data_4ZDK # _model_server_result.job_id TOPHTjO5YGFKH1VeU4nD1A _model_server_result.datetime_utc '2024-10-28 14:29:46' _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 4zdk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":603}' # _entry.id 4ZDK # _exptl.entry_id 4ZDK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 484.141 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE 5'-TRIPHOSPHATE" _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 4ZDK _cell.length_a 121.732 _cell.length_b 194.724 _cell.length_c 207.457 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4ZDK _symmetry.cell_setting ? _symmetry.Int_Tables_number 24 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 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 ? tetrameric 4 author_defined_assembly 1 PISA tetrameric 4 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 B,G,H,I,J 1 1 A,C,D,E,F 1 2 B,G,H,I,J 1 4 A,C,D,E,F 1 6 A,C,D,E,F 2 1,5 B,G,H,I,J 2 3,6 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_545 x+1/2,-y-1/2,-z 1 0 0 0 -1 0 0 0 -1 60.866 -97.362 0 3 'crystal symmetry operation' 4_445 x-1/2,-y-1/2,-z 1 0 0 0 -1 0 0 0 -1 -60.866 -97.362 0 4 'crystal symmetry operation' 6_645 -x+1,-y-1/2,z -1 0 0 0 -1 0 0 0 1 121.732 -97.362 0 5 'crystal symmetry operation' 6_545 -x,-y-1/2,z -1 0 0 0 -1 0 0 0 1 0 -97.362 0 6 'crystal symmetry operation' 7_555 -x+1/2,y,-z -1 0 0 0 1 0 0 0 -1 60.866 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 E N N ? 4 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 covale ? covale1 A SG CYS 393 A CYS 393 1_555 C CE ONL . A ONL 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? covale ? covale2 B SG CYS 393 B CYS 393 1_555 G CE ONL . B ONL 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.797 ? metalc ? metalc1 A OD1 ASP 78 A ASP 78 1_555 F MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.738 ? metalc ? metalc2 A OD2 ASP 78 A ASP 78 1_555 F MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? metalc ? metalc3 A OE1 GLU 152 A GLU 152 1_555 F MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.991 ? metalc ? metalc4 A OE2 GLU 152 A GLU 152 1_555 F MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.664 ? metalc ? metalc5 D O3G ACP . A ACP 602 1_555 F MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? metalc ? metalc6 D O1B ACP . A ACP 602 1_555 F MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.699 ? metalc ? metalc7 B OD2 ASP 78 B ASP 78 1_555 J MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.622 ? metalc ? metalc8 B OE2 GLU 152 B GLU 152 1_555 J MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.671 ? metalc ? metalc9 H O1B ACP . B ACP 602 1_555 J MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? # _chem_comp.formula 'C9 H15 N2 O15 P3' _chem_comp.formula_weight 484.141 _chem_comp.id UTP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE 5'-TRIPHOSPHATE" _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 PA O1A UTP doub 427 n n PA O2A UTP sing 428 n n PA O3A UTP sing 429 n n PA O5' UTP sing 430 n n O2A H2A UTP sing 431 n n O3A PB UTP sing 432 n n O5' C5' UTP sing 433 n n PB O1B UTP sing 434 n n PB O2B UTP doub 435 n n PB O3B UTP sing 436 n n O1B H1B UTP sing 437 n n O3B PG UTP sing 438 n n PG O1G UTP sing 439 n n PG O2G UTP doub 440 n n PG O3G UTP sing 441 n n O1G H1G UTP sing 442 n n O3G H3G UTP sing 443 n n C5' C4' UTP sing 444 n n C5' "H5'1" UTP sing 445 n n C5' "H5'2" UTP sing 446 n n C4' O4' UTP sing 