 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 P U . . . F 3 39.333 1.197 38.956 1 85.69 ? P U 402 A 1 HETATM 2 O OP1 U . . . F 3 38.174 1.886 38.253 1 58.19 ? OP1 U 402 A 1 HETATM 3 O OP2 U . . . F 3 40.689 1.859 38.764 1 82.55 ? OP2 U 402 A 1 HETATM 4 O O5' U . . . F 3 39.006 1.062 40.526 1 98.14 ? O5' U 402 A 1 HETATM 5 C C5' U . . . F 3 37.643 0.91 40.947 1 107.4 ? C5' U 402 A 1 HETATM 6 C C4' U . . . F 3 37.376 -0.433 41.618 1 109.59 ? C4' U 402 A 1 HETATM 7 O O4' U . . . F 3 37.866 -0.416 42.972 1 120.34 ? O4' U 402 A 1 HETATM 8 C C3' U . . . F 3 35.874 -0.732 41.707 1 117.17 ? C3' U 402 A 1 HETATM 9 O O3' U . . . F 3 35.319 -1.926 41.172 1 124.91 ? O3' U 402 A 1 HETATM 10 C C2' U . . . F 3 35.643 -0.695 43.222 1 131.08 ? C2' U 402 A 1 HETATM 11 O O2' U . . . F 3 35.645 -2.049 43.699 1 143.99 ? O2' U 402 A 1 HETATM 12 C C1' U . . . F 3 36.832 -0.01 43.907 1 126.88 ? C1' U 402 A 1 HETATM 13 N N1 U . . . F 3 36.92 1.436 44.096 1 114.63 ? N1 U 402 A 1 HETATM 14 C C2 U . . . F 3 35.787 2.175 44.517 1 104.71 ? C2 U 402 A 1 HETATM 15 O O2 U . . . F 3 34.67 1.63 44.704 1 100.28 ? O2 U 402 A 1 HETATM 16 N N3 U . . . F 3 35.913 3.49 44.689 1 102.32 ? N3 U 402 A 1 HETATM 17 C C4 U . . . F 3 37.087 4.101 44.499 1 95.95 ? C4 U 402 A 1 HETATM 18 O O4 U . . . F 3 37.167 5.328 44.669 1 88.77 ? O4 U 402 A 1 HETATM 19 C C5 U . . . F 3 38.214 3.408 44.116 1 94.58 ? C5 U 402 A 1 HETATM 20 C C6 U . . . F 3 38.112 2.043 43.943 1 103.84 ? C6 U 402 A 1 HETATM 21 H H5' U . . . F 3 37.395 1.712 41.645 1 128.88 ? H5' U 402 A 1 HETATM 22 H "H5''" U . . . F 3 36.99 1.008 40.077 1 128.88 ? "H5''" U 402 A 1 HETATM 23 H H4' U . . . F 3 37.886 -1.195 41.013 1 131.51 ? H4' U 402 A 1 HETATM 24 H H3' U . . . F 3 35.36 -0.011 41.056 1 140.6 ? H3' U 402 A 1 HETATM 25 H H2' U . . . F 3 34.701 -0.17 43.436 1 157.3 ? H2' U 402 A 1 HETATM 26 H HO2' U . . . F 3 36.547 -2.396 43.678 1 172.78 ? HO2' U 402 A 1 HETATM 27 H H1' U . . . F 3 36.824 -0.31 44.964 1 152.26 ? H1' U 402 A 1 HETATM 28 H H3 U . . . F 3 35.085 4.05 44.976 1 122.78 ? H3 U 402 A 1 HETATM 29 H H5 U . . . F 3 39.154 3.92 43.953 1 113.5 ? H5 U 402 A 1 HETATM 30 H H6 U . . . F 3 38.989 1.462 43.686 1 124.61 ? H6 U 402 A 1 # _model_server_stats.io_time_ms 35 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 327 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 30 #