data_6G63 # _model_server_result.job_id Tnq-VBBV5A4ydxWkhH-Kew _model_server_result.datetime_utc '2024-10-19 16:37:48' _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 6g63 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":601}' # _entry.id 6G63 # _exptl.entry_id 6G63 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 324.181 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-MONOPHOSPHATE" _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 120 _cell.entry_id 6G63 _cell.length_a 110.63 _cell.length_b 110.63 _cell.length_c 466.02 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6G63 _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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 _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 H _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 SG CYS 404 A CYS 404 1_555 F ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc2 A SG CYS 407 A CYS 407 1_555 F ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.437 ? metalc ? metalc3 F ZN ZN . A ZN 601 1_555 B SG CYS 404 G CYS 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc4 F ZN ZN . A ZN 601 1_555 B SG CYS 407 G CYS 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.527 ? metalc ? metalc5 C SG CYS 404 L CYS 404 1_555 G ZN ZN . L ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc6 C SG CYS 407 L CYS 407 1_555 G ZN ZN . L ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.531 ? metalc ? metalc7 G ZN ZN . L ZN 601 1_555 D SG CYS 404 N CYS 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc8 G ZN ZN . L ZN 601 1_555 D SG CYS 407 N CYS 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.579 ? hydrog WATSON-CRICK hydrog1 E N1 A 4 B A 3 1_555 E N3 U 25 B U 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 E N6 A 4 B A 3 1_555 E O4 U 25 B U 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 E N1 A 5 B A 4 1_555 E N3 U 24 B U 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 E N6 A 5 B A 4 1_555 E O4 U 24 B U 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 E N1 A 6 B A 5 1_555 E N3 U 23 B U 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 E N6 A 6 B A 5 1_555 E O4 U 23 B U 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 E N1 A 7 B A 6 1_555 E N3 U 22 B U 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 E N6 A 7 B A 6 1_555 E O4 U 22 B U 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 E N1 A 8 B A 7 1_555 E N3 U 21 B U 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 E N6 A 8 B A 7 1_555 E O4 U 21 B U 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 E N1 A 10 B A 9 1_555 E N3 U 20 B U 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 E N6 A 10 B A 9 1_555 E O4 U 20 B U 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 395 n n OP3 HOP3 U sing 396 n n P OP1 U doub 397 n n P OP2 U sing 398 n n P O5' U sing 399 n n OP2 HOP2 U sing 400 n n O5' C5' U sing 401 n n C5' C4' U sing 402 n n C5' H5' U sing 403 n n C5' "H5''" U sing 404 n n C4' O4' U sing 405 n n C4' C3' U sing 406 n n C4' H4' U sing 407 n n O4' C1' U sing 408 n n C3' O3' U sing 409 n n C3' C2' U sing 410 n n C3' H3' U sing 411 n n O3' HO3' U sing 412 n n C2' O2' U sing 413 n n C2' C1' U sing 414 n n C2' H2' U sing 415 n n O2' HO2' U sing 416 n n C1' N1 U sing 417 n n C1' H1' U sing 418 n n N1 C2 U sing 419 n n N1 C6 U sing 420 n n C2 O2 U doub 421 n n C2 N3 U sing 422 n n N3 C4 U sing 423 n n N3 H3 U sing 424 n n C4 O4 U doub 425 n n C4 C5 U sing 426 n n C5 C6 U doub 427 n n C5 H5 U sing 428 n n C6 H6 U sing 429 n n # _atom_sites.entry_id 6G63 _atom_sites.fract_transf_matrix[1][1] 0.009039 _atom_sites.fract_transf_matrix[1][2] 0.005219 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010437 _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] 0.002146 _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 F 3 ZN A 1 601 1 ZN ZN . G 3 ZN L 1 601 1 ZN ZN . H 4 U N 1 601 1 U U . # 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 . . . H 4 40.497 -52.221 25.44 1 296.92 ? P U 601 N 1 HETATM 2 O OP1 U . . . H 4 40.818 -53.445 26.217 1 297.16 ? OP1 U 601 N 1 HETATM 3 O OP2 U . . . H 4 40.168 -50.964 26.16 1 297.09 ? OP2 U 601 N 1 HETATM 4 O O5' U . . . H 4 39.303 -52.566 24.446 1 296.89 ? O5' U 601 N 1 HETATM 5 C C5' U . . . H 4 38.293 -53.5 24.797 1 296.77 ? C5' U 601 N 1 HETATM 6 C C4' U . . . H 4 37.129 -52.81 25.458 1 296.66 ? C4' U 601 N 1 HETATM 7 O O4' U . . . H 4 35.939 -53.586 25.235 1 296.57 ? O4' U 601 N 1 HETATM 8 C C3' U . . . H 4 37.199 -52.698 26.971 1 296.8 ? C3' U 601 N 1 HETATM 9 O O3' U . . . H 4 37.955 -51.58 27.402 1 297.16 ? O3' U 601 N 1 HETATM 10 C C2' U . . . H 4 35.725 -52.581 27.38 1 296.88 ? C2' U 601 N 1 HETATM 11 O O2' U . . . H 4 35.321 -51.222 27.449 1 297.43 ? O2' U 601 N 1 HETATM 12 C C1' U . . . H 4 34.989 -53.259 26.216 1 296.57 ? C1' U 601 N 1 HETATM 13 N N1 U . . . H 4 34.271 -54.487 26.627 1 296.41 ? N1 U 601 N 1 HETATM 14 C C2 U . . . H 4 32.889 -54.462 26.571 1 296.4 ? C2 U 601 N 1 HETATM 15 O O2 U . . . H 4 32.245 -53.489 26.217 1 296.7 ? O2 U 601 N 1 HETATM 16 N N3 U . . . H 4 32.273 -55.623 26.957 1 296.29 ? N3 U 601 N 1 HETATM 17 C C4 U . . . H 4 32.885 -56.785 27.378 1 296.45 ? C4 U 601 N 1 HETATM 18 O O4 U . . . H 4 32.188 -57.751 27.692 1 296.57 ? O4 U 601 N 1 HETATM 19 C C5 U . . . H 4 34.315 -56.739 27.404 1 296.7 ? C5 U 601 N 1 HETATM 20 C C6 U . . . H 4 34.943 -55.617 27.034 1 296.55 ? C6 U 601 N 1 HETATM 21 H H5' U . . . H 4 38.664 -54.157 25.408 1 137.67 ? H5' U 601 N 1 HETATM 22 H "H5''" U . . . H 4 37.984 -53.953 23.997 1 137.67 ? "H5''" U 601 N 1 HETATM 23 H H4' U . . . H 4 37.023 -51.924 25.077 1 137.67 ? H4' U 601 N 1 HETATM 24 H H3' U . . . H 4 37.576 -53.52 27.321 1 137.67 ? H3' U 601 N 1 HETATM 25 H HO3' U . . . H 4 38.717 -51.439 27.078 1 137.67 ? HO3' U 601 N 1 HETATM 26 H H2' U . . . H 4 35.56 -53.052 28.211 1 137.67 ? H2' U 601 N 1 HETATM 27 H HO2' U . . . H 4 36.003 -50.738 27.529 1 137.67 ? HO2' U 601 N 1 HETATM 28 H H1' U . . . H 4 34.347 -52.635 25.842 1 137.67 ? H1' U 601 N 1 HETATM 29 H H3 U . . . H 4 31.413 -55.628 26.934 1 137.67 ? H3 U 601 N 1 HETATM 30 H H5 U . . . H 4 34.804 -57.482 27.677 1 137.67 ? H5 U 601 N 1 HETATM 31 H H6 U . . . H 4 35.872 -55.6 27.053 1 137.67 ? H6 U 601 N 1 # _model_server_stats.io_time_ms 138 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 67 _model_server_stats.query_time_ms 252 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 31 #