data_6MXG # _model_server_result.job_id pXZZDh205tBRl6yKsGsWfw _model_server_result.datetime_utc '2024-10-18 23:25:42' _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 6mxg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 6MXG # _exptl.entry_id 6MXG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 365.213 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "XANTHOSINE-5'-MONOPHOSPHATE" _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 111.97 _cell.angle_gamma 90 _cell.entry_id 6MXG _cell.length_a 117.57 _cell.length_b 94.37 _cell.length_c 45 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6MXG _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _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,J,K,L _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 ? 2 C N N ? 2 G 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 OD1 ASP 40 A ASP 34 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.886 ? metalc ? metalc2 A OD2 ASP 40 A ASP 34 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc3 D MG MG . A MG 302 1_555 K O HOH . A HOH 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc4 D MG MG . A MG 302 1_555 K O HOH . A HOH 420 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc5 E MG MG . A MG 303 1_555 K O HOH . A HOH 422 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc6 E MG MG . A MG 303 1_555 K O HOH . A HOH 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc7 B OE2 GLU 119 B GLU 113 1_555 I MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc8 B OD1 ASP 120 B ASP 114 1_555 I MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? metalc ? metalc9 B OD2 ASP 120 B ASP 114 1_555 I MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.947 ? metalc ? metalc10 B OD1 ASP 179 B ASP 173 1_555 H MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? metalc ? metalc11 B OD2 ASP 179 B ASP 173 1_555 H MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc12 G O2' XMP . B XMP 301 1_555 H MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? metalc ? metalc13 H MG MG . B MG 302 1_555 L O HOH . B HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? # _chem_comp.formula 'C10 H14 N4 O9 P 1' _chem_comp.formula_weight 365.213 _chem_comp.id XMP _chem_comp.mon_nstd_flag . _chem_comp.name "XANTHOSINE-5'-MONOPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '5-MONOPHOSPHATE-9-BETA-D-RIBOFURANOSYL XANTHINE' # 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 P O1P XMP sing 380 n n P O2P XMP sing 381 n n P O5' XMP sing 382 n n P O3P XMP doub 383 n n O1P HOP1 XMP sing 384 n n O2P HOP2 XMP sing 385 n n O5' C5' XMP sing 386 n n C5' C4' XMP sing 387 n n C5' "H5'2" XMP sing 388 n n C5' "H5'1" XMP sing 389 n n C4' O4' XMP sing 390 n n C4' C3' XMP sing 391 n n C4' H4' XMP sing 392 n n O4' C1' XMP sing 393 n n C1' N9 XMP sing 394 n n C1' C2' XMP sing 395 n n C1' H1' XMP sing 396 n n N9 C4 XMP sing 397 n y N9 C8 XMP sing 398 n y C4 N3 XMP sing 399 n n C4 C5 XMP doub 400 n y N3 C2 XMP sing 401 n n N3 H3 XMP sing 402 n n N1 C2 XMP sing 403 n n N1 C6 XMP sing 404 n n N1 H1 XMP sing 405 n n C2 O2 XMP doub 406 n n C6 O6 XMP doub 407 n n C6 C5 XMP sing 408 n n C5 N7 XMP sing 409 n y N7 C8 XMP doub 410 n y N7 H7 XMP sing 411 n n C8 H8 XMP sing 412 n n C2' O2' XMP sing 413 n n C2' C3' XMP sing 414 n n C2' H2' XMP sing 415 n n O2' H2O1 XMP sing 416 n n C3' O3' XMP sing 417 n n C3' H3' XMP sing 418 n n O3' H3O1 XMP sing 419 n n # _atom_sites.entry_id 6MXG _atom_sites.fract_transf_matrix[1][1] 0.008506 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003431 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010597 _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] 0.023962 _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 XMP A 1 301 301 XMP XMP . D 3 MG A 1 302 4 MG MG . E 3 MG A 1 303 5 MG MG . F 4 SO4 A 1 304 1 SO4 SO4 . G 2 XMP B 1 301 300 XMP XMP . H 3 MG B 1 302 1 MG MG . I 3 MG B 1 303 3 MG MG . J 4 SO4 B 1 304 2 SO4 SO4 . K 5 HOH A 1 401 28 HOH HOH . K 5 HOH A 2 402 47 HOH HOH . K 5 HOH A 3 403 88 HOH HOH . K 5 HOH A 4 404 35 HOH HOH . K 5 HOH A 5 405 75 HOH HOH . K 5 HOH A 6 406 40 HOH HOH . K 5 HOH A 7 407 14 HOH HOH . K 5 HOH A 8 408 5 HOH HOH . K 5 HOH A 9 409 84 HOH HOH . K 5 HOH A 10 410 85 HOH HOH . K 5 HOH A 11 411 80 HOH HOH . K 5 HOH A 12 412 38 HOH HOH . K 5 HOH A 13 413 69 HOH HOH . K 5 HOH A 14 414 20 HOH HOH . K 5 HOH A 15 415 64 HOH HOH . K 5 HOH A 16 416 16 HOH HOH . K 5 HOH A 17 417 33 HOH HOH . K 5 HOH A 18 418 61 HOH HOH . K 5 HOH A 19 419 59 HOH HOH . K 5 HOH A 20 420 48 HOH HOH . K 5 HOH A 21 421 73 HOH HOH . K 5 HOH A 22 422 44 HOH HOH . K 5 HOH A 23 423 65 HOH HOH . K 5 HOH A 24 424 66 HOH HOH . K 5 HOH A 25 425 74 HOH HOH . K 5 HOH A 26 426 50 HOH HOH . K 5 HOH A 27 427 70 HOH HOH . K 5 HOH A 28 428 42 HOH HOH . L 5 HOH B 1 401 18 HOH HOH . L 5 HOH B 2 402 27 HOH HOH . L 5 HOH B 3 403 4 HOH HOH . L 5 HOH B 4 404 43 HOH HOH . L 5 HOH B 5 405 10 HOH HOH . L 5 HOH B 6 406 22 HOH HOH . L 5 HOH B 7 407 31 HOH HOH . L 5 HOH B 8 408 87 HOH HOH . L 5 HOH B 9 409 19 HOH HOH . L 5 HOH B 10 410 24 HOH HOH . L 5 HOH B 11 411 23 HOH HOH . L 5 HOH B 12 412 32 HOH HOH . L 5 HOH B 13 413 7 HOH HOH . L 5 HOH B 14 414 3 HOH HOH . L 5 HOH B 15 415 2 HOH HOH . L 5 HOH B 16 416 13 HOH HOH . L 5 HOH B 17 417 63 HOH HOH . L 5 HOH B 18 418 9 HOH HOH . L 5 HOH B 19 419 26 HOH HOH . L 5 HOH B 20 420 39 HOH HOH . L 5 HOH B 21 421 54 HOH HOH . L 5 HOH B 22 422 58 HOH HOH . L 5 HOH B 23 423 21 HOH HOH . L 5 HOH B 24 424 25 HOH HOH . L 5 HOH B 25 425 8 HOH HOH . L 5 HOH B 26 426 55 HOH HOH . L 5 HOH B 27 427 67 HOH HOH . L 5 HOH B 28 428 11 HOH HOH . L 5 HOH B 29 429 30 HOH HOH . L 5 HOH B 30 430 86 HOH HOH . L 5 HOH B 31 431 56 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 