data_7ZI8 # _model_server_result.job_id Jjc4nSZZGKp674Kaul-Mpw _model_server_result.datetime_utc '2024-11-22 21:18:11' _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 7zi8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 7ZI8 # _exptl.entry_id 7ZI8 _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 7ZI8 _cell.length_a 68.618 _cell.length_b 68.618 _cell.length_c 121.247 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7ZI8 _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 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc2 A O SER 65 A SER 45 1_555 D NA NA . A NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? metalc ? metalc3 A O TRP 68 A TRP 48 1_555 D NA NA . A NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc4 D NA NA . A NA 403 1_555 E O HOH . A HOH 529 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? # _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 438 n n N1 C6 UDP sing 439 n n N1 C1' UDP sing 440 n n C2 N3 UDP sing 441 n n C2 O2 UDP doub 442 n n N3 C4 UDP sing 443 n n N3 HN3 UDP sing 444 n n C4 C5 UDP sing 445 n n C4 O4 UDP doub 446 n n C5 C6 UDP doub 447 n n C5 H5 UDP sing 448 n n C6 H6 UDP sing 449 n n C1' C2' UDP sing 450 n n C1' O4' UDP sing 451 n n C1' H1' UDP sing 452 n n C2' O2' UDP sing 453 n n C2' C3' UDP sing 454 n n C2' H2' UDP sing 455 n n O2' HO2' UDP sing 456 n n C3' C4' UDP sing 457 n n C3' O3' UDP sing 458 n n C3' H3' UDP sing 459 n n C4' O4' UDP sing 460 n n C4' C5' UDP sing 461 n n C4' H4' UDP sing 462 n n O3' HO3' UDP sing 463 n n C5' O5' UDP sing 464 n n C5' "H5'1" UDP sing 465 n n C5' "H5'2" UDP sing 466 n n O5' PA UDP sing 467 n n PA O1A UDP doub 468 n n PA O2A UDP sing 469 n n PA O3A UDP sing 470 n n O2A HOA2 UDP sing 471 n n O3A PB UDP sing 472 n n PB O1B UDP doub 473 n n PB O2B UDP sing 474 n n PB O3B UDP sing 475 n n O2B HOB2 UDP sing 476 n n O3B HOB3 UDP sing 477 n n # _atom_sites.entry_id 7ZI8 _atom_sites.fract_transf_matrix[1][1] 0.014573 _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] 0.014573 _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] 0.008248 _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 1 401 401 UDP UDP . C 3 J5U A 1 402 402 J5U DRG . D 4 NA A 1 403 1 NA NA . E 5 HOH A 1 501 17 HOH HOH . E 5 HOH A 2 502 31 HOH HOH . E 5 HOH A 3 503 21 HOH HOH . E 5 HOH A 4 504 19 HOH HOH . E 5 HOH A 5 505 15 HOH HOH . E 5 HOH A 6 506 4 HOH HOH . E 5 HOH A 7 507 2 HOH HOH . E 5 HOH A 8 508 1 HOH HOH . E 5 HOH A 9 509 13 HOH HOH . E 5 HOH A 10 510 14 HOH HOH . E 5 HOH A 11 511 32 HOH HOH . E 5 HOH A 12 512 9 HOH HOH . E 5 HOH A 13 513 27 HOH HOH . E 5 HOH A 14 514 25 HOH HOH . E 5 HOH A 15 515 20 HOH HOH . E 5 HOH A 16 516 24 HOH HOH . E 5 HOH A 17 517 33 HOH HOH . E 5 HOH A 18 518 12 HOH HOH . E 5 HOH A 19 519 6 HOH HOH . E 5 HOH A 20 520 23 HOH HOH . E 5 HOH A 21 521 3 HOH HOH . E 5 HOH A 22 522 29 HOH HOH . E 5 HOH A 23 523 18 HOH HOH . E 5 HOH A 24 524 5 HOH HOH . E 5 HOH A 25 525 10 HOH HOH . E 5 HOH A 26 526 28 HOH HOH . E 5 HOH A 27 527 26 HOH HOH . E 5 HOH A 28 528 22 HOH HOH . E 5 HOH A 29 529 7 HOH HOH . E 5 HOH A 30 530 11 HOH HOH . E 5 HOH A 31 531 16 HOH HOH . E 5 HOH A 32 532 8 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 -28.367 -25.521 17.472 1 57.91 ? N1 UDP 401 A 1 HETATM 2 C C2 UDP . . . B 2 -29.464 -25.544 18.369 1 60.52 ? C2 UDP 401 A 1 HETATM 3 N N3 UDP . . . B 2 -29.538 -24.638 19.353 1 58.92 ? N3 UDP 401 A 1 HETATM 4 C C4 UDP . . . B 2 -28.58 -23.732 19.505 1 60.78 ? C4 UDP 401 A 1 HETATM 5 C C5 UDP . . . B 2 -27.476 -23.7 18.678 1 58.79 ? C5 UDP 401 A 1 HETATM 6 C C6 UDP . . . B 2 -27.388 -24.61 17.642 1 62.66 ? C6 UDP 401 A 1 HETATM 7 O O2 UDP . . . B 2 -30.386 -26.388 18.245 1 60.91 ? O2 UDP 401 A 1 HETATM 8 O O4 UDP . . . B 2 -28.662 -22.919 20.425 1 71.25 ? O4 UDP 401 A 1 HETATM 9 C C1' UDP . . . B 2 -28.229 -26.504 16.41 1 52.6 ? C1' UDP 401 A 1 HETATM 10 C C2' UDP . . . B 2 -28.145 -25.943 14.997 1 57.79 ? C2' UDP 401 A 1 HETATM 11 O O2' UDP . . . B 2 -29.418 -25.625 14.382 1 54.19 ? O2' UDP 401 A 1 HETATM 12 C C3' UDP . . . B 2 -27.414 -27.103 14.322 1 64.07 ? C3' UDP 401 A 1 HETATM 13 C C4' UDP . . . B 2 -26.428 -27.583 15.394 1 52.98 ? C4' UDP 401 A 1 HETATM 14 O O4' UDP . . . B 2 -26.987 -27.21 16.669 1 53.77 ? O4' UDP 401 A 1 HETATM 15 O O3' UDP . . . B 2 -28.273 -28.205 13.957 1 55.97 ? O3' UDP 401 A 1 HETATM 16 C C5' UDP . . . B 2 -25.075 -26.936 15.176 1 52.91 ? C5' UDP 401 A 1 HETATM 17 O O5' UDP . . . B 2 -25.146 -25.504 15.12 1 48.99 ? O5' UDP 401 A 1 HETATM 18 P PA UDP . . . B 2 -24.227 -24.694 14.134 1 50.53 ? PA UDP 401 A 1 HETATM 19 O O1A UDP . . . B 2 -24.315 -25.371 12.818 1 49.45 ? O1A UDP 401 A 1 HETATM 20 O O2A UDP . . . B 2 -24.461 -23.223 14.162 1 55.57 ? O2A UDP 401 A 1 HETATM 21 O O3A UDP . . . B 2 -22.749 -25.015 14.8 1 47.67 ? O3A UDP 401 A 1 HETATM 22 P PB UDP . . . B 2 -21.287 -24.549 14.264 1 48.37 ? PB UDP 401 A 1 HETATM 23 O O1B UDP . . . B 2 -21.525 -23.479 13.261 1 43.88 ? O1B UDP 401 A 1 HETATM 24 O O2B UDP . . . B 2 -20.682 -25.848 13.768 1 48.05 ? O2B UDP 401 A 1 HETATM 25 O O3B UDP . . . B 2 -20.604 -24.027 15.529 1 43.05 ? O3B UDP 401 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #