data_8D5G # _model_server_result.job_id -tIKTUk-O65IlxIR1xxtqA _model_server_result.datetime_utc '2024-11-25 22:25:41' _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 8d5g # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":301}' # _entry.id 8D5G # _exptl.entry_id 8D5G _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 353.123 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 6-HYDROXYMETHYLPTERIN-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 120 _cell.entry_id 8D5G _cell.length_a 101.54 _cell.length_b 101.54 _cell.length_c 207.009 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8D5G _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall 'P 64 2 (x,y,z+1/6)' _symmetry.space_group_name_H-M 'P 64 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,I 1 1,2 B,G,H,J 2 1,3 # 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' 8_555 x-y,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 3 'crystal symmetry operation' 11_555 -x+y,y,-z -1 0 0 0 1 0 0 0 -1 0 0 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 # _chem_comp.formula 'C7 H9 N5 O8 P2' _chem_comp.formula_weight 353.123 _chem_comp.id HH2 _chem_comp.mon_nstd_flag . _chem_comp.name 6-HYDROXYMETHYLPTERIN-DIPHOSPHATE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '[PTERIN-6-YL METHANYL]-PHOSPHONOPHOSPHATE' # 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 HH2 doub 129 n y N1 C9 HH2 sing 130 n y C2 C3 HH2 sing 131 n y C2 C11 HH2 sing 132 n n C3 N4 HH2 doub 133 n y C3 H31 HH2 sing 134 n n N4 C10 HH2 sing 135 n y N5 C6 HH2 doub 136 n y N5 C10 HH2 sing 137 n y C6 N6 HH2 sing 138 n n C6 N7 HH2 sing 139 n y N6 HN61 HH2 sing 140 n n N6 HN62 HH2 sing 141 n n N7 C8 HH2 sing 142 n y N7 HN7 HH2 sing 143 n n C8 O8 HH2 doub 144 n n C8 C9 HH2 sing 145 n y C9 C10 HH2 doub 146 n y C11 O4 HH2 sing 147 n n C11 H111 HH2 sing 148 n n C11 H112 HH2 sing 149 n n O4 P1 HH2 sing 150 n n P1 O1P HH2 doub 151 n n P1 O2P HH2 sing 152 n n P1 O3P HH2 sing 153 n n O2P HOP2 HH2 sing 154 n n O3P P2 HH2 sing 155 n n P2 O4P HH2 doub 156 n n P2 O5P HH2 sing 157 n n P2 O6P HH2 sing 158 n n O5P HOP5 HH2 sing 159 n n O6P HOP6 HH2 sing 160 n n # _atom_sites.entry_id 8D5G _atom_sites.fract_transf_matrix[1][1] 0.009848 _atom_sites.fract_transf_matrix[1][2] 0.005686 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011372 _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] 0.004831 _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 HH2 A 1 301 1 HH2 HH2 . D 3 CL A 1 302 1 CL CL . E 3 CL A 1 303 2 CL CL . F 3 