data_7ZI2 # _model_server_result.job_id tl30d_CLRs-xuVZBiCaPgA _model_server_result.datetime_utc '2024-11-13 05:23:10' _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 7zi2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 7ZI2 # _exptl.entry_id 7ZI2 _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 90 _cell.angle_gamma 90 _cell.entry_id 7ZI2 _cell.length_a 68.836 _cell.length_b 68.836 _cell.length_c 123.656 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7ZI2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 91 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 1,2 # 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' 5_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 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 # 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 A O LYS 62 A LYS 42 1_555 D NA NA . A NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc2 A O SER 65 A SER 45 1_555 D NA NA . A NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.593 ? metalc ? metalc3 A O TRP 68 A TRP 48 1_555 D NA NA . A NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc4 D NA NA . A NA 303 1_555 E O HOH . A HOH 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.447 ? # _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 431 n n N1 C6 UDP sing 432 n n N1 C1' UDP sing 433 n n C2 N3 UDP sing 434 n n C2 O2 UDP doub 435 n n N3 C4 UDP sing 436 n n N3 HN3 UDP sing 437 n n C4 C5 UDP sing 438 n n C4 O4 UDP doub 439 n n C5 C6 UDP doub 440 n n C5 H5 UDP sing 441 n n C6 H6 UDP sing 442 n n C1' C2' UDP sing 443 n n C1' O4' UDP sing 444 n n C1' H1' UDP sing 445 n n C2' O2' UDP sing 446 n n C2' C3' UDP sing 447 n n C2' H2' UDP sing 448 n n O2' HO2' UDP sing 449 n n C3' C4' UDP sing 450 n n C3' O3' UDP sing 451 n n C3' H3' UDP sing 452 n n C4' O4' UDP sing 453 n n C4' C5' UDP sing 454 n n C4' H4' UDP sing 455 n n O3' HO3' UDP sing 456 n n C5' O5' UDP sing 457 n n C5' "H5'1" UDP sing 458 n n C5' "H5'2" UDP sing 459 n n O5' PA UDP sing 460 n n PA O1A UDP doub 461 n n PA O2A UDP sing 462 n n PA O3A UDP sing 463 n n O2A HOA2 UDP sing 464 n n O3A PB UDP sing 465 n n PB O1B UDP doub 466 n n PB O2B UDP sing 467 n n PB O3B UDP sing 468 n n O2B HOB2 UDP sing 469 n n O3B HOB3 UDP sing 470 n n # _atom_sites.entry_id 7ZI2 _atom_sites.fract_transf_matrix[1][1] 0.014527 _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] 0.014527 _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] 0.008087 _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 1 301 301 UDP UDP . C 3 J7W A 1 302 401 J7W LIG . D 4 NA A 1 303 1 NA NA . E 5 HOH A 1 401 7 HOH HOH . E 5 HOH A 2 402 27 HOH HOH . E 5 HOH A 3 403 14 HOH HOH . E 5 HOH A 4 404 2 HOH HOH . E 5 HOH A 5 405 5 HOH HOH . E 5 HOH A 6 406 30 HOH HOH . E 5 HOH A 7 407 24 HOH HOH . E 5 HOH A 8 408 1 HOH HOH . E 5 HOH A 9 409 39 HOH HOH . E 5 HOH A 10 410 12 HOH HOH . E 5 HOH A 11 411 11 HOH HOH . E 5 HOH A 12 412 20 HOH HOH . E 5 HOH A 13 413 31 HOH HOH . E 5 HOH A 14 414 13 HOH HOH . E 5 HOH A 15 415 38 HOH HOH . E 5 HOH A 16 416 10 HOH HOH . E 5 HOH A 17 417 36 HOH HOH . E 5 HOH A 18 418 21 HOH HOH . E 5 HOH A 19 419 23 HOH HOH . E 5 HOH A 20 420 17 HOH HOH . E 5 HOH A 21 421 22 HOH HOH . E 5 HOH A 22 422 18 HOH HOH . E 5 HOH A 23 423 15 HOH HOH . E 5 HOH A 24 424 4 HOH HOH . E 5 HOH A 25 425 6 HOH HOH . E 5 HOH A 26 426 3 HOH HOH . E 5 HOH A 27 427 16 HOH HOH . E 5 HOH A 28 428 34 HOH HOH . E 5 HOH A 29 429 25 HOH HOH . E 5 HOH A 30 430 29 HOH HOH . E 5 HOH A 31 431 33 HOH HOH . E 5 HOH A 32 432 9 HOH HOH . E 5 HOH A 33 433 26 HOH HOH . E 5 HOH A 34 434 8 HOH HOH . E 5 HOH A 35 435 37 HOH HOH . E 5 HOH A 36 436 35 HOH HOH . E 5 HOH A 37 437 40 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 -28.522 -25.606 18.176 1 52.11 ? N1 UDP 301 A 1 HETATM 2 C C2 UDP . . . B 2 -29.596 -25.64 19.097 1 56.92 ? C2 UDP 301 A 1 HETATM 3 N N3 UDP . . . B 2 -29.652 -24.762 20.096 1 55.93 ? N3 UDP 301 A 1 HETATM 4 C C4 UDP . . . B 2 -28.7 -23.853 20.243 1 56.05 ? C4 UDP 301 A 1 HETATM 5 C C5 UDP . . . B 2 -27.606 -23.812 19.384 1 49.1 ? C5 UDP 301 A 1 HETATM 6 C C6 UDP . . . B 2 -27.528 -24.713 18.343 1 54.75 ? C6 UDP 301 A 1 HETATM 7 O O2 UDP . . . B 2 -30.516 -26.467 18.989 1 59.32 ? O2 UDP 301 A 1 HETATM 8 O O4 UDP . . . B 2 -28.781 -23.053 21.197 1 60.25 ? O4 UDP 301 A 1 HETATM 9 C C1' UDP . . . B 2 -28.445 -26.566 17.112 1 45.3 ? C1' UDP 301 A 1 HETATM 10 C C2' UDP . . . B 2 -28.401 -25.991 15.725 1 51.33 ? C2' UDP 301 A 1 HETATM 11 O O2' UDP . . . B 2 -29.679 -25.679 15.184 1 51.57 ? O2' UDP 301 A 1 HETATM 12 C C3' UDP . . . B 2 -27.649 -27.101 14.975 1 55.58 ? C3' UDP 301 A 1 HETATM 13 C C4' UDP . . . B 2 -26.691 -27.652 16.037 1 50.02 ? C4' UDP 301 A 1 HETATM 14 O O4' UDP . . . B 2 -27.198 -27.244 17.312 1 50.47 ? O4' UDP 301 A 1 HETATM 15 O O3' UDP . . . B 2 -28.515 -28.159 14.486 1 55.94 ? O3' UDP 301 A 1 HETATM 16 C C5' UDP . . . B 2 -25.254 -27.142 15.902 1 50.59 ? C5' UDP 301 A 1 HETATM 17 O O5' UDP . . . B 2 -25.134 -25.725 15.94 1 48.79 ? O5' UDP 301 A 1 HETATM 18 P PA UDP . . . B 2 -24.37 -24.917 14.769 1 45.59 ? PA UDP 301 A 1 HETATM 19 O O1A UDP . . . B 2 -24.612 -25.547 13.449 1 48.09 ? O1A UDP 301 A 1 HETATM 20 O O2A UDP . . . B 2 -24.703 -23.476 14.883 1 51.24 ? O2A UDP 301 A 1 HETATM 21 O O3A UDP . . . B 2 -22.846 -25.212 15.291 1 44.53 ? O3A UDP 301 A 1 HETATM 22 P PB UDP . . . B 2 -21.422 -24.712 14.719 1 43.23 ? PB UDP 301 A 1 HETATM 23 O O1B UDP . . . B 2 -21.683 -23.69 13.675 1 42.19 ? O1B UDP 301 A 1 HETATM 24 O O2B UDP . . . B 2 -20.668 -25.856 14.125 1 46.45 ? O2B UDP 301 A 1 HETATM 25 O O3B UDP . . . B 2 -20.781 -24.212 15.998 1 38.25 ? O3B UDP 301 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 25 #