data_6J5T # _model_server_result.job_id ZjBVe2_YwXS3CfACpIKpqQ _model_server_result.datetime_utc '2025-09-04 15:06:55' _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 6j5t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":501}' # _entry.id 6J5T # _exptl.entry_id 6J5T _exptl.method 'ELECTRON MICROSCOPY' # _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 10 _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 6J5T _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6J5T _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details pentadecameric _pdbx_struct_assembly.oligomeric_count 15 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA _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 ? _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 ? 4 P N N ? 4 Q N N ? 4 S N N ? 4 T N N ? 4 V N N ? 4 W N N ? 4 Y N N ? 4 Z N N ? 4 BA N N ? 4 CA 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 A OG SER 253 I SER 253 1_555 P P U5P . I U5P 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.601 ? covale ? covale2 A OG1 THR 254 I THR 254 1_555 Q P U5P . I U5P 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.642 ? covale ? covale3 D OG SER 253 A SER 253 1_555 S P U5P . A U5P 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.602 ? covale ? covale4 D OG1 THR 254 A THR 254 1_555 T P U5P . A U5P 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.644 ? covale ? covale5 G OG SER 253 D SER 253 1_555 V P U5P . D U5P 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.602 ? covale ? covale6 G OG1 THR 254 D THR 254 1_555 W P U5P . D U5P 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.643 ? covale ? covale7 J OG SER 253 J SER 253 1_555 Y P U5P . J U5P 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.602 ? covale ? covale8 J OG1 THR 254 J THR 254 1_555 Z P U5P . J U5P 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.643 ? covale ? covale9 M OG SER 253 M SER 253 1_555 BA P U5P . M U5P 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.601 ? covale ? covale10 M OG1 THR 254 M THR 254 1_555 CA P U5P . M U5P 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.646 ? # _chem_comp.formula 'C9 H13 N2 O9 P' _chem_comp.formula_weight 324.181 _chem_comp.id U5P _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-MONOPHOSPHATE" _chem_comp.type non-polymer _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 U5P sing 404 n n N1 C6 U5P sing 405 n n N1 C1' U5P sing 406 n n C2 N3 U5P sing 407 n n C2 O2 U5P doub 408 n n N3 C4 U5P sing 409 n n N3 HN3 U5P sing 410 n n C4 C5 U5P sing 411 n n C4 O4 U5P doub 412 n n C5 C6 U5P doub 413 n n C5 H5 U5P sing 414 n n C6 H6 U5P sing 415 n n C1' C2' U5P sing 416 n n C1' O4' U5P sing 417 n n C1' H1' U5P sing 418 n n C2' O2' U5P sing 419 n n C2' C3' U5P sing 420 n n C2' H2' U5P sing 421 n n O2' HO2' U5P sing 422 n n C3' C4' U5P sing 423 n n C3' O3' U5P sing 424 n n C3' H3' U5P sing 425 n n C4' O4' U5P sing 426 n n C4' C5' U5P sing 427 n n C4' H4' U5P sing 428 n n O3' HO3' U5P sing 429 n n C5' O5' U5P sing 430 n n C5' "H5'1" U5P sing 431 n n C5' "H5'2" U5P sing 432 n n O5' P U5P sing 433 n n P O1P U5P doub 434 n n P O2P U5P sing 435 n n P O3P U5P sing 436 n n O2P HOP2 U5P sing 437 n n O3P HOP3 U5P sing 438 n n # _atom_sites.entry_id 6J5T _atom_sites.fract_transf_matrix[1][1] 0.002546 _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] 0.002546 _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] 0.002546 _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 P 4 U5P I 1 501 2 U5P U5P . Q 4 U5P I 1 502 1 U5P U5P . R 5 DTP G 1 901 901 DTP DTP . S 4 U5P A 1 501 2 U5P U5P . T 4 U5P A 1 502 1 U5P U5P . U 5 DTP C 1 901 901 DTP DTP . V 4 U5P D 1 501 2 U5P U5P . W 4 U5P D 1 502 1 U5P U5P . X 5 DTP F 1 901 901 DTP DTP . Y 4 U5P J 1 501 2 U5P U5P . Z 4 U5P J 1 502 1 U5P U5P . AA 5 DTP L 1 901 901 DTP DTP . BA 4 U5P M 1 501 2 U5P U5P . CA 4 U5P M 1 502 1 U5P U5P . DA 5 DTP O 1 901 901 DTP DTP . # 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 U5P . . . V 4 233.213 108.251 199.695 0 184.02 ? N1 U5P 501 D 1 HETATM 2 C C2 U5P . . . V 4 232.984 108.907 200.93 0 184.02 ? C2 U5P 501 D 1 HETATM 3 N N3 U5P . . . V 4 233.124 108.233 202.075 0 184.02 ? N3 U5P 501 D 1 HETATM 4 C C4 U5P . . . V 4 233.476 106.942 202.082 0 184.02 ? C4 U5P 501 D 1 HETATM 5 C C5 U5P . . . V 4 233.702 106.27 200.888 0 184.02 ? C5 U5P 501 D 1 HETATM 6 C C6 U5P . . . V 4 233.558 106.96 199.692 0 184.02 ? C6 U5P 501 D 1 HETATM 7 O O2 U5P . . . V 4 232.656 110.106 201.004 0 184.02 ? O2 U5P 501 D 1 HETATM 8 O O4 U5P . . . V 4 233.597 106.337 203.167 0 184.02 ? O4 U5P 501 D 1 HETATM 9 C C1' U5P . . . V 4 233.08 108.899 198.386 0 184.02 ? C1' U5P 501 D 1 HETATM 10 C C2' U5P . . . V 4 231.62 108.98 197.998 0 184.02 ? C2' U5P 501 D 1 HETATM 11 O O2' U5P . . . V 4 231.437 108.232 196.803 0 184.02 ? O2' U5P 501 D 1 HETATM 12 C C3' U5P . . . V 4 231.351 110.433 197.703 0 184.02 ? C3' U5P 501 D 1 HETATM 13 C C4' U5P . . . V 4 232.703 111.121 197.774 0 184.02 ? C4' U5P 501 D 1 HETATM 14 O O3' U5P . . . V 4 230.791 110.56 196.391 0 184.02 ? O3' U5P 501 D 1 HETATM 15 O O4' U5P . . . V 4 233.644 110.212 198.342 0 184.02 ? O4' U5P 501 D 1 HETATM 16 C C5' U5P . . . V 4 232.593 112.344 198.654 0 184.02 ? C5' U5P 501 D 1 HETATM 17 O O5' U5P . . . V 4 233.776 113.104 198.524 0 184.02 ? O5' U5P 501 D 1 HETATM 18 P P U5P . . . V 4 233.558 114.685 198.55 0 184.02 ? P U5P 501 D 1 HETATM 19 O O2P U5P . . . V 4 233.652 115.219 197.145 0 184.02 ? O2P U5P 501 D 1 HETATM 20 O O3P U5P . . . V 4 232.185 114.96 199.11 0 184.02 ? O3P U5P 501 D 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 61 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #