data_8TX9 # _model_server_result.job_id hEOly9ckrK2OR9151mB02A _model_server_result.datetime_utc '2024-11-27 00:15:19' _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 8tx9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":301}' # _entry.id 8TX9 # _exptl.entry_id 8TX9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 301.188 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-mannopyranose _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 8TX9 _cell.length_a 147.577 _cell.length_b 147.577 _cell.length_c 82.311 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8TX9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 79 _symmetry.space_group_name_Hall 'I 4' _symmetry.space_group_name_H-M 'I 4' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,M,N,O,P _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 E N N ? 2 G N N ? 2 I N N ? 2 K 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 covale ? covale1 B C ASN 100 C ASN 100 1_555 B N MSE 101 C MSE 101 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.322 ? covale ? covale2 B C GLU 141 C GLU 141 1_555 B N MSE 142 C MSE 142 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.324 ? covale ? covale3 B C MSE 142 C MSE 142 1_555 B N LYS 143 C LYS 143 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale4 B C PRO 238 C PRO 238 1_555 B N MSE 239 C MSE 239 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.336 ? covale ? covale5 B C MSE 239 C MSE 239 1_555 B N LEU 240 C LEU 240 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.336 ? metalc ? metalc1 A OG SER 225 A SER 225 1_555 F NA NA . A NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.183 ? metalc ? metalc2 D OG SER 97 B SER 97 1_555 L NA NA . B NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.999 ? # _chem_comp.formula 'C8 H16 N O9 P' _chem_comp.formula_weight 301.188 _chem_comp.id BMX _chem_comp.mon_nstd_flag n _chem_comp.name 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-mannopyranose _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms 2-(ACETYLAMINO)-2-DEOXY-6-O-PHOSPHONO-ALPHA-D-MANNOPYRANOSE;N-acetyl-6-O-phosphono-alpha-D-mannosamine;2-acetamido-2-deoxy-6-O-phosphono-alpha-D-mannose;2-acetamido-2-deoxy-6-O-phosphono-D-mannose;2-acetamido-2-deoxy-6-O-phosphono-mannose # 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 C1 O1 BMX sing 70 n n C1 C2 BMX sing 71 n n C1 O5 BMX sing 72 n n C2 N2 BMX sing 73 n n C2 C3 BMX sing 74 n n N2 C7 BMX sing 75 n n C7 O7 BMX doub 76 n n C7 C8 BMX sing 77 n n C3 O3 BMX sing 78 n n C3 C4 BMX sing 79 n n C4 O4 BMX sing 80 n n C4 C5 BMX sing 81 n n C5 C6 BMX sing 82 n n C5 O5 BMX sing 83 n n C6 O6 BMX sing 84 n n O6 P BMX sing 85 n n P O17 BMX doub 86 n n P O18 BMX sing 87 n n P O19 BMX sing 88 n n C1 H1 BMX sing 89 n n O1 HO1 BMX sing 90 n n C2 H2 BMX sing 91 n n N2 HN2 BMX sing 92 n n C3 H3 BMX sing 93 n n C8 H81 BMX sing 94 n n C8 H82 BMX sing 95 n n C8 H83 BMX sing 96 n n O3 HO3 BMX sing 97 n n C4 H4 BMX sing 98 n n O4 HO4 BMX sing 99 n n C5 H5 BMX sing 100 n n C6 H61 BMX sing 101 n n C6 H62 BMX sing 102 n n O18 H18 BMX sing 103 n n O19 H19 BMX sing 104 n n # _pdbx_chem_comp_identifier.comp_id BMX _pdbx_chem_comp_identifier.identifier a-D-ManpNAc6PO3 _pdbx_chem_comp_identifier.type 'IUPAC CARBOHYDRATE SYMBOL' _pdbx_chem_comp_identifier.program PDB-CARE _pdbx_chem_comp_identifier.program_version 1 # _atom_sites.entry_id 8TX9 _atom_sites.fract_transf_matrix[1][1] 0.006776 _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] 0.006776 _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] 0.012149 _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 BMX A 1 301 301 BMX BMX . F 3 NA A 1 302 2 NA NA . G 2 BMX C 1 301 301 BMX BMX . H 3 NA C 1 302 1 NA NA . I 2 BMX D 1 301 301 BMX BMX . J 3 NA D 1 302 4 NA NA . K 2 BMX B 1 301 301 BMX BMX . L 3 NA B 1 302 3 NA NA . M 4 HOH A 1 401 114 HOH HOH . M 4 HOH A 2 402 175 HOH HOH . M 4 HOH A 3 403 141 HOH HOH . M 4 HOH A 4 404 119 HOH HOH . M 4 HOH A 5 405 163 HOH HOH . M 4 HOH A 6 406 30 HOH HOH . M 4 HOH A 7 407 153 HOH HOH . M 4 HOH A 8 408 17 HOH HOH . M 4 HOH A 9 409 91 HOH HOH . M 4 HOH A 10 410 3 HOH HOH . M 4 HOH A 11 411 109 HOH HOH . M 4 HOH A 12 412 75 HOH HOH . M 4 HOH A 13 413 182 HOH HOH . M 4 HOH A 14 414 18 HOH HOH . M 4 HOH A 15 415 86 HOH HOH . M 4 HOH A 16 416 99 HOH HOH . M 4 HOH A 17 417 74 HOH HOH . M 4 HOH A 18 418 194 HOH HOH . M 4 HOH A 19 419 162 HOH HOH . M 4 HOH A 20 420 58 HOH HOH . M 4 HOH A 21 421 166 HOH HOH . N 4 HOH C 1 401 16 HOH HOH . N 4 HOH C 2 402 97 HOH HOH . N 4 HOH C 3 403 42 HOH HOH . N 4 HOH C 4 404 73 HOH HOH . N 4 HOH C 5 405 144 HOH HOH . N 4 HOH C 6 406 31 HOH HOH . N 4 HOH C 7 407 32 HOH HOH . N 4 HOH C 8 408 108 HOH HOH . N 4 HOH C 9 409 4 HOH HOH . N 4 HOH C 10 410 51 HOH HOH . N 4 HOH C 11 411 57 HOH HOH . N 4 HOH C 12 412 38 HOH HOH . N 4 HOH C 13 413 93 HOH HOH . N 4 HOH C 14 414 83 HOH HOH . N 4 HOH C 15 415 1 HOH HOH . N 4 HOH C 16 416 131 HOH HOH . N 4 HOH C 17 417 84 HOH HOH . N 4 HOH C 18 418 68 HOH HOH . N 4 HOH C 19 419 53 HOH HOH . N 4 HOH C 20 420 142 HOH HOH . N 4 HOH C 21 421 12 HOH HOH . N 4 HOH C 22 422 10 HOH HOH . N 4 HOH C 23 423 40 HOH HOH . N 4 HOH C 24 424 110 HOH HOH . N 4 HOH C 25 425 171 HOH HOH . N 4 HOH C 26 426 50 HOH HOH . N 4 HOH C 27 427 189 HOH HOH . N 4 HOH C 28 428 152 HOH HOH . N 4 HOH C 29 429 6 HOH HOH . N 4 HOH C 30 430 21 HOH HOH . N 4 HOH C 31 431 8 HOH HOH . N 4 HOH C 32 432 60 HOH HOH . N 4 HOH C 33 433 20 HOH HOH . N 4 HOH C 34 434 33 HOH HOH . N 4 HOH C 35 435 143 HOH HOH . N 4 HOH C 36 436 192 HOH HOH . N 4 HOH C 37 437 23 HOH HOH . N 4 HOH C 38 438 69 HOH HOH . N 4 HOH C 39 439 94 HOH HOH . N 4 HOH C 40 440 167 HOH HOH . N 4 HOH C 41 441 