data_2E9Z # _model_server_result.job_id 9DxBRikgQCEiaB2t4O5rrw _model_server_result.datetime_utc '2024-12-26 06:11:55' _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 2e9z # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":993}' # _entry.id 2E9Z # _exptl.entry_id 2E9Z _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 484.141 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE 5'-TRIPHOSPHATE" _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 2E9Z _cell.length_a 94.11 _cell.length_b 94.11 _cell.length_c 99.362 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2E9Z _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 5 _struct_asym.id F _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 C OD1 ASP 238 A ASP 238 1_555 D MG MG . A MG 1030 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.825 ? metalc ? metalc2 C O TYR 241 A TYR 241 1_555 E MG MG . A MG 1031 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.116 ? metalc ? metalc3 C OD2 ASP 339 A ASP 339 1_555 D MG MG . A MG 1030 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.943 ? metalc ? metalc4 C O THR 384 A THR 384 1_555 D MG MG . A MG 1030 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.114 ? metalc ? metalc5 F O3A UTP . A UTP 993 1_555 E MG MG . A MG 1031 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.867 ? hydrog 'U-A PAIR' hydrog1 A N3 U 3 B U 904 1_555 B N1 A 7 C A 921 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-C PAIR' hydrog2 A N1 G 4 B G 905 1_555 B N3 C 6 C C 920 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A N1 G 5 B G 906 1_555 B N3 C 5 C C 919 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N2 G 5 B G 906 1_555 B O2 C 5 C C 919 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A O6 G 5 B G 906 1_555 B N4 C 5 C C 919 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-C PAIR' hydrog6 A N1 G 6 B G 907 1_555 B N3 C 4 C C 918 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N3 C 7 B C 908 1_555 B N1 G 3 C G 917 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N4 C 7 B C 908 1_555 B O6 G 3 C G 917 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A O2 C 7 B C 908 1_555 B N2 G 3 C G 917 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-G PAIR' hydrog10 A O2 C 8 B C 909 1_555 B N1 G 2 C G 916 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-G PAIR' hydrog11 A O2 C 9 B C 910 1_555 B N1 G 1 C G 915 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 520 n n PA O2A UTP sing 521 n n PA O3A UTP sing 522 n n PA O5' UTP sing 523 n n O2A H2A UTP sing 524 n n O3A PB UTP sing 525 n n O5' C5' UTP sing 526 n n PB O1B UTP sing 527 n n PB O2B UTP doub 528 n n PB O3B UTP sing 529 n n O1B H1B UTP sing 530 n n O3B PG UTP sing 531 n n PG O1G UTP sing 532 n n PG O2G UTP doub 533 n n PG O3G UTP sing 534 n n O1G H1G UTP sing 535 n n O3G H3G UTP sing 536 n n C5' C4' UTP sing 537 n n C5' "H5'1" UTP sing 538 n n C5' "H5'2" UTP sing 539 n n C4' O4' UTP sing 540 n n C4' C3' UTP sing 541 n n C4' H4' UTP sing 542 n n O4' C1' UTP sing 543 n n C1' C2' UTP sing 544 n n C1' N1 UTP sing 545 n n C1' H1' UTP sing 546 n n C2' O2' UTP sing 547 n n C2' C3' UTP sing 548 n n C2' H2' UTP sing 549 n n O2' HA UTP sing 550 n n C3' O3' UTP sing 551 n n C3' H3' UTP sing 552 n n O3' HB UTP sing 553 n n N1 C6 UTP sing 554 n y N1 C2 UTP sing 555 n y C6 C5 UTP doub 556 n y C6 H6 UTP sing 557 n n C2 O2 UTP doub 558 n n C2 N3 UTP sing 559 n y N3 C4 UTP sing 560 n y N3 H3 UTP sing 561 n n C4 O4 UTP doub 562 n n C4 C5 UTP sing 563 n y C5 H5 UTP sing 564 n n # _atom_sites.entry_id 2E9Z _atom_sites.fract_transf_matrix[1][1] 0.010626 _atom_sites.fract_transf_matrix[1][2] 0.006135 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01227 _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] 0.010064 _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 D 4 MG A 1 1030 1030 MG MG . E 4 MG A 1 1031 1031 MG MG . F 5 UTP A 1 993 993 UTP UTP . G 6 PPV A 1 665 665 PPV PPV . H 7 HOH B 1 516 516 HOH HOH . H 7 HOH B 2 523 523 HOH HOH . I 7 HOH C 1 517 517 HOH HOH . I 7 HOH C 2 522 522 HOH HOH . I 7 HOH C 3 527 527 HOH HOH . J 7 HOH A 1 1032 236 HOH HOH . J 7 HOH A 2 1033 501 HOH HOH . J 7 HOH A 3 1034 502 HOH HOH . J 7 HOH A 4 1035 505 HOH HOH . J 7 HOH A 5 1036 507 HOH HOH . J 7 HOH A 6 1037 508 HOH HOH . J 7 HOH A 7 1038 510 HOH HOH . J 7 HOH A 8 1039 511 HOH HOH . J 7 HOH A 9 1040 512 HOH HOH . J 7 HOH A 10 1041 513 HOH HOH . J 7 HOH A 11 1042 520 HOH HOH . J 7 HOH A 12 1043 524 HOH HOH . J 7 HOH A 13 1044 525 HOH HOH . J 7 HOH A 14 1045 526 HOH HOH . J 7 HOH A 15 1046 528 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 PA UTP . . . F 5 19.645 26.156 16.094 0.5 98.66 ? PA UTP 993 A 1 HETATM 2 O O1A UTP . . . F 5 18.109 25.865 15.846 0.5 98.3 ? O1A UTP 993 A 1 HETATM 3 O O2A UTP . . . F 5 20.35 27.496 16.407 0.5 98.62 ? O2A UTP 993 A 1 HETATM 4 O O3A UTP . . . F 5 20.386 25.547 14.729 0.5 96.95 ? O3A UTP 993 A 1 HETATM 5 O O5' UTP . . . F 5 19.68 26.131 17.618 0.5 98.51 ? O5' UTP 993 A 1 HETATM 6 P PB UTP . . . F 5 19.581 25.431 13.275 0.5 95.83 ? PB UTP 993 A 1 HETATM 7 O O1B UTP . . . F 5 19.135 26.863 12.855 0.5 95.31 ? O1B UTP 993 A 1 HETATM 8 O O2B UTP . . . F 5 18.367 24.467 13.391 0.5 95.34 ? O2B UTP 993 A 1 HETATM 9 O O3B UTP . . . F 5 20.671 24.602 12.332 0.5 94.93 ? O3B UTP 993 A 1 HETATM 10 P PG UTP . . . F 5 21.065 24.649 10.696 0.5 94.35 ? PG UTP 993 A 1 HETATM 11 O O1G UTP . . . F 5 22.121 25.721 10.423 0.5 94.24 ? O1G UTP 993 A 1 HETATM 12 O O2G UTP . . . F 5 21.62 23.218 10.487 0.6 94.14 ? O2G UTP 993 A 1 HETATM 13 O O3G UTP . . . F 5 19.726 24.984 10.028 0.5 94.21 ? O3G UTP 993 A 1 HETATM 14 C C5' UTP . . . F 5 19.108 26.595 18.891 0.5 98.86 ? C5' UTP 993 A 1 HETATM 15 C C4' UTP . . . F 5 18.616 25.36 19.717 0.5 99.18 ? C4' UTP 993 A 1 HETATM 16 O O4' UTP . . . F 5 17.42 25.607 20.512 0.5 99.44 ? O4' UTP 993 A 1 HETATM 17 C C1' UTP . . . F 5 16.385 24.675 20.135 0.5 100.21 ? C1' UTP 993 A 1 HETATM 18 C C2' UTP . . . F 5 16.951 23.8 19.011 0.5 100.06 ? C2' UTP 993 A 1 HETATM 19 O O2' UTP . . . F 5 16.901 22.423 19.48 0.5 100.45 ? O2' UTP 993 A 1 HETATM 20 C C3' UTP . . . F 5 18.406 24.182 18.758 0.5 99.65 ? C3' UTP 993 A 1 HETATM 21 O O3' UTP . . . F 5 19.527 23.241 18.801 0.5 99.25 ? O3' UTP 993 A 1 HETATM 22 N N1 UTP . . . F 5 15.094 25.38 19.93 0.5 100.63 ? N1 UTP 993 A 1 HETATM 23 C C6 UTP . . . F 5 14.933 26.795 20.087 0.5 100.6 ? C6 UTP 993 A 1 HETATM 24 C C2 UTP . . . F 5 13.975 24.555 19.56 0.5 100.48 ? C2 UTP 993 A 1 HETATM 25 O O2 UTP . . . F 5 14.004 23.336 19.402 0.5 100.03 ? O2 UTP 993 A 1 HETATM 26 N N3 UTP . . . F 5 12.77 25.244 19.373 0.5 100.6 ? N3 UTP 993 A 1 HETATM 27 C C4 UTP . . . F 5 12.549 26.638 19.512 0.5 100.75 ? C4 UTP 993 A 1 HETATM 28 O O4 UTP . . . F 5 11.433 27.097 19.315 0.5 101.09 ? O4 UTP 993 A 1 HETATM 29 C C5 UTP . . . F 5 13.732 27.42 19.893 0.5 100.56 ? C5 UTP 993 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 29 #