CL A 1 304 3 CL CL . G 2 HH2 B 1 301 2 HH2 HH2 . H 3 CL B 1 302 4 CL CL . I 4 HOH A 1 401 107 HOH HOH . I 4 HOH A 2 402 106 HOH HOH . I 4 HOH A 3 403 85 HOH HOH . I 4 HOH A 4 404 81 HOH HOH . I 4 HOH A 5 405 11 HOH HOH . I 4 HOH A 6 406 7 HOH HOH . I 4 HOH A 7 407 94 HOH HOH . I 4 HOH A 8 408 15 HOH HOH . I 4 HOH A 9 409 23 HOH HOH . I 4 HOH A 10 410 18 HOH HOH . I 4 HOH A 11 411 86 HOH HOH . I 4 HOH A 12 412 91 HOH HOH . I 4 HOH A 13 413 14 HOH HOH . I 4 HOH A 14 414 25 HOH HOH . I 4 HOH A 15 415 90 HOH HOH . I 4 HOH A 16 416 93 HOH HOH . I 4 HOH A 17 417 34 HOH HOH . I 4 HOH A 18 418 6 HOH HOH . I 4 HOH A 19 419 62 HOH HOH . I 4 HOH A 20 420 26 HOH HOH . I 4 HOH A 21 421 3 HOH HOH . I 4 HOH A 22 422 28 HOH HOH . I 4 HOH A 23 423 101 HOH HOH . I 4 HOH A 24 424 104 HOH HOH . I 4 HOH A 25 425 55 HOH HOH . I 4 HOH A 26 426 40 HOH HOH . I 4 HOH A 27 427 50 HOH HOH . I 4 HOH A 28 428 24 HOH HOH . I 4 HOH A 29 429 105 HOH HOH . I 4 HOH A 30 430 51 HOH HOH . I 4 HOH A 31 431 61 HOH HOH . I 4 HOH A 32 432 87 HOH HOH . I 4 HOH A 33 433 48 HOH HOH . I 4 HOH A 34 434 58 HOH HOH . I 4 HOH A 35 435 96 HOH HOH . I 4 HOH A 36 436 54 HOH HOH . I 4 HOH A 37 437 56 HOH HOH . I 4 HOH A 38 438 47 HOH HOH . I 4 HOH A 39 439 60 HOH HOH . I 4 HOH A 40 440 52 HOH HOH . I 4 HOH A 41 441 53 HOH HOH . I 4 HOH A 42 442 57 HOH HOH . I 4 HOH A 43 443 80 HOH HOH . I 4 HOH A 44 444 49 HOH HOH . I 4 HOH A 45 445 83 HOH HOH . I 4 HOH A 46 446 95 HOH HOH . I 4 HOH A 47 447 82 HOH HOH . J 4 HOH B 1 401 9 HOH HOH . J 4 HOH B 2 402 99 HOH HOH . J 4 HOH B 3 403 21 HOH HOH . J 4 HOH B 4 404 30 HOH HOH . J 4 HOH B 5 405 103 HOH HOH . J 4 HOH B 6 406 89 HOH HOH . J 4 HOH B 7 407 92 HOH HOH . J 4 HOH B 8 408 12 HOH HOH . J 4 HOH B 9 409 38 HOH HOH . J 4 HOH B 10 410 35 HOH HOH . J 4 HOH B 11 411 17 HOH HOH . J 4 HOH B 12 412 8 HOH HOH . J 4 HOH B 13 413 37 HOH HOH . J 4 HOH B 14 414 100 HOH HOH . J 4 HOH B 15 415 41 HOH HOH . J 4 HOH B 16 416 22 HOH HOH . J 4 HOH B 17 417 76 HOH HOH . J 4 HOH B 18 418 88 HOH HOH . J 4 HOH B 19 419 42 HOH HOH . J 4 HOH B 20 420 4 HOH HOH . J 4 HOH B 21 421 29 HOH HOH . J 4 HOH B 22 422 39 HOH HOH . J 4 HOH B 23 423 36 HOH HOH . J 4 HOH B 24 424 102 HOH HOH . J 4 HOH B 25 425 45 HOH HOH . J 4 HOH B 26 426 46 HOH HOH . J 4 HOH B 27 427 5 HOH HOH . J 4 HOH B 28 428 32 HOH HOH . J 4 HOH B 29 429 74 HOH HOH . J 4 HOH B 30 430 73 HOH HOH . J 4 HOH B 31 431 59 HOH HOH . J 4 HOH B 32 432 44 HOH HOH . J 4 HOH B 33 433 20 HOH HOH . J 4 HOH B 34 434 43 HOH HOH . J 4 HOH B 35 435 27 HOH HOH . J 4 HOH B 36 436 19 HOH HOH . J 4 HOH B 37 437 33 HOH HOH . J 4 HOH B 38 438 16 HOH HOH . J 4 HOH B 39 439 10 HOH HOH . J 4 HOH B 40 440 71 HOH HOH . J 4 HOH B 41 441 77 HOH HOH . J 4 HOH B 42 442 75 HOH HOH . J 4 HOH B 43 443 66 HOH HOH . J 4 HOH B 44 444 2 HOH HOH . J 4 HOH B 45 445 84 HOH HOH . J 4 HOH B 46 446 98 HOH HOH . J 4 HOH B 47 447 70 HOH HOH . J 4 HOH B 48 448 108 HOH HOH . J 4 HOH B 49 449 79 HOH HOH . J 4 HOH B 50 450 65 HOH HOH . J 4 HOH B 51 451 63 HOH HOH . J 4 HOH B 52 452 64 HOH HOH . J 4 HOH B 53 453 78 HOH HOH . J 4 HOH B 54 454 69 HOH HOH . J 4 HOH B 55 455 97 HOH HOH . J 4 HOH B 56 456 1 HOH HOH . J 4 HOH B 57 457 13 HOH HOH . J 4 HOH B 58 458 67 HOH HOH . J 4 HOH B 59 459 31 HOH HOH . J 4 HOH B 60 460 72 HOH HOH . J 4 HOH B 61 461 68 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 HH2 . . . G 2 15.708 26.431 -11.197 1 56.78 ? N1 HH2 301 B 1 HETATM 2 C C2 HH2 . . . G 2 16.362 25.352 -11.624 1 53.57 ? C2 HH2 301 B 1 HETATM 3 C C3 HH2 . . . G 2 16.469 25.098 -12.999 1 52.92 ? C3 HH2 301 B 1 HETATM 4 N N4 HH2 . . . G 2 15.92 25.928 -13.865 1 48.23 ? N4 HH2 301 B 1 HETATM 5 N N5 HH2 . . . G 2 14.694 27.88 -14.297 1 49.82 ? N5 HH2 301 B 1 HETATM 6 C C6 HH2 . . . G 2 14.024 28.987 -13.859 1 44.47 ? C6 HH2 301 B 1 HETATM 7 N N6 HH2 . . . G 2 13.486 29.789 -14.933 1 34.27 ? N6 HH2 301 B 1 HETATM 8 N N7 HH2 . . . G 2 13.915 29.245 -12.507 1 45.62 ? N7 HH2 301 B 1 HETATM 9 C C8 HH2 . . . G 2 14.461 28.417 -11.636 1 49.27 ? C8 HH2 301 B 1 HETATM 10 O O8 HH2 . . . G 2 14.371 28.633 -10.482 1 47.22 ? O8 HH2 301 B 1 HETATM 11 C C9 HH2 . . . G 2 15.146 27.284 -12.086 1 52.93 ? C9 HH2 301 B 1 HETATM 12 C C10 HH2 . . . G 2 15.248 27.039 -13.419 1 50.38 ? C10 HH2 301 B 1 HETATM 13 C C11 HH2 . . . G 2 16.938 24.498 -10.491 1 60.4 ? C11 HH2 301 B 1 HETATM 14 O O4 HH2 . . . G 2 16.329 23.26 -10.494 1 75.2 ? O4 HH2 301 B 1 HETATM 15 P P1 HH2 . . . G 2 15.057 23.018 -9.539 1 82.02 ? P1 HH2 301 B 1 HETATM 16 O O1P HH2 . . . G 2 14.202 24.266 -9.485 1 67.93 ? O1P HH2 301 B 1 HETATM 17 O O2P HH2 . . . G 2 15.529 22.647 -8.127 1 67.44 ? O2P HH2 301 B 1 HETATM 18 O O3P HH2 . . . G 2 14.178 21.761 -10.182 1 71.71 ? O3P HH2 301 B 1 HETATM 19 P P2 HH2 . . . G 2 14.961 20.375 -10.803 1 91.91 ? P2 HH2 301 B 1 HETATM 20 O O4P HH2 . . . G 2 14.98 20.443 -12.337 1 76.22 ? O4P HH2 301 B 1 HETATM 21 O O5P HH2 . . . G 2 14.232 19.114 -10.341 1 82.95 ? O5P HH2 301 B 1 HETATM 22 O O6P HH2 . . . G 2 16.395 20.345 -10.273 1 77.48 ? O6P HH2 301 B 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 22 #