data_3MJR # _model_server_result.job_id k8ZdRjaLiUw4cA6qwMfKxQ _model_server_result.datetime_utc '2024-10-13 00:25:09' _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 3mjr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":261}' # _entry.id 3MJR # _exptl.entry_id 3MJR _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 4 _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 3MJR _cell.length_a 97.31 _cell.length_b 97.31 _cell.length_c 121.5 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3MJR _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41' # 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,L,M 1 1 C,D,I,J,K,N,O 2 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 F N N ? 3 H N N ? 3 I N N ? 3 K 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 386 n n N1 C6 UDP sing 387 n n N1 C1' UDP sing 388 n n C2 N3 UDP sing 389 n n C2 O2 UDP doub 390 n n N3 C4 UDP sing 391 n n N3 HN3 UDP sing 392 n n C4 C5 UDP sing 393 n n C4 O4 UDP doub 394 n n C5 C6 UDP doub 395 n n C5 H5 UDP sing 396 n n C6 H6 UDP sing 397 n n C1' C2' UDP sing 398 n n C1' O4' UDP sing 399 n n C1' H1' UDP sing 400 n n C2' O2' UDP sing 401 n n C2' C3' UDP sing 402 n n C2' H2' UDP sing 403 n n O2' HO2' UDP sing 404 n n C3' C4' UDP sing 405 n n C3' O3' UDP sing 406 n n C3' H3' UDP sing 407 n n C4' O4' UDP sing 408 n n C4' C5' UDP sing 409 n n C4' H4' UDP sing 410 n n O3' HO3' UDP sing 411 n n C5' O5' UDP sing 412 n n C5' "H5'1" UDP sing 413 n n C5' "H5'2" UDP sing 414 n n O5' PA UDP sing 415 n n PA O1A UDP doub 416 n n PA O2A UDP sing 417 n n PA O3A UDP sing 418 n n O2A HOA2 UDP sing 419 n n O3A PB UDP sing 420 n n PB O1B UDP doub 421 n n PB O2B UDP sing 422 n n PB O3B UDP sing 423 n n O2B HOB2 UDP sing 424 n n O3B HOB3 UDP sing 425 n n # _atom_sites.entry_id 3MJR _atom_sites.fract_transf_matrix[1][1] 0.010276 _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] 0.010276 _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] 0.00823 _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 E 2 AC2 A 1 301 301 AC2 AC2 . F 3 UDP A 1 261 301 UDP UDP . G 2 AC2 B 1 401 401 AC2 AC2 . H 3 UDP B 1 261 401 UDP UDP . I 3 UDP C 1 501 501 UDP UDP . J 2 AC2 D 1 601 601 AC2 AC2 . K 3 UDP D 1 261 601 UDP UDP . L 4 HOH A 1 262 5 HOH HOH . L 4 HOH A 2 263 7 HOH HOH . L 4 HOH A 3 264 10 HOH HOH . L 4 HOH A 4 265 14 HOH HOH . L 4 HOH A 5 266 20 HOH HOH . L 4 HOH A 6 267 21 HOH HOH . L 4 HOH A 7 268 27 HOH HOH . L 4 HOH A 8 269 29 HOH HOH . L 4 HOH A 9 270 31 HOH HOH . L 4 HOH A 10 271 32 HOH HOH . L 4 HOH A 11 272 35 HOH HOH . L 4 HOH A 12 273 41 HOH HOH . L 4 HOH A 13 274 55 HOH HOH . L 4 HOH A 14 275 68 HOH HOH . L 4 HOH A 15 276 71 HOH HOH . L 4 HOH A 16 277 73 HOH HOH . L 4 HOH A 17 278 74 HOH HOH . L 4 HOH A 18 279 77 HOH HOH . L 4 HOH A 19 280 78 HOH HOH . L 4 HOH A 20 281 80 HOH HOH . L 4 HOH A 21 282 88 HOH HOH . L 4 HOH A 22 283 91 HOH HOH . M 4 HOH B 1 262 2 HOH HOH . M 4 HOH B 2 263 3 HOH HOH . M 4 HOH B 3 264 4 HOH HOH . M 4 HOH B 4 265 6 HOH HOH . M 4 HOH B 5 266 8 HOH HOH . M 4 HOH B 6 267 9 HOH HOH . M 4 HOH B 7 268 15 HOH HOH . M 4 HOH B 8 269 18 HOH HOH . M 4 HOH B 9 270 19 HOH HOH . M 4 HOH B 10 271 22 HOH HOH . M 4 HOH B 11 272 23 HOH HOH . M 4 HOH B 12 273 24 HOH HOH . M 4 HOH B 13 274 26 HOH HOH . M 4 HOH B 14 275 30 HOH HOH . M 4 HOH B 15 276 33 HOH HOH . M 4 HOH B 16 277 38 HOH HOH . M 4 HOH B 17 278 42 HOH HOH . M 4 HOH B 18 279 44 HOH HOH . M 4 HOH B 19 280 45 HOH HOH . M 4 HOH B 20 281 50 HOH HOH . M 4 HOH B 21 282 54 HOH HOH . M 4 HOH B 22 283 57 HOH HOH . M 4 HOH B 23 284 69 HOH HOH . M 4 HOH B 24 285 70 HOH HOH . M 4 HOH B 25 286 83 HOH HOH . M 4 HOH B 26 287 87 HOH HOH . M 4 HOH B 27 288 89 HOH HOH . M 4 HOH B 28 289 90 HOH HOH . M 4 HOH B 29 290 94 HOH HOH . M 4 HOH B 30 291 96 HOH HOH . M 4 HOH B 31 292 97 HOH HOH . M 4 HOH B 32 293 99 HOH HOH . N 4 HOH C 1 261 11 HOH HOH . N 4 HOH C 2 262 40 HOH HOH . N 4 HOH C 3 263 53 HOH HOH . N 4 HOH C 4 264 63 HOH HOH . N 4 HOH C 5 265 72 HOH HOH . N 4 HOH C 6 266 75 HOH HOH . N 4 HOH C 7 267 82 HOH HOH . O 4 HOH D 1 262 39 HOH HOH . O 4 HOH D 2 263 52 HOH HOH . O 4 HOH D 3 264 62 HOH HOH . O 4 HOH D 4 265 84 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 . . . H 3 38.123 51.055 -18.518 1 30.4 ? N1 UDP 261 B 1 HETATM 2 C C2 UDP . . . H 3 38.902 51.763 -19.427 1 32.04 ? C2 UDP 261 B 1 HETATM 3 N N3 UDP . . . H 3 38.294 52.536 -20.395 1 30.05 ? N3 UDP 261 B 1 HETATM 4 C C4 UDP . . . H 3 36.918 52.589 -20.462 1 29.25 ? C4 UDP 261 B 1 HETATM 5 C C5 UDP . . . H 3 36.125 51.873 -19.564 1 28.57 ? C5 UDP 261 B 1 HETATM 6 C C6 UDP . . . H 3 36.749 51.084 -18.601 1 29.96 ? C6 UDP 261 B 1 HETATM 7 O O2 UDP . . . H 3 40.138 51.733 -19.38 1 34.5 ? O2 UDP 261 B 1 HETATM 8 O O4 UDP . . . H 3 36.405 53.27 -21.338 1 29.58 ? O4 UDP 261 B 1 HETATM 9 C C1' UDP . . . H 3 38.788 50.247 -17.485 1 31.67 ? C1' UDP 261 B 1 HETATM 10 C C2' UDP . . . H 3 38.471 50.813 -16.115 1 32.31 ? C2' UDP 261 B 1 HETATM 11 O O2' UDP . . . H 3 39.381 51.83 -15.744 1 33.55 ? O2' UDP 261 B 1 HETATM 12 C C3' UDP . . . H 3 38.574 49.595 -15.228 1 32.51 ? C3' UDP 261 B 1 HETATM 13 C C4' UDP . . . H 3 38.29 48.411 -16.139 1 31.91 ? C4' UDP 261 B 1 HETATM 14 O O4' UDP . . . H 3 38.368 48.883 -17.474 1 31.28 ? O4' UDP 261 B 1 HETATM 15 O O3' UDP . . . H 3 39.884 49.509 -14.733 1 33.99 ? O3' UDP 261 B 1 HETATM 16 C C5' UDP . . . H 3 36.919 47.801 -15.869 1 31.3 ? C5' UDP 261 B 1 HETATM 17 O O5' UDP . . . H 3 35.91 48.777 -16.056 1 31.23 ? O5' UDP 261 B 1 HETATM 18 P PA UDP . . . H 3 34.618 48.872 -15.091 1 31.97 ? PA UDP 261 B 1 HETATM 19 O O1A UDP . . . H 3 34.925 48.599 -13.665 1 31.29 ? O1A UDP 261 B 1 HETATM 20 O O2A UDP . . . H 3 33.999 50.199 -15.234 1 31.28 ? O2A UDP 261 B 1 HETATM 21 O O3A UDP . . . H 3 33.782 47.644 -15.706 1 28.08 ? O3A UDP 261 B 1 HETATM 22 P PB UDP . . . H 3 32.382 47.067 -15.165 1 25.45 ? PB UDP 261 B 1 HETATM 23 O O1B UDP . . . H 3 31.907 47.904 -14.04 1 25.38 ? O1B UDP 261 B 1 HETATM 24 O O2B UDP . . . H 3 32.532 45.69 -14.676 1 23.29 ? O2B UDP 261 B 1 HETATM 25 O O3B UDP . . . H 3 31.488 47.09 -16.348 1 21 ? O3B UDP 261 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #