data_4JLM # _model_server_result.job_id OcNU1-ky2n1hYrsbMrcdiQ _model_server_result.datetime_utc '2024-11-23 01:34:40' _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 4jlm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":303}' # _entry.id 4JLM # _exptl.entry_id 4JLM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 3 _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 4JLM _cell.length_a 68.516 _cell.length_b 68.516 _cell.length_c 121.285 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4JLM _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41' # _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,G,H,I _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 G N N # _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 411 n n N1 C6 UDP sing 412 n n N1 C1' UDP sing 413 n n C2 N3 UDP sing 414 n n C2 O2 UDP doub 415 n n N3 C4 UDP sing 416 n n N3 HN3 UDP sing 417 n n C4 C5 UDP sing 418 n n C4 O4 UDP doub 419 n n C5 C6 UDP doub 420 n n C5 H5 UDP sing 421 n n C6 H6 UDP sing 422 n n C1' C2' UDP sing 423 n n C1' O4' UDP sing 424 n n C1' H1' UDP sing 425 n n C2' O2' UDP sing 426 n n C2' C3' UDP sing 427 n n C2' H2' UDP sing 428 n n O2' HO2' UDP sing 429 n n C3' C4' UDP sing 430 n n C3' O3' UDP sing 431 n n C3' H3' UDP sing 432 n n C4' O4' UDP sing 433 n n C4' C5' UDP sing 434 n n C4' H4' UDP sing 435 n n O3' HO3' UDP sing 436 n n C5' O5' UDP sing 437 n n C5' "H5'1" UDP sing 438 n n C5' "H5'2" UDP sing 439 n n O5' PA UDP sing 440 n n PA O1A UDP doub 441 n n PA O2A UDP sing 442 n n PA O3A UDP sing 443 n n O2A HOA2 UDP sing 444 n n O3A PB UDP sing 445 n n PB O1B UDP doub 446 n n PB O2B UDP sing 447 n n PB O3B UDP sing 448 n n O2B HOB2 UDP sing 449 n n O3B HOB3 UDP sing 450 n n # _atom_sites.entry_id 4JLM _atom_sites.fract_transf_matrix[1][1] 0.014595 _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] 0.014595 _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] 0.008245 _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 1NN A 1 301 301 1NN 1NN . D 2 1NN A 1 302 302 1NN 1NN . E 3 UDP A 1 303 401 UDP UDP . F 2 1NN B 1 301 301 1NN 1NN . G 3 UDP B 1 302 401 UDP UDP . H 4 HOH A 1 401 2 HOH HOH . H 4 HOH A 2 402 3 HOH HOH . H 4 HOH A 3 403 5 HOH HOH . H 4 HOH A 4 404 6 HOH HOH . H 4 HOH A 5 405 7 HOH HOH . H 4 HOH A 6 406 9 HOH HOH . H 4 HOH A 7 407 14 HOH HOH . H 4 HOH A 8 408 19 HOH HOH . H 4 HOH A 9 409 21 HOH HOH . H 4 HOH A 10 410 26 HOH HOH . H 4 HOH A 11 411 27 HOH HOH . H 4 HOH A 12 412 32 HOH HOH . H 4 HOH A 13 413 33 HOH HOH . H 4 HOH A 14 414 34 HOH HOH . H 4 HOH A 15 415 37 HOH HOH . H 4 HOH A 16 416 41 HOH HOH . H 4 HOH A 17 417 46 HOH HOH . H 4 HOH A 18 418 47 HOH HOH . H 4 HOH A 19 419 51 HOH HOH . H 4 HOH A 20 420 52 HOH HOH . H 4 HOH A 21 421 53 HOH HOH . H 4 HOH A 22 422 54 HOH HOH . H 4 HOH A 23 423 63 HOH HOH . H 4 HOH A 24 424 64 HOH HOH . H 4 HOH A 25 425 66 HOH HOH . H 4 HOH A 26 426 68 HOH HOH . H 4 HOH A 27 427 69 HOH HOH . H 4 HOH A 28 428 71 HOH HOH . H 4 HOH A 29 429 72 HOH HOH . H 4 HOH A 30 430 73 HOH HOH . H 4 HOH A 31 431 75 HOH HOH . H 4 HOH A 32 432 78 HOH HOH . H 4 HOH A 33 433 83 HOH HOH . H 4 HOH A 34 434 84 HOH HOH . H 4 HOH A 35 435 86 HOH HOH . H 4 HOH A 36 436 87 HOH HOH . H 4 HOH A 37 437 89 HOH HOH . H 4 HOH A 38 438 91 HOH HOH . H 4 HOH A 39 439 92 HOH HOH . H 4 HOH A 40 440 93 HOH HOH . H 4 HOH A 41 441 94 HOH HOH . H 4 HOH A 42 442 95 HOH HOH . H 4 HOH A 43 443 96 HOH HOH . H 4 HOH A 44 444 97 HOH HOH . H 4 HOH A 45 445 99 HOH HOH . H 4 HOH A 46 446 103 HOH HOH . H 4 HOH A 47 447 106 HOH HOH . H 4 HOH A 48 448 107 HOH HOH . H 4 HOH A 49 449 114 HOH HOH . H 4 HOH A 50 450 116 HOH HOH . H 4 HOH A 51 451 118 HOH HOH . H 4 HOH A 52 452 120 HOH HOH . H 4 HOH A 53 453 121 HOH HOH . H 4 HOH A 54 454 123 HOH HOH . H 4 HOH A 55 455 124 HOH HOH . H 4 HOH A 56 456 131 HOH HOH . H 4 HOH A 57 457 132 HOH HOH . I 4 HOH B 1 401 1 HOH HOH . I 4 HOH B 2 402 4 HOH HOH . I 4 HOH B 3 403 10 HOH HOH . I 4 HOH B 4 404 11 HOH HOH . I 4 HOH B 5 405 12 HOH HOH . I 4 HOH B 6 406 15 HOH HOH . I 4 HOH B 7 407 16 HOH HOH . I 4 HOH B 8 408 17 HOH HOH . I 4 HOH B 9 409 18 HOH HOH . I 4 HOH B 10 410 20 HOH HOH . I 4 HOH B 11 411 24 HOH HOH . I 4 HOH B 12 412 30 HOH HOH . I 4 HOH B 13 413 31 HOH HOH . I 4 HOH B 14 414 35 HOH HOH . I 4 HOH B 15 415 36 HOH HOH . I 4 HOH B 16 416 38 HOH HOH . I 4 HOH B 17 417 39 HOH HOH . I 4 HOH B 18 418 40 HOH HOH . I 4 HOH B 19 419 42 HOH HOH . I 4 HOH B 20 420 43 HOH HOH . I 4 HOH B 21 421 44 HOH HOH . I 4 HOH B 22 422 45 HOH HOH . I 4 HOH B 23 423 48 HOH HOH . I 4 HOH B 24 424 49 HOH HOH . I 4 HOH B 25 425 50 HOH HOH . I 4 HOH B 26 426 55 HOH HOH . I 4 HOH B 27 427 56 HOH HOH . I 4 HOH B 28 428 57 HOH HOH . I 4 HOH B 29 429 59 HOH HOH . I 4 HOH B 30 430 60 HOH HOH . I 4 HOH B 31 431 61 HOH HOH . I 4 HOH B 32 432 62 HOH HOH . I 4 HOH B 33 433 67 HOH HOH . I 4 HOH B 34 434 77 HOH HOH . I 4 HOH B 35 435 79 HOH HOH . I 4 HOH B 36 436 80 HOH HOH . I 4 HOH B 37 437 81 HOH HOH . I 4 HOH B 38 438 82 HOH HOH . I 4 HOH B 39 439 90 HOH HOH . I 4 HOH B 40 440 98 HOH HOH . I 4 HOH B 41 441 100 HOH HOH . I 4 HOH B 42 442 101 HOH HOH . I 4 HOH B 43 443 102 HOH HOH . I 4 HOH B 44 444 108 HOH HOH . I 4 HOH B 45 445 109 HOH HOH . I 4 HOH B 46 446 110 HOH HOH . I 4 HOH B 47 447 111 HOH HOH . I 4 HOH B 48 448 112 HOH HOH . I 4 HOH B 49 449 113 HOH HOH . I 4 HOH B 50 450 119 HOH HOH . I 4 HOH B 51 451 125 HOH HOH . I 4 HOH B 52 452 126 HOH HOH . I 4 HOH B 53 453 127 HOH HOH . I 4 HOH B 54 454 128 HOH HOH . I 4 HOH B 55 455 129 HOH HOH . I 4 HOH B 56 456 130 HOH HOH . I 4 HOH B 57 457 133 HOH HOH . I 4 HOH B 58 458 134 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 3 -25.051 28.918 3.669 1 60.54 ? N1 UDP 303 A 1 HETATM 2 C C2 UDP . . . E 3 -24.728 30.202 4.177 1 65.62 ? C2 UDP 303 A 1 HETATM 3 N N3 UDP . . . E 3 -23.764 30.331 5.116 1 62.47 ? N3 UDP 303 A 1 HETATM 4 C C4 UDP . . . E 3 -23.108 29.244 5.572 1 61.19 ? C4 UDP 303 A 1 HETATM 5 C C5 UDP . . . E 3 -23.41 27.967 5.08 1 54.12 ? C5 UDP 303 A 1 HETATM 6 C C6 UDP . . . E 3 -24.394 27.824 4.107 1 57.78 ? C6 UDP 303 A 1 HETATM 7 O O2 UDP . . . E 3 -25.347 31.212 3.754 1 64.45 ? O2 UDP 303 A 1 HETATM 8 O O4 UDP . . . E 3 -22.232 29.365 6.455 1 56.91 ? O4 UDP 303 A 1 HETATM 9 C C1' UDP . . . E 3 -26.088 28.79 2.657 1 59.11 ? C1' UDP 303 A 1 HETATM 10 C C2' UDP . . . E 3 -25.433 28.733 1.299 1 57.68 ? C2' UDP 303 A 1 HETATM 11 O O2' UDP . . . E 3 -25.237 30.027 0.737 1 65.45 ? O2' UDP 303 A 1 HETATM 12 C C3' UDP . . . E 3 -26.411 27.894 0.499 1 63.67 ? C3' UDP 303 A 1 HETATM 13 C C4' UDP . . . E 3 -26.972 26.924 1.54 1 55.8 ? C4' UDP 303 A 1 HETATM 14 O O4' UDP . . . E 3 -26.834 27.566 2.811 1 57.65 ? O4' UDP 303 A 1 HETATM 15 O O3' UDP . . . E 3 -27.428 28.723 -0.13 1 61.65 ? O3' UDP 303 A 1 HETATM 16 C C5' UDP . . . E 3 -26.265 25.551 1.548 1 59.67 ? C5' UDP 303 A 1 HETATM 17 O O5' UDP . . . E 3 -24.842 25.584 1.335 1 52.28 ? O5' UDP 303 A 1 HETATM 18 P PA UDP . . . E 3 -24.073 24.649 0.258 1 54.67 ? PA UDP 303 A 1 HETATM 19 O O1A UDP . . . E 3 -24.709 24.72 -1.099 1 54.7 ? O1A UDP 303 A 1 HETATM 20 O O2A UDP . . . E 3 -22.603 24.952 0.362 1 59.2 ? O2A UDP 303 A 1 HETATM 21 O O3A UDP . . . E 3 -24.427 23.249 0.998 1 53.01 ? O3A UDP 303 A 1 HETATM 22 P PB UDP . . . E 3 -23.965 21.804 0.493 1 47.32 ? PB UDP 303 A 1 HETATM 23 O O1B UDP . . . E 3 -22.822 22.136 -0.422 1 52.29 ? O1B UDP 303 A 1 HETATM 24 O O2B UDP . . . E 3 -25.169 21.269 -0.25 1 56.63 ? O2B UDP 303 A 1 HETATM 25 O O3B UDP . . . E 3 -23.616 21.194 1.821 1 49.12 ? O3B UDP 303 A 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 25 #