data_4M55 # _model_server_result.job_id FYXT4RlMbwVp-gdVsazfxg _model_server_result.datetime_utc '2024-10-13 19:18:31' _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 4m55 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":502}' # _entry.id 4M55 # _exptl.entry_id 4M55 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE" _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 4M55 _cell.length_a 83.171 _cell.length_b 85.145 _cell.length_c 292.549 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4M55 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 K N N ? 5 Q N N # _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 445 n n N1 C6 UDP sing 446 n n N1 C1' UDP sing 447 n n C2 N3 UDP sing 448 n n C2 O2 UDP doub 449 n n N3 C4 UDP sing 450 n n N3 HN3 UDP sing 451 n n C4 C5 UDP sing 452 n n C4 O4 UDP doub 453 n n C5 C6 UDP doub 454 n n C5 H5 UDP sing 455 n n C6 H6 UDP sing 456 n n C1' C2' UDP sing 457 n n C1' O4' UDP sing 458 n n C1' H1' UDP sing 459 n n C2' O2' UDP sing 460 n n C2' C3' UDP sing 461 n n C2' H2' UDP sing 462 n n O2' HO2' UDP sing 463 n n C3' C4' UDP sing 464 n n C3' O3' UDP sing 465 n n C3' H3' UDP sing 466 n n C4' O4' UDP sing 467 n n C4' C5' UDP sing 468 n n C4' H4' UDP sing 469 n n O3' HO3' UDP sing 470 n n C5' O5' UDP sing 471 n n C5' "H5'1" UDP sing 472 n n C5' "H5'2" UDP sing 473 n n O5' PA UDP sing 474 n n PA O1A UDP doub 475 n n PA O2A UDP sing 476 n n PA O3A UDP sing 477 n n O2A HOA2 UDP sing 478 n n O3A PB UDP sing 479 n n PB O1B UDP doub 480 n n PB O2B UDP sing 481 n n PB O3B UDP sing 482 n n O2B HOB2 UDP sing 483 n n O3B HOB3 UDP sing 484 n n # _atom_sites.entry_id 4M55 _atom_sites.fract_transf_matrix[1][1] 0.012023 _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] 0.011745 _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] 0.003418 _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 G 2 NAD A 1 501 800 NAD NAD . H 3 POP A 1 502 503 POP POP . I 4 SO4 A 1 503 1 SO4 SO4 . J 2 NAD B 1 501 800 NAD NAD . K 5 UDP B 1 502 901 UDP UDP . L 4 SO4 B 1 503 2 SO4 SO4 . M 2 NAD C 1 501 800 NAD NAD . N 3 POP C 1 502 503 POP POP . O 4 SO4 C 1 503 3 SO4 SO4 . P 2 NAD D 1 501 800 NAD NAD . Q 5 UDP D 1 502 901 UDP UDP . R 2 NAD E 1 800 800 NAD NAD . S 2 NAD F 1 800 800 NAD NAD . # 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 . . . K 5 -10.812 24.145 336.818 1 118.1 ? N1 UDP 502 B 1 HETATM 2 C C2 UDP . . . K 5 -10.191 24.482 338.009 1 111.76 ? C2 UDP 502 B 1 HETATM 3 N N3 UDP . . . K 5 -10.323 23.65 339.101 1 113.6 ? N3 UDP 502 B 1 HETATM 4 C C4 UDP . . . K 5 -11.067 22.495 338.993 1 116.31 ? C4 UDP 502 B 1 HETATM 5 C C5 UDP . . . K 5 -11.676 22.165 337.795 1 114.35 ? C5 UDP 502 B 1 HETATM 6 C C6 UDP . . . K 5 -11.706 23.117 336.785 1 114.91 ? C6 UDP 502 B 1 HETATM 7 O O2 UDP . . . K 5 -9.53 25.522 338.097 1 101.31 ? O2 UDP 502 B 1 HETATM 8 O O4 UDP . . . K 5 -11.177 21.761 339.964 1 122.98 ? O4 UDP 502 B 1 HETATM 9 C C1' UDP . . . K 5 -10.665 25.033 335.652 1 130.41 ? C1' UDP 502 B 1 HETATM 10 C C2' UDP . . . K 5 -10.149 24.235 334.462 1 133.54 ? C2' UDP 502 B 1 HETATM 11 O O2' UDP . . . K 5 -8.926 24.764 334.012 1 138.68 ? O2' UDP 502 B 1 HETATM 12 C C3' UDP . . . K 5 -11.213 24.404 333.398 1 132.12 ? C3' UDP 502 B 1 HETATM 13 C C4' UDP . . . K 5 -12.044 25.589 333.868 1 137.1 ? C4' UDP 502 B 1 HETATM 14 O O4' UDP . . . K 5 -11.894 25.627 335.275 1 137.71 ? O4' UDP 502 B 1 HETATM 15 O O3' UDP . . . K 5 -10.616 24.693 332.159 1 126.71 ? O3' UDP 502 B 1 HETATM 16 C C5' UDP . . . K 5 -13.513 25.474 333.464 1 137.64 ? C5' UDP 502 B 1 HETATM 17 O O5' UDP . . . K 5 -14.047 24.253 333.935 1 139.23 ? O5' UDP 502 B 1 HETATM 18 P PA UDP . . . K 5 -15.1 23.438 333.033 1 130.63 ? PA UDP 502 B 1 HETATM 19 O O1A UDP . . . K 5 -16.13 24.391 332.559 1 128.34 ? O1A UDP 502 B 1 HETATM 20 O O2A UDP . . . K 5 -15.702 22.293 333.76 1 131.57 ? O2A UDP 502 B 1 HETATM 21 O O3A UDP . . . K 5 -14.169 22.957 331.805 1 323.04 ? O3A UDP 502 B 1 HETATM 22 P PB UDP . . . K 5 -13.828 21.415 331.466 1 171.91 ? PB UDP 502 B 1 HETATM 23 O O1B UDP . . . K 5 -15.079 20.623 331.416 1 174.53 ? O1B UDP 502 B 1 HETATM 24 O O2B UDP . . . K 5 -12.962 20.841 332.52 1 171.04 ? O2B UDP 502 B 1 HETATM 25 O O3B UDP . . . K 5 -13.136 21.365 330.156 1 170.51 ? O3B UDP 502 B 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #