data_7ZI1 # _model_server_result.job_id RdCZOl2NP_CpX2SQwa9LUg _model_server_result.datetime_utc '2024-11-13 05:10:12' _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 7zi1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 7ZI1 # _exptl.entry_id 7ZI1 _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 7ZI1 _cell.length_a 68.625 _cell.length_b 68.625 _cell.length_c 120.809 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7ZI1 _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,F _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 E NA NA . A NA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc2 A O SER 65 A SER 45 1_555 E NA NA . A NA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc3 A O TRP 68 A TRP 48 1_555 E NA NA . A NA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc4 E NA NA . A NA 304 1_555 F O HOH . A HOH 424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? metalc ? metalc5 E NA NA . A NA 304 1_555 F O HOH . A HOH 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? # _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 429 n n N1 C6 UDP sing 430 n n N1 C1' UDP sing 431 n n C2 N3 UDP sing 432 n n C2 O2 UDP doub 433 n n N3 C4 UDP sing 434 n n N3 HN3 UDP sing 435 n n C4 C5 UDP sing 436 n n C4 O4 UDP doub 437 n n C5 C6 UDP doub 438 n n C5 H5 UDP sing 439 n n C6 H6 UDP sing 440 n n C1' C2' UDP sing 441 n n C1' O4' UDP sing 442 n n C1' H1' UDP sing 443 n n C2' O2' UDP sing 444 n n C2' C3' UDP sing 445 n n C2' H2' UDP sing 446 n n O2' HO2' UDP sing 447 n n C3' C4' UDP sing 448 n n C3' O3' UDP sing 449 n n C3' H3' UDP sing 450 n n C4' O4' UDP sing 451 n n C4' C5' UDP sing 452 n n C4' H4' UDP sing 453 n n O3' HO3' UDP sing 454 n n C5' O5' UDP sing 455 n n C5' "H5'1" UDP sing 456 n n C5' "H5'2" UDP sing 457 n n O5' PA UDP sing 458 n n PA O1A UDP doub 459 n n PA O2A UDP sing 460 n n PA O3A UDP sing 461 n n O2A HOA2 UDP sing 462 n n O3A PB UDP sing 463 n n PB O1B UDP doub 464 n n PB O2B UDP sing 465 n n PB O3B UDP sing 466 n n O2B HOB2 UDP sing 467 n n O3B HOB3 UDP sing 468 n n # _atom_sites.entry_id 7ZI1 _atom_sites.fract_transf_matrix[1][1] 0.014572 _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] 0.014572 _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] 0.008278 _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 JCA A 1 302 401 JCA LIG . D 3 JCA A 1 303 501 JCA LIG . E 4 NA A 1 304 1 NA NA . F 5 HOH A 1 401 27 HOH HOH . F 5 HOH A 2 402 67 HOH HOH . F 5 HOH A 3 403 68 HOH HOH . F 5 HOH A 4 404 36 HOH HOH . F 5 HOH A 5 405 43 HOH HOH . F 5 HOH A 6 406 10 HOH HOH . F 5 HOH A 7 407 55 HOH HOH . F 5 HOH A 8 408 25 HOH HOH . F 5 HOH A 9 409 86 HOH HOH . F 5 HOH A 10 410 17 HOH HOH . F 5 HOH A 11 411 58 HOH HOH . F 5 HOH A 12 412 56 HOH HOH . F 5 HOH A 13 413 88 HOH HOH . F 5 HOH A 14 414 83 HOH HOH . F 5 HOH A 15 415 21 HOH HOH . F 5 HOH A 16 416 34 HOH HOH . F 5 HOH A 17 417 8 HOH HOH . F 5 HOH A 18 418 37 HOH HOH . F 5 HOH A 19 419 77 HOH HOH . F 5 HOH A 20 420 39 HOH HOH . F 5 HOH A 21 421 59 HOH HOH . F 5 HOH A 22 422 50 HOH HOH . F 5 HOH A 23 423 40 HOH HOH . F 5 HOH A 24 424 82 HOH HOH . F 5 HOH A 25 425 24 HOH HOH . F 5 HOH A 26 426 22 HOH HOH . F 5 HOH A 27 427 74 HOH HOH . F 5 HOH A 28 428 11 HOH HOH . F 5 HOH A 29 429 23 HOH HOH . F 5 HOH A 30 430 79 HOH HOH . F 5 HOH A 31 431 75 HOH HOH . F 5 HOH A 32 432 20 HOH HOH . F 5 HOH A 33 433 3 HOH HOH . F 5 HOH A 34 434 5 HOH HOH . F 5 HOH A 35 435 52 HOH HOH . F 5 HOH A 36 436 13 HOH HOH . F 5 HOH A 37 437 90 HOH HOH . F 5 HOH A 38 438 62 HOH HOH . F 5 HOH A 39 439 6 HOH HOH . F 5 HOH A 40 440 66 HOH HOH . F 5 HOH A 41 441 26 HOH HOH . F 5 HOH A 42 442 30 HOH HOH . F 5 HOH A 43 443 73 HOH HOH . F 5 HOH A 44 444 78 HOH HOH . F 5 HOH A 45 445 44 HOH HOH . F 5 HOH A 46 446 54 HOH HOH . F 5 HOH A 47 447 48 HOH HOH . F 5 HOH A 48 448 45 HOH HOH . F 5 HOH A 49 449 16 HOH HOH . F 5 HOH A 50 450 32 HOH HOH . F 5 HOH A 51 451 53 HOH HOH . F 5 HOH A 52 452 51 HOH HOH . F 5 HOH A 53 453 42 HOH HOH . F 5 HOH A 54 454 9 HOH HOH . F 5 HOH A 55 455 92 HOH HOH . F 5 HOH A 56 456 72 HOH HOH . F 5 HOH A 57 457 2 HOH HOH . F 5 HOH A 58 458 7 HOH HOH . F 5 HOH A 59 459 33 HOH HOH . F 5 HOH A 60 460 46 HOH HOH . F 5 HOH A 61 461 19 HOH HOH . F 5 HOH A 62 462 47 HOH HOH . F 5 HOH A 63 463 70 HOH HOH . F 5 HOH A 64 464 76 HOH HOH . F 5 HOH A 65 465 71 HOH HOH . F 5 HOH A 66 466 49 HOH HOH . F 5 HOH A 67 467 57 HOH HOH . F 5 HOH A 68 468 4 HOH HOH . F 5 HOH A 69 469 60 HOH HOH . F 5 HOH A 70 470 31 HOH HOH . F 5 HOH A 71 471 93 HOH HOH . F 5 HOH A 72 472 1 HOH HOH . F 5 HOH A 73 473 28 HOH HOH . F 5 HOH A 74 474 81 HOH HOH . F 5 HOH A 75 475 18 HOH HOH . F 5 HOH A 76 476 35 HOH HOH . F 5 HOH A 77 477 38 HOH HOH . F 5 HOH A 78 478 94 HOH HOH . F 5 HOH A 79 479 64 HOH HOH . F 5 HOH A 80 480 61 HOH HOH . F 5 HOH A 81 481 80 HOH HOH . F 5 HOH A 82 482 14 HOH HOH . F 5 HOH A 83 483 65 HOH HOH . F 5 HOH A 84 484 84 HOH HOH . F 5 HOH A 85 485 15 HOH HOH . F 5 HOH A 86 486 41 HOH HOH . F 5 HOH A 87 487 12 HOH HOH . F 5 HOH A 88 488 29 HOH HOH . F 5 HOH A 89 489 63 HOH HOH . F 5 HOH A 90 490 89 HOH HOH . F 5 HOH A 91 491 87 HOH HOH . F 5 HOH A 92 492 91 HOH HOH . F 5 HOH A 93 493 69 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 -28.049 -25.728 17.776 1 34.91 ? N1 UDP 301 A 1 HETATM 2 C C2 UDP . . . B 2 -29.19 -25.643 18.616 1 37.54 ? C2 UDP 301 A 1 HETATM 3 N N3 UDP . . . B 2 -29.238 -24.707 19.581 1 34.54 ? N3 UDP 301 A 1 HETATM 4 C C4 UDP . . . B 2 -28.207 -23.851 19.756 1 39.24 ? C4 UDP 301 A 1 HETATM 5 C C5 UDP . . . B 2 -27.043 -23.909 18.952 1 35.86 ? C5 UDP 301 A 1 HETATM 6 C C6 UDP . . . B 2 -27.009 -24.861 17.94 1 37.34 ? C6 UDP 301 A 1 HETATM 7 O O2 UDP . . . B 2 -30.123 -26.459 18.425 1 39.11 ? O2 UDP 301 A 1 HETATM 8 O O4 UDP . . . B 2 -28.238 -23.016 20.679 1 38.96 ? O4 UDP 301 A 1 HETATM 9 C C1' UDP . . . B 2 -28.004 -26.734 16.739 1 35.92 ? C1' UDP 301 A 1 HETATM 10 C C2' UDP . . . B 2 -27.954 -26.142 15.348 1 36.17 ? C2' UDP 301 A 1 HETATM 11 O O2' UDP . . . B 2 -29.2 -25.888 14.759 1 36.98 ? O2' UDP 301 A 1 HETATM 12 C C3' UDP . . . B 2 -27.184 -27.205 14.595 1 37.1 ? C3' UDP 301 A 1 HETATM 13 C C4' UDP . . . B 2 -26.209 -27.755 15.633 1 33.81 ? C4' UDP 301 A 1 HETATM 14 O O4' UDP . . . B 2 -26.759 -27.454 16.915 1 34 ? O4' UDP 301 A 1 HETATM 15 O O3' UDP . . . B 2 -28.005 -28.28 14.122 1 36.31 ? O3' UDP 301 A 1 HETATM 16 C C5' UDP . . . B 2 -24.808 -27.158 15.545 1 36.38 ? C5' UDP 301 A 1 HETATM 17 O O5' UDP . . . B 2 -24.84 -25.741 15.442 1 32.41 ? O5' UDP 301 A 1 HETATM 18 P PA UDP . . . B 2 -23.911 -24.926 14.4 1 31.33 ? PA UDP 301 A 1 HETATM 19 O O1A UDP . . . B 2 -24.026 -25.529 13.057 1 31.32 ? O1A UDP 301 A 1 HETATM 20 O O2A UDP . . . B 2 -24.236 -23.463 14.516 1 33.21 ? O2A UDP 301 A 1 HETATM 21 O O3A UDP . . . B 2 -22.442 -25.228 15.03 1 28.95 ? O3A UDP 301 A 1 HETATM 22 P PB UDP . . . B 2 -20.974 -24.723 14.549 1 27.94 ? PB UDP 301 A 1 HETATM 23 O O1B UDP . . . B 2 -21.164 -23.766 13.383 1 25.44 ? O1B UDP 301 A 1 HETATM 24 O O2B UDP . . . B 2 -20.289 -25.948 14.009 1 30.51 ? O2B UDP 301 A 1 HETATM 25 O O3B UDP . . . B 2 -20.405 -24.223 15.831 1 24.84 ? O3B UDP 301 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 25 #