126 HOH HOH . N 4 HOH C 42 442 72 HOH HOH . N 4 HOH C 43 443 27 HOH HOH . N 4 HOH C 44 444 11 HOH HOH . N 4 HOH C 45 445 26 HOH HOH . N 4 HOH C 46 446 85 HOH HOH . N 4 HOH C 47 447 127 HOH HOH . N 4 HOH C 48 448 188 HOH HOH . N 4 HOH C 49 449 196 HOH HOH . N 4 HOH C 50 450 104 HOH HOH . N 4 HOH C 51 451 124 HOH HOH . N 4 HOH C 52 452 46 HOH HOH . N 4 HOH C 53 453 52 HOH HOH . N 4 HOH C 54 454 147 HOH HOH . N 4 HOH C 55 455 155 HOH HOH . N 4 HOH C 56 456 39 HOH HOH . N 4 HOH C 57 457 168 HOH HOH . N 4 HOH C 58 458 165 HOH HOH . N 4 HOH C 59 459 115 HOH HOH . N 4 HOH C 60 460 29 HOH HOH . N 4 HOH C 61 461 195 HOH HOH . N 4 HOH C 62 462 148 HOH HOH . N 4 HOH C 63 463 179 HOH HOH . N 4 HOH C 64 464 133 HOH HOH . N 4 HOH C 65 465 173 HOH HOH . N 4 HOH C 66 466 170 HOH HOH . N 4 HOH C 67 467 149 HOH HOH . N 4 HOH C 68 468 125 HOH HOH . N 4 HOH C 69 469 159 HOH HOH . N 4 HOH C 70 470 180 HOH HOH . N 4 HOH C 71 471 92 HOH HOH . N 4 HOH C 72 472 102 HOH HOH . N 4 HOH C 73 473 156 HOH HOH . N 4 HOH C 74 474 134 HOH HOH . N 4 HOH C 75 475 101 HOH HOH . O 4 HOH D 1 401 41 HOH HOH . O 4 HOH D 2 402 105 HOH HOH . O 4 HOH D 3 403 65 HOH HOH . O 4 HOH D 4 404 120 HOH HOH . O 4 HOH D 5 405 45 HOH HOH . O 4 HOH D 6 406 81 HOH HOH . O 4 HOH D 7 407 117 HOH HOH . O 4 HOH D 8 408 128 HOH HOH . O 4 HOH D 9 409 5 HOH HOH . O 4 HOH D 10 410 82 HOH HOH . O 4 HOH D 11 411 44 HOH HOH . O 4 HOH D 12 412 36 HOH HOH . O 4 HOH D 13 413 34 HOH HOH . O 4 HOH D 14 414 80 HOH HOH . O 4 HOH D 15 415 113 HOH HOH . O 4 HOH D 16 416 87 HOH HOH . O 4 HOH D 17 417 2 HOH HOH . O 4 HOH D 18 418 136 HOH HOH . O 4 HOH D 19 419 178 HOH HOH . O 4 HOH D 20 420 56 HOH HOH . O 4 HOH D 21 421 14 HOH HOH . O 4 HOH D 22 422 98 HOH HOH . O 4 HOH D 23 423 35 HOH HOH . O 4 HOH D 24 424 55 HOH HOH . O 4 HOH D 25 425 89 HOH HOH . O 4 HOH D 26 426 90 HOH HOH . O 4 HOH D 27 427 62 HOH HOH . O 4 HOH D 28 428 132 HOH HOH . O 4 HOH D 29 429 64 HOH HOH . O 4 HOH D 30 430 63 HOH HOH . O 4 HOH D 31 431 139 HOH HOH . O 4 HOH D 32 432 130 HOH HOH . O 4 HOH D 33 433 9 HOH HOH . O 4 HOH D 34 434 13 HOH HOH . O 4 HOH D 35 435 95 HOH HOH . O 4 HOH D 36 436 28 HOH HOH . O 4 HOH D 37 437 122 HOH HOH . O 4 HOH D 38 438 146 HOH HOH . O 4 HOH D 39 439 48 HOH HOH . O 4 HOH D 40 440 25 HOH HOH . O 4 HOH D 41 441 66 HOH HOH . O 4 HOH D 42 442 15 HOH HOH . O 4 HOH D 43 443 37 HOH HOH . O 4 HOH D 44 444 71 HOH HOH . O 4 HOH D 45 445 186 HOH HOH . O 4 HOH D 46 446 129 HOH HOH . O 4 HOH D 47 447 88 HOH HOH . O 4 HOH D 48 448 59 HOH HOH . O 4 HOH D 49 449 187 HOH HOH . O 4 HOH D 50 450 160 HOH HOH . O 4 HOH D 51 451 19 HOH HOH . O 4 HOH D 52 452 70 HOH HOH . O 4 HOH D 53 453 145 HOH HOH . O 4 HOH D 54 454 49 HOH HOH . O 4 HOH D 55 455 157 HOH HOH . O 4 HOH D 56 456 181 HOH HOH . O 4 HOH D 57 457 190 HOH HOH . O 4 HOH D 58 458 184 HOH HOH . O 4 HOH D 59 459 164 HOH HOH . O 4 HOH D 60 460 185 HOH HOH . P 4 HOH B 1 401 7 HOH HOH . P 4 HOH B 2 402 158 HOH HOH . P 4 HOH B 3 403 137 HOH HOH . P 4 HOH B 4 404 61 HOH HOH . P 4 HOH B 5 405 103 HOH HOH . P 4 HOH B 6 406 76 HOH HOH . P 4 HOH B 7 407 77 HOH HOH . P 4 HOH B 8 408 100 HOH HOH . P 4 HOH B 9 409 79 HOH HOH . P 4 HOH B 10 410 169 HOH HOH . P 4 HOH B 11 411 43 HOH HOH . P 4 HOH B 12 412 22 HOH HOH . P 4 HOH B 13 413 121 HOH HOH . P 4 HOH B 14 414 111 HOH HOH . P 4 HOH B 15 415 67 HOH HOH . P 4 HOH B 16 416 24 HOH HOH . P 4 HOH B 17 417 54 HOH HOH . P 4 HOH B 18 418 78 HOH HOH . P 4 HOH B 19 419 154 HOH HOH . P 4 HOH B 20 420 191 HOH HOH . P 4 HOH B 21 421 138 HOH HOH . P 4 HOH B 22 422 112 HOH HOH . P 4 HOH B 23 423 123 HOH HOH . P 4 HOH B 24 424 150 HOH HOH . P 4 HOH B 25 425 161 HOH HOH . P 4 HOH B 26 426 193 HOH HOH . P 4 HOH B 27 427 176 HOH HOH . P 4 HOH B 28 428 96 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 C C1 BMX . . . I 2 -1.143 -36.869 -39.173 1 56.77 ? C1 BMX 301 D 1 HETATM 2 C C2 BMX . . . I 2 -1.498 -35.771 -40.138 1 59.3 ? C2 BMX 301 D 1 HETATM 3 C C3 BMX . . . I 2 -0.329 -34.84 -40.214 1 52.23 ? C3 BMX 301 D 1 HETATM 4 C C4 BMX . . . I 2 0.064 -34.235 -38.888 1 50.12 ? C4 BMX 301 D 1 HETATM 5 C C5 BMX . . . I 2 0.266 -35.34 -37.858 1 43.24 ? C5 BMX 301 D 1 HETATM 6 C C6 BMX . . . I 2 0.395 -34.76 -36.521 1 47.09 ? C6 BMX 301 D 1 HETATM 7 C C7 BMX . . . I 2 -3.747 -34.667 -40.506 1 63.27 ? C7 BMX 301 D 1 HETATM 8 C C8 BMX . . . I 2 -4.962 -33.948 -39.874 1 74.37 ? C8 BMX 301 D 1 HETATM 9 N N2 BMX . . . I 2 -2.701 -35.106 -39.602 1 63.77 ? N2 BMX 301 D 1 HETATM 10 O O1 BMX . . . I 2 -0.024 -37.419 -39.728 1 54.28 ? O1 BMX 301 D 1 HETATM 11 O O3 BMX . . . I 2 -0.5 -33.727 -41.134 1 46.28 ? O3 BMX 301 D 1 HETATM 12 O O4 BMX . . . I 2 1.249 -33.444 -39.127 1 49.7 ? O4 BMX 301 D 1 HETATM 13 O O5 BMX . . . I 2 -0.827 -36.301 -37.838 1 41.54 ? O5 BMX 301 D 1 HETATM 14 O O6 BMX . . . I 2 -0.812 -34.269 -36.003 1 41.09 ? O6 BMX 301 D 1 HETATM 15 O O7 BMX . . . I 2 -3.674 -34.871 -41.682 1 58.46 ? O7 BMX 301 D 1 HETATM 16 P P BMX . . . I 2 -0.663 -33.301 -34.796 1 61.11 ? P BMX 301 D 1 HETATM 17 O O19 BMX . . . I 2 -0.318 -34.228 -33.742 1 41.08 ? O19 BMX 301 D 1 HETATM 18 O O17 BMX . . . I 2 0.493 -32.354 -34.973 1 45.68 ? O17 BMX 301 D 1 HETATM 19 O O18 BMX . . . I 2 -1.965 -32.642 -34.473 1 42.58 ? O18 BMX 301 D 1 HETATM 20 H H1 BMX . . . I 2 -1.843 -37.53 -39.05 1 56.77 ? H1 BMX 301 D 1 HETATM 21 H H2 BMX . . . I 2 -1.718 -36.08 -41.03 1 59.3 ? H2 BMX 301 D 1 HETATM 22 H H3 BMX . . . I 2 0.371 -35.411 -40.566 1 52.23 ? H3 BMX 301 D 1 HETATM 23 H H4 BMX . . . I 2 -0.603 -33.633 -38.524 1 50.12 ? H4 BMX 301 D 1 HETATM 24 H H5 BMX . . . I 2 1.088 -35.803 -38.082 1 43.24 ? H5 BMX 301 D 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 33 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 24 #