447 n n C4' C3' UTP sing 448 n n C4' H4' UTP sing 449 n n O4' C1' UTP sing 450 n n C1' C2' UTP sing 451 n n C1' N1 UTP sing 452 n n C1' H1' UTP sing 453 n n C2' O2' UTP sing 454 n n C2' C3' UTP sing 455 n n C2' H2' UTP sing 456 n n O2' HA UTP sing 457 n n C3' O3' UTP sing 458 n n C3' H3' UTP sing 459 n n O3' HB UTP sing 460 n n N1 C6 UTP sing 461 n y N1 C2 UTP sing 462 n y C6 C5 UTP doub 463 n y C6 H6 UTP sing 464 n n C2 O2 UTP doub 465 n n C2 N3 UTP sing 466 n y N3 C4 UTP sing 467 n y N3 H3 UTP sing 468 n n C4 O4 UTP doub 469 n n C4 C5 UTP sing 470 n y C5 H5 UTP sing 471 n n # _atom_sites.entry_id 4ZDK _atom_sites.fract_transf_matrix[1][1] 0.008215 _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] 0.005135 _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] 0.00482 _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 C 2 ONL A 1 601 601 ONL ONL . D 3 ACP A 1 602 1 ACP ACP . E 4 UTP A 1 603 3 UTP UTP . F 5 MG A 1 604 5 MG MG . G 2 ONL B 1 601 601 ONL ONL . H 3 ACP B 1 602 2 ACP ACP . I 4 UTP B 1 603 4 UTP UTP . J 5 MG B 1 604 6 MG MG . # 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 PA UTP . . . I 4 54.221 -35.267 -5.616 1 166.17 ? PA UTP 603 B 1 HETATM 2 O O1A UTP . . . I 4 53.37 -34.162 -6.272 1 166.69 ? O1A UTP 603 B 1 HETATM 3 O O2A UTP . . . I 4 55.357 -34.697 -4.858 1 166.36 ? O2A UTP 603 B 1 HETATM 4 O O3A UTP . . . I 4 53.29 -36.093 -4.622 1 165.85 ? O3A UTP 603 B 1 HETATM 5 O O5' UTP . . . I 4 54.675 -36.311 -6.73 1 165.51 ? O5' UTP 603 B 1 HETATM 6 P PB UTP . . . I 4 51.721 -36.054 -4.361 1 166.14 ? PB UTP 603 B 1 HETATM 7 O O1B UTP . . . I 4 51.218 -37.42 -4.089 1 165.48 ? O1B UTP 603 B 1 HETATM 8 O O2B UTP . . . I 4 51.033 -35.413 -5.568 1 166.92 ? O2B UTP 603 B 1 HETATM 9 O O3B UTP . . . I 4 51.515 -35.096 -3.106 1 166.87 ? O3B UTP 603 B 1 HETATM 10 P PG UTP . . . I 4 51.628 -33.512 -2.985 1 167.74 ? PG UTP 603 B 1 HETATM 11 O O1G UTP . . . I 4 50.449 -33.029 -2.237 1 168.79 ? O1G UTP 603 B 1 HETATM 12 O O2G UTP . . . I 4 51.663 -32.982 -4.442 1 167.84 ? O2G UTP 603 B 1 HETATM 13 O O3G UTP . . . I 4 52.975 -33.201 -2.277 1 166.95 ? O3G UTP 603 B 1 HETATM 14 C C5' UTP . . . I 4 53.824 -37.338 -7.28 1 164.67 ? C5' UTP 603 B 1 HETATM 15 C C4' UTP . . . I 4 54.642 -38.582 -7.51 1 163.42 ? C4' UTP 603 B 1 HETATM 16 O O4' UTP . . . I 4 54.763 -39.328 -6.287 1 162.4 ? O4' UTP 603 B 1 HETATM 17 C C1' UTP . . . I 4 55.128 -40.635 -6.66 1 162.4 ? C1' UTP 603 B 1 HETATM 18 C C2' UTP . . . I 4 54.341 -40.951 -7.933 1 163.17 ? C2' UTP 603 B 1 HETATM 19 O O2' UTP . . . I 4 55.097 -41.795 -8.795 1 163.82 ? O2' UTP 603 B 1 HETATM 20 C C3' UTP . . . I 4 54.062 -39.558 -8.534 1 163.6 ? C3' UTP 603 B 1 HETATM 21 O O3' UTP . . . I 4 54.69 -39.357 -9.791 1 164.13 ? O3' UTP 603 B 1 HETATM 22 N N1 UTP . . . I 4 54.869 -41.56 -5.536 1 162.23 ? N1 UTP 603 B 1 HETATM 23 C C6 UTP . . . I 4 53.801 -41.38 -4.672 1 162.62 ? C6 UTP 603 B 1 HETATM 24 C C2 UTP . . . I 4 55.761 -42.602 -5.368 1 162.2 ? C2 UTP 603 B 1 HETATM 25 O O2 UTP . . . I 4 56.72 -42.784 -6.101 1 162.04 ? O2 UTP 603 B 1 HETATM 26 N N3 UTP . . . I 4 55.51 -43.413 -4.282 1 162.61 ? N3 UTP 603 B 1 HETATM 27 C C4 UTP . . . I 4 54.483 -43.284 -3.367 1 163.36 ? C4 UTP 603 B 1 HETATM 28 O O4 UTP . . . I 4 54.416 -44.072 -2.412 1 164.64 ? O4 UTP 603 B 1 HETATM 29 C C5 UTP . . . I 4 53.588 -42.19 -3.616 1 162.95 ? C5 UTP 603 B 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 237 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 29 #