data_3C4Q # _model_server_result.job_id 7rmC9qtxULzI9EToqVl86w _model_server_result.datetime_utc '2024-11-17 08:39:18' _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 3c4q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":600}' # _entry.id 3C4Q # _exptl.entry_id 3C4Q _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 3C4Q _cell.length_a 224.245 _cell.length_b 224.245 _cell.length_c 125.112 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3C4Q _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA hexadecameric 16 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,I 1 1,2 B,F,G,H,J 2 1,3 A,B,C,D,E,F,G,H,I,J 3 1,4,5,6,3,7,2,8 # 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' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 3 'crystal symmetry operation' 5_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 224.245 0 0 4 'crystal symmetry operation' 2_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 224.245 224.245 0 5 'crystal symmetry operation' 3_655 -y+1,x,z 0 -1 0 1 0 0 0 0 1 224.245 0 0 6 'crystal symmetry operation' 4_565 y,-x+1,z 0 1 0 -1 0 0 0 0 1 0 224.245 0 7 'crystal symmetry operation' 6_565 x,-y+1,-z 1 0 0 0 -1 0 0 0 -1 0 224.245 0 8 'crystal symmetry operation' 8_665 -y+1,-x+1,-z 0 -1 0 -1 0 0 0 0 -1 224.245 224.245 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 E N N ? 4 H N 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 ALA 306 A ALA 306 1_555 C MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc2 A OG1 THR 330 A THR 330 1_555 C MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc3 C MG MG . A MG 602 1_555 I O HOH . A HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? metalc ? metalc4 B O ALA 306 B ALA 306 1_555 F MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc5 F MG MG . B MG 602 1_555 J O HOH . B HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? # _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 362 n n N1 C6 UDP sing 363 n n N1 C1' UDP sing 364 n n C2 N3 UDP sing 365 n n C2 O2 UDP doub 366 n n N3 C4 UDP sing 367 n n N3 HN3 UDP sing 368 n n C4 C5 UDP sing 369 n n C4 O4 UDP doub 370 n n C5 C6 UDP doub 371 n n C5 H5 UDP sing 372 n n C6 H6 UDP sing 373 n n C1' C2' UDP sing 374 n n C1' O4' UDP sing 375 n n C1' H1' UDP sing 376 n n C2' O2' UDP sing 377 n n C2' C3' UDP sing 378 n n C2' H2' UDP sing 379 n n O2' HO2' UDP sing 380 n n C3' C4' UDP sing 381 n n C3' O3' UDP sing 382 n n C3' H3' UDP sing 383 n n C4' O4' UDP sing 384 n n C4' C5' UDP sing 385 n n C4' H4' UDP sing 386 n n O3' HO3' UDP sing 387 n n C5' O5' UDP sing 388 n n C5' "H5'1" UDP sing 389 n n C5' "H5'2" UDP sing 390 n n O5' PA UDP sing 391 n n PA O1A UDP doub 392 n n PA O2A UDP sing 393 n n PA O3A UDP sing 394 n n O2A HOA2 UDP sing 395 n n O3A PB UDP sing 396 n n PB O1B UDP doub 397 n n PB O2B UDP sing 398 n n PB O3B UDP sing 399 n n O2B HOB2 UDP sing 400 n n O3B HOB3 UDP sing 401 n n # _atom_sites.entry_id 3C4Q _atom_sites.fract_transf_matrix[1][1] 0.004459 _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] 0.004459 _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] 0.007993 _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 C 2 MG A 1 602 602 MG MG . D 3 SO4 A 1 603 1 SO4 SO4 . E 4 UDP A 1 600 600 UDP UDP . F 2 MG B 1 602 602 MG MG . G 3 SO4 B 1 603 2 SO4 SO4 . H 4 UDP B 1 600 600 UDP UDP . I 5 HOH A 1 604 4 HOH HOH . I 5 HOH A 2 605 10 HOH HOH . I 5 HOH A 3 606 12 HOH HOH . I 5 HOH A 4 607 13 HOH HOH . I 5 HOH A 5 608 14 HOH HOH . I 5 HOH A 6 609 15 HOH HOH . I 5 HOH A 7 610 16 HOH HOH . I 5 HOH A 8 611 29 HOH HOH . I 5 HOH A 9 612 32 HOH HOH . I 5 HOH A 10 613 33 HOH HOH . I 5 HOH A 11 614 34 HOH HOH . I 5 HOH A 12 615 35 HOH HOH . I 5 HOH A 13 616 37 HOH HOH . I 5 HOH A 14 617 38 HOH HOH . I 5 HOH A 15 618 41 HOH HOH . I 5 HOH A 16 619 42 HOH HOH . I 5 HOH A 17 620 43 HOH HOH . I 5 HOH A 18 621 44 HOH HOH . I 5 HOH A 19 622 45 HOH HOH . I 5 HOH A 20 623 46 HOH HOH . I 5 HOH A 21 624 48 HOH HOH . I 5 HOH A 22 625 49 HOH HOH . I 5 HOH A 23 626 52 HOH HOH . I 5 HOH A 24 627 54 HOH HOH . I 5 HOH A 25 628 55 HOH HOH . I 5 HOH A 26 629 56 HOH HOH . I 5 HOH A 27 630 73 HOH HOH . I 5 HOH A 28 631 74 HOH HOH . J 5 HOH B 1 604 6 HOH HOH . J 5 HOH B 2 605 8 HOH HOH . J 5 HOH B 3 606 18 HOH HOH . J 5 HOH B 4 607 19 HOH HOH . J 5 HOH B 5 608 20 HOH HOH . J 5 HOH B 6 609 21 HOH HOH . J 5 HOH B 7 610 25 HOH HOH . J 5 HOH B 8 611 26 HOH HOH . J 5 HOH B 9 612 27 HOH HOH . J 5 HOH B 10 613 30 HOH HOH . J 5 HOH B 11 614 31 HOH HOH . J 5 HOH B 12 615 57 HOH HOH . J 5 HOH B 13 616 58 HOH HOH . J 5 HOH B 14 617 59 HOH HOH . J 5 HOH B 15 618 61 HOH HOH . J 5 HOH B 16 619 62 HOH HOH . J 5 HOH B 17 620 63 HOH HOH . J 5 HOH B 18 621 64 HOH HOH . J 5 HOH B 19 622 65 HOH HOH . J 5 HOH B 20 623 66 HOH HOH . J 5 HOH B 21 624 67 HOH HOH . J 5 HOH B 22 625 68 HOH HOH . J 5 HOH B 23 626 69 HOH HOH . J 5 HOH B 24 627 71 HOH HOH . J 5 HOH B 25 628 75 HOH HOH . J 5 HOH B 26 629 76 HOH HOH . J 5 HOH B 27 630 77 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 . . . E 4 81.599 45.608 12.436 1 14.92 ? N1 UDP 600 A 1 HETATM 2 C C2 UDP . . . E 4 81.859 44.522 11.635 1 14.78 ? C2 UDP 600 A 1 HETATM 3 N N3 UDP . . . E 4 83.034 44.436 10.937 1 13.55 ? N3 UDP 600 A 1 HETATM 4 C C4 UDP . . . E 4 83.936 45.465 11.045 1 15.97 ? C4 UDP 600 A 1 HETATM 5 C C5 UDP . . . E 4 83.666 46.574 11.848 1 15.32 ? C5 UDP 600 A 1 HETATM 6 C C6 UDP . . . E 4 82.383 46.72 12.363 1 14.43 ? C6 UDP 600 A 1 HETATM 7 O O2 UDP . . . E 4 81.014 43.621 11.537 1 17.18 ? O2 UDP 600 A 1 HETATM 8 O O4 UDP . . . E 4 84.993 45.389 10.419 1 17.9 ? O4 UDP 600 A 1 HETATM 9 C C1' UDP . . . E 4 80.311 45.607 13.142 1 17.63 ? C1' UDP 600 A 1 HETATM 10 C C2' UDP . . . E 4 80.374 45.356 14.649 1 19.81 ? C2' UDP 600 A 1 HETATM 11 O O2' UDP . . . E 4 80.407 43.972 15.019 1 17.02 ? O2' UDP 600 A 1 HETATM 12 C C3' UDP . . . E 4 79.136 46.106 15.135 1 21.41 ? C3' UDP 600 A 1 HETATM 13 C C4' UDP . . . E 4 78.767 47.056 13.996 1 25.03 ? C4' UDP 600 A 1 HETATM 14 O O4' UDP . . . E 4 79.774 46.884 13.039 1 21.63 ? O4' UDP 600 A 1 HETATM 15 O O3' UDP . . . E 4 78.102 45.181 15.371 1 18.71 ? O3' UDP 600 A 1 HETATM 16 C C5' UDP . . . E 4 78.84 48.554 14.257 1 32.24 ? C5' UDP 600 A 1 HETATM 17 O O5' UDP . . . E 4 78.256 48.828 15.503 1 42.8 ? O5' UDP 600 A 1 HETATM 18 P PA UDP . . . E 4 78.14 50.366 16.03 1 49.84 ? PA UDP 600 A 1 HETATM 19 O O1A UDP . . . E 4 77.103 50.36 17.105 1 48.3 ? O1A UDP 600 A 1 HETATM 20 O O2A UDP . . . E 4 79.41 50.965 16.6 1 49.36 ? O2A UDP 600 A 1 HETATM 21 O O3A UDP . . . E 4 77.683 51.136 14.668 1 43.07 ? O3A UDP 600 A 1 HETATM 22 P PB UDP . . . E 4 76.255 51.824 14.865 1 37.55 ? PB UDP 600 A 1 HETATM 23 O O1B UDP . . . E 4 76.472 53.081 15.597 1 35.54 ? O1B UDP 600 A 1 HETATM 24 O O2B UDP . . . E 4 75.287 50.932 15.497 1 35.72 ? O2B UDP 600 A 1 HETATM 25 O O3B UDP . . . E 4 75.685 52.039 13.54 1 43.37 ? O3B UDP 600 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 25 #