data_3MJR # _model_server_result.job_id FbBfrCrYeb2TfDycE02Stw _model_server_result.datetime_utc '2024-11-21 17:25:24' _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":"I","auth_seq_id":501}' # _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 . . . I 3 -39.325 52.893 -15.03 1 60.91 ? N1 UDP 501 C 1 HETATM 2 C C2 UDP . . . I 3 -40.145 53.706 -14.259 1 61 ? C2 UDP 501 C 1 HETATM 3 N N3 UDP . . . I 3 -39.596 54.744 -13.525 1 61.22 ? N3 UDP 501 C 1 HETATM 4 C C4 UDP . . . I 3 -38.232 54.978 -13.562 1 61.14 ? C4 UDP 501 C 1 HETATM 5 C C5 UDP . . . I 3 -37.421 54.161 -14.342 1 61.2 ? C5 UDP 501 C 1 HETATM 6 C C6 UDP . . . I 3 -37.964 53.002 -14.887 1 61.08 ? C6 UDP 501 C 1 HETATM 7 O O2 UDP . . . I 3 -41.358 53.512 -14.213 1 60.88 ? O2 UDP 501 C 1 HETATM 8 O O4 UDP . . . I 3 -37.741 55.9 -12.913 1 61.09 ? O4 UDP 501 C 1 HETATM 9 C C1' UDP . . . I 3 -39.913 51.786 -15.826 1 60.67 ? C1' UDP 501 C 1 HETATM 10 C C2' UDP . . . I 3 -39.88 52.149 -17.307 1 60.35 ? C2' UDP 501 C 1 HETATM 11 O O2' UDP . . . I 3 -41.164 51.989 -17.866 1 60.94 ? O2' UDP 501 C 1 HETATM 12 C C3' UDP . . . I 3 -38.896 51.17 -17.925 1 60.19 ? C3' UDP 501 C 1 HETATM 13 C C4' UDP . . . I 3 -38.758 50.05 -16.902 1 59.99 ? C4' UDP 501 C 1 HETATM 14 O O4' UDP . . . I 3 -39.201 50.57 -15.658 1 60.22 ? O4' UDP 501 C 1 HETATM 15 O O3' UDP . . . I 3 -39.349 50.676 -19.164 1 59.36 ? O3' UDP 501 C 1 HETATM 16 C C5' UDP . . . I 3 -37.33 49.515 -16.784 1 58.94 ? C5' UDP 501 C 1 HETATM 17 O O5' UDP . . . I 3 -36.396 50.452 -17.279 1 58.72 ? O5' UDP 501 C 1 HETATM 18 P PA UDP . . . I 3 -35.262 50.054 -18.359 1 58.13 ? PA UDP 501 C 1 HETATM 19 O O1A UDP . . . I 3 -35.798 50.2 -19.728 1 57.99 ? O1A UDP 501 C 1 HETATM 20 O O2A UDP . . . I 3 -34.067 50.91 -18.184 1 58.89 ? O2A UDP 501 C 1 HETATM 21 O O3A UDP . . . I 3 -34.909 48.502 -18.088 1 57 ? O3A UDP 501 C 1 HETATM 22 P PB UDP . . . I 3 -33.42 47.928 -18.338 1 55.28 ? PB UDP 501 C 1 HETATM 23 O O1B UDP . . . I 3 -32.486 48.681 -17.471 1 53.47 ? O1B UDP 501 C 1 HETATM 24 O O2B UDP . . . I 3 -33.026 48.077 -19.757 1 54.3 ? O2B UDP 501 C 1 HETATM 25 O O3B UDP . . . I 3 -33.421 46.489 -17.996 1 55 ? O3B UDP 501 C 1 # _model_server_stats.io_time_ms 50 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #