data_7W11 # _model_server_result.job_id bol3ya5mlVkdG99GJv4ICg _model_server_result.datetime_utc '2024-10-18 23:31:55' _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 7w11 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 7W11 # _exptl.entry_id 7W11 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE" _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 97.194 _cell.angle_gamma 90 _cell.entry_id 7W11 _cell.length_a 50.753 _cell.length_b 76.533 _cell.length_c 63.21 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7W11 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id C _struct_conn.ptnr1_label_atom_id C1 _struct_conn.ptnr1_label_comp_id GLC _struct_conn.ptnr1_label_seq_id . _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id GLC _struct_conn.ptnr1_auth_seq_id 502 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id D _struct_conn.ptnr2_label_atom_id O32 _struct_conn.ptnr2_label_comp_id DTX _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id DTX _struct_conn.ptnr2_auth_seq_id 503 _struct_conn.ptnr2_symmetry 1_555 _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 1.417 _struct_conn.pdbx_value_order ? # _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 447 n n N1 C6 UDP sing 448 n n N1 C1' UDP sing 449 n n C2 N3 UDP sing 450 n n C2 O2 UDP doub 451 n n N3 C4 UDP sing 452 n n N3 HN3 UDP sing 453 n n C4 C5 UDP sing 454 n n C4 O4 UDP doub 455 n n C5 C6 UDP doub 456 n n C5 H5 UDP sing 457 n n C6 H6 UDP sing 458 n n C1' C2' UDP sing 459 n n C1' O4' UDP sing 460 n n C1' H1' UDP sing 461 n n C2' O2' UDP sing 462 n n C2' C3' UDP sing 463 n n C2' H2' UDP sing 464 n n O2' HO2' UDP sing 465 n n C3' C4' UDP sing 466 n n C3' O3' UDP sing 467 n n C3' H3' UDP sing 468 n n C4' O4' UDP sing 469 n n C4' C5' UDP sing 470 n n C4' H4' UDP sing 471 n n O3' HO3' UDP sing 472 n n C5' O5' UDP sing 473 n n C5' "H5'1" UDP sing 474 n n C5' "H5'2" UDP sing 475 n n O5' PA UDP sing 476 n n PA O1A UDP doub 477 n n PA O2A UDP sing 478 n n PA O3A UDP sing 479 n n O2A HOA2 UDP sing 480 n n O3A PB UDP sing 481 n n PB O1B UDP doub 482 n n PB O2B UDP sing 483 n n PB O3B UDP sing 484 n n O2B HOB2 UDP sing 485 n n O3B HOB3 UDP sing 486 n n # _atom_sites.entry_id 7W11 _atom_sites.fract_transf_matrix[1][1] 0.019703 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002487 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013066 _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] 0.015946 _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 B 2 UDP A 1 501 502 UDP UDP . C 3 GLC A 1 502 503 GLC D3G . D 4 DTX A 1 503 503 DTX D3G . E 5 HOH A 1 601 3 HOH HOH . E 5 HOH A 2 602 2 HOH HOH . E 5 HOH A 3 603 1 HOH HOH . E 5 HOH A 4 604 86 HOH HOH . E 5 HOH A 5 605 15 HOH HOH . E 5 HOH A 6 606 85 HOH HOH . E 5 HOH A 7 607 92 HOH HOH . E 5 HOH A 8 608 70 HOH HOH . E 5 HOH A 9 609 17 HOH HOH . E 5 HOH A 10 610 94 HOH HOH . E 5 HOH A 11 611 71 HOH HOH . E 5 HOH A 12 612 93 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 N N1 UDP . . . B 2 -22.605 -1.464 -10.365 1 25.94 ? N1 UDP 501 A 1 HETATM 2 C C2 UDP . . . B 2 -23.446 -0.751 -9.659 1 25.97 ? C2 UDP 501 A 1 HETATM 3 N N3 UDP . . . B 2 -24.14 0.254 -10.149 1 26.61 ? N3 UDP 501 A 1 HETATM 4 C C4 UDP . . . B 2 -24.005 0.562 -11.421 1 25.57 ? C4 UDP 501 A 1 HETATM 5 C C5 UDP . . . B 2 -23.128 -0.167 -12.219 1 25.12 ? C5 UDP 501 A 1 HETATM 6 C C6 UDP . . . B 2 -22.406 -1.213 -11.646 1 24.25 ? C6 UDP 501 A 1 HETATM 7 O O2 UDP . . . B 2 -23.575 -1.084 -8.318 1 25.6 ? O2 UDP 501 A 1 HETATM 8 O O4 UDP . . . B 2 -24.756 1.616 -11.952 1 25.5 ? O4 UDP 501 A 1 HETATM 9 C C1' UDP . . . B 2 -21.898 -2.547 -9.651 1 26.25 ? C1' UDP 501 A 1 HETATM 10 C C2' UDP . . . B 2 -22.286 -3.924 -10.228 1 26.82 ? C2' UDP 501 A 1 HETATM 11 O O2' UDP . . . B 2 -23.468 -4.367 -9.68 1 22.38 ? O2' UDP 501 A 1 HETATM 12 C C3' UDP . . . B 2 -21.036 -4.782 -9.878 1 25.01 ? C3' UDP 501 A 1 HETATM 13 C C4' UDP . . . B 2 -20.017 -3.947 -9.927 1 23.79 ? C4' UDP 501 A 1 HETATM 14 O O4' UDP . . . B 2 -20.597 -2.454 -9.793 1 25.39 ? O4' UDP 501 A 1 HETATM 15 O O3' UDP . . . B 2 -21.127 -5.366 -8.502 1 25.28 ? O3' UDP 501 A 1 HETATM 16 C C5' UDP . . . B 2 -19.327 -4.014 -11.266 1 23.53 ? C5' UDP 501 A 1 HETATM 17 O O5' UDP . . . B 2 -18.472 -5.101 -11.214 1 21.41 ? O5' UDP 501 A 1 HETATM 18 P PA UDP . . . B 2 -18.133 -5.904 -12.601 1 21.58 ? PA UDP 501 A 1 HETATM 19 O O1A UDP . . . B 2 -19.444 -6.283 -13.238 1 27.52 -1 O1A UDP 501 A 1 HETATM 20 O O2A UDP . . . B 2 -17.369 -7.158 -12.268 1 23.64 ? O2A UDP 501 A 1 HETATM 21 O O3A UDP . . . B 2 -17.294 -4.995 -13.685 1 24.35 ? O3A UDP 501 A 1 HETATM 22 P PB UDP . . . B 2 -16.1 -3.899 -13.376 1 27.29 ? PB UDP 501 A 1 HETATM 23 O O1B UDP . . . B 2 -15.371 -3.679 -14.686 1 28.56 ? O1B UDP 501 A 1 HETATM 24 O O2B UDP . . . B 2 -16.744 -2.617 -12.915 1 26.43 -1 O2B UDP 501 A 1 HETATM 25 O O3B UDP . . . B 2 -15.084 -4.401 -12.367 1 25.92 ? O3B UDP 501 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 33 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 25 #