P P XMP . . . C 2 230.072 -42.596 90.057 1 25.28 ? P XMP 301 A 1 HETATM 2 O O1P XMP . . . C 2 229.606 -43.74 90.928 1 25.19 ? O1P XMP 301 A 1 HETATM 3 O O2P XMP . . . C 2 231.062 -41.609 90.629 1 25.24 ? O2P XMP 301 A 1 HETATM 4 O O5' XMP . . . C 2 228.765 -41.777 89.664 1 52.21 ? O5' XMP 301 A 1 HETATM 5 O O3P XMP . . . C 2 230.666 -43.162 88.79 1 33.36 ? O3P XMP 301 A 1 HETATM 6 C C5' XMP . . . C 2 227.479 -42.266 90.01 1 53.8 ? C5' XMP 301 A 1 HETATM 7 C C4' XMP . . . C 2 226.386 -41.428 89.399 1 51.36 ? C4' XMP 301 A 1 HETATM 8 O O4' XMP . . . C 2 225.198 -42.244 89.22 1 47.67 ? O4' XMP 301 A 1 HETATM 9 C C1' XMP . . . C 2 224.042 -41.493 89.517 1 38.52 ? C1' XMP 301 A 1 HETATM 10 N N9 XMP . . . C 2 223.385 -42.104 90.688 1 38.77 ? N9 XMP 301 A 1 HETATM 11 C C4 XMP . . . C 2 222.337 -41.65 91.427 1 34.52 ? C4 XMP 301 A 1 HETATM 12 N N3 XMP . . . C 2 221.527 -40.445 91.348 1 36.67 ? N3 XMP 301 A 1 HETATM 13 N N1 XMP . . . C 2 220.19 -41.178 93.311 1 38.01 ? N1 XMP 301 A 1 HETATM 14 C C2 XMP . . . C 2 220.458 -40.217 92.292 1 26.71 ? C2 XMP 301 A 1 HETATM 15 O O2 XMP . . . C 2 219.791 -39.214 92.218 1 24.66 ? O2 XMP 301 A 1 HETATM 16 C C6 XMP . . . C 2 220.977 -42.338 93.382 1 41.03 ? C6 XMP 301 A 1 HETATM 17 O O6 XMP . . . C 2 220.757 -43.161 94.243 1 30.14 ? O6 XMP 301 A 1 HETATM 18 C C5 XMP . . . C 2 222.084 -42.563 92.397 1 31.57 ? C5 XMP 301 A 1 HETATM 19 N N7 XMP . . . C 2 222.963 -43.579 92.258 1 24.59 ? N7 XMP 301 A 1 HETATM 20 C C8 XMP . . . C 2 223.766 -43.297 91.201 1 37.98 ? C8 XMP 301 A 1 HETATM 21 C C2' XMP . . . C 2 224.482 -40.055 89.775 1 42.51 ? C2' XMP 301 A 1 HETATM 22 O O2' XMP . . . C 2 224.448 -39.348 88.545 1 49.7 ? O2' XMP 301 A 1 HETATM 23 C C3' XMP . . . C 2 225.915 -40.254 90.244 1 44.57 ? C3' XMP 301 A 1 HETATM 24 O O3' XMP . . . C 2 226.725 -39.104 90.077 1 40.81 ? O3' XMP 301 A 1 HETATM 25 H "H5'2" XMP . . . C 2 227.392 -43.189 89.691 1 64.56 ? "H5'2" XMP 301 A 1 HETATM 26 H "H5'1" XMP . . . C 2 227.384 -42.254 90.985 1 64.56 ? "H5'1" XMP 301 A 1 HETATM 27 H H4' XMP . . . C 2 226.684 -41.098 88.528 1 61.63 ? H4' XMP 301 A 1 HETATM 28 H H1' XMP . . . C 2 223.432 -41.516 88.752 1 46.22 ? H1' XMP 301 A 1 HETATM 29 H H3 XMP . . . C 2 221.695 -39.829 90.697 1 44.01 ? H3 XMP 301 A 1 HETATM 30 H H1 XMP . . . C 2 219.517 -41.04 93.91 1 45.61 ? H1 XMP 301 A 1 HETATM 31 H H7 XMP . . . C 2 223.009 -44.323 92.783 1 29.5 ? H7 XMP 301 A 1 HETATM 32 H H8 XMP . . . C 2 224.494 -43.856 90.87 1 45.57 ? H8 XMP 301 A 1 HETATM 33 H H2' XMP . . . C 2 223.932 -39.625 90.46 1 51.01 ? H2' XMP 301 A 1 HETATM 34 H H2O1 XMP . . . C 2 223.834 -38.706 88.59 1 59.64 ? H2O1 XMP 301 A 1 HETATM 35 H H3' XMP . . . C 2 225.913 -40.514 91.187 1 53.48 ? H3' XMP 301 A 1 HETATM 36 H H3O1 XMP . . . C 2 227.143 -38.922 90.842 1 48.98 ? H3O1 XMP 301 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 36 #