data_7KMA # _model_server_result.job_id cHQVYQTsQukjqIqCuMLIgA _model_server_result.datetime_utc '2024-11-06 01:25:06' _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 7kma # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":401}' # _entry.id 7KMA # _exptl.entry_id 7KMA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 260.136 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 6-O-phosphono-alpha-D-mannopyranose _entity.pdbx_number_of_molecules 8 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 103.893 _cell.angle_gamma 90 _cell.entry_id 7KMA _cell.length_a 71.2 _cell.length_b 155.54 _cell.length_c 140.11 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7KMA _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 1' # 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 PISA dimeric 2 author_and_software_defined_assembly 3 PISA dimeric 2 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,I,J,L,R,T 1 1 B,H,K,Q,S,Y 2 1 D,E,M,N,U,V 3 1 F,G,O,P,W,X 4 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 I N N ? 2 K N N ? 2 L N N ? 2 M N N ? 2 N N N ? 2 O N N ? 2 P N N ? 2 Q N N # _chem_comp.formula 'C6 H13 O9 P' _chem_comp.formula_weight 260.136 _chem_comp.id M6P _chem_comp.mon_nstd_flag n _chem_comp.name 6-O-phosphono-alpha-D-mannopyranose _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms ALPHA-D-MANNOSE-6-PHOSPHATE;6-O-phosphono-alpha-D-mannose;6-O-phosphono-D-mannose;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 C2 M6P sing 224 n n C1 O1 M6P sing 225 n n C1 O5 M6P sing 226 n n C1 H1 M6P sing 227 n n C2 C3 M6P sing 228 n n C2 O2 M6P sing 229 n n C2 H2 M6P sing 230 n n C3 C4 M6P sing 231 n n C3 O3 M6P sing 232 n n C3 H3 M6P sing 233 n n C4 C5 M6P sing 234 n n C4 O4 M6P sing 235 n n C4 H4 M6P sing 236 n n C5 C6 M6P sing 237 n n C5 O5 M6P sing 238 n n C5 H5 M6P sing 239 n n C6 O6 M6P sing 240 n n C6 H61 M6P sing 241 n n C6 H62 M6P sing 242 n n O1 HO1 M6P sing 243 n n O2 HO2 M6P sing 244 n n O3 HO3 M6P sing 245 n n O4 HO4 M6P sing 246 n n O6 P M6P sing 247 n n P O1P M6P doub 248 n n P O2P M6P sing 249 n n P O3P M6P sing 250 n n O2P HOP2 M6P sing 251 n n O3P HOP3 M6P sing 252 n n # _pdbx_chem_comp_identifier.comp_id M6P _pdbx_chem_comp_identifier.identifier a-D-Manp6PO3 _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 7KMA _atom_sites.fract_transf_matrix[1][1] 0.014045 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003474 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006429 _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] 0.007352 _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 I 2 M6P A 1 401 401 M6P M6P . J 3 ACT A 1 402 501 ACT ACT . K 2 M6P B 1 401 401 M6P M6P . L 2 M6P C 1 401 401 M6P M6P . M 2 M6P D 1 401 401 M6P M6P . N 2 M6P E 1 401 401 M6P M6P . O 2 M6P F 1 401 401 M6P M6P . P 2 M6P G 1 401 401 M6P M6P . Q 2 M6P H 1 401 401 M6P M6P . R 4 HOH A 1 501 116 HOH HOH . R 4 HOH A 2 502 114 HOH HOH . R 4 HOH A 3 503 75 HOH HOH . R 4 HOH A 4 504 8 HOH HOH . R 4 HOH A 5 505 107 HOH HOH . R 4 HOH A 6 506 42 HOH HOH . R 4 HOH A 7 507 6 HOH HOH . R 4 HOH A 8 508 36 HOH HOH . R 4 HOH A 9 509 22 HOH HOH . R 4 HOH A 10 510 20 HOH HOH . R 4 HOH A 11 511 16 HOH HOH . R 4 HOH A 12 512 127 HOH HOH . R 4 HOH A 13 513 7 HOH HOH . R 4 HOH A 14 514 111 HOH HOH . R 4 HOH A 15 515 74 HOH HOH . R 4 HOH A 16 516 68 HOH HOH . R 4 HOH A 17 517 11 HOH HOH . R 4 HOH A 18 518 10 HOH HOH . R 4 HOH A 19 519 93 HOH HOH . R 4 HOH A 20 520 128 HOH HOH . R 4 HOH A 21 521 41 HOH HOH . R 4 HOH A 22 522 101 HOH HOH . S 4 HOH B 1 501 115 HOH HOH . S 4 HOH B 2 502 46 HOH HOH . S 4 HOH B 3 503 72 HOH HOH . S 4 HOH B 4 504 15 HOH HOH . S 4 HOH B 5 505 19 HOH HOH . S 4 HOH B 6 506 26 HOH HOH . S 4 HOH B 7 507 58 HOH HOH . S 4 HOH B 8 508 60 HOH HOH . S 4 HOH B 9 509 57 HOH HOH . S 4 HOH B 10 510 47 HOH HOH . S 4 HOH B 11 511 92 HOH HOH . S 4 HOH B 12 512 73 HOH HOH . S 4 HOH B 13 513 109 HOH HOH . S 4 HOH B 14 514 37 HOH HOH . S 4 HOH B 15 515 17 HOH HOH . S 4 HOH B 16 516 67 HOH HOH . S 4 HOH B 17 517 45 HOH HOH . S 4 HOH B 18 518 82 HOH HOH . S 4 HOH B 19 519 153 HOH HOH . S 4 HOH B 20 520 130 HOH HOH . S 4 HOH B 21 521 91 HOH HOH . S 4 HOH B 22 522 123 HOH HOH . S 4 HOH B 23 523 44 HOH HOH . S 4 HOH B 24 524 88 HOH HOH . S 4 HOH B 25 525 48 HOH HOH . S 4 HOH B 26 526 129 HOH HOH . S 4 HOH B 27 527 89 HOH HOH . S 4 HOH B 28 528 122 HOH HOH . T 4 HOH C 1 501 135 HOH HOH . T 4 HOH C 2 502 125 HOH HOH . T 4 HOH C 3 503 142 HOH HOH . T 4 HOH C 4 504 59 HOH HOH . T 4 HOH C 5 505 102 HOH HOH . T 4 HOH C 6 506 64 HOH HOH . T 4 HOH C 7 507 131 HOH HOH . T 4 HOH C 8 508 134 HOH HOH . T 4 HOH C 9 509 108 HOH HOH . T 4 HOH C 10 510 79 HOH HOH . T 4 HOH C 11 511 132 HOH HOH . T 4 HOH C 12 512 137 HOH HOH . T 4 HOH C 13 513 87 HOH HOH . T 4 HOH C 14 514 143 HOH HOH . T 4 HOH C 15 515 69 HOH HOH . T 4 HOH C 16 516 103 HOH HOH . T 4 HOH C 17 517 144 HOH HOH . T 4 HOH C 18 518 133 HOH HOH . T 4 HOH C 19 519 136 HOH HOH . U 4 HOH D 1 501 110 HOH HOH . U 4 HOH D 2 502 94 HOH HOH . U 4 HOH D 3 503 77 HOH HOH . U 4 HOH D 4 504 152 HOH HOH . U 4 HOH D 5 505 149 HOH HOH . U 4 HOH D 6 506 62 HOH HOH . U 4 HOH D 7 507 12 HOH HOH . U 4 HOH D 8 508 54 HOH HOH . U 4 HOH D 9 509 63 HOH HOH . U 4 HOH D 10 510 50 HOH HOH . U 4 HOH D 11 511 112 HOH HOH . U 4 HOH D 12 512 25 HOH HOH . U 4 HOH D 13 513 138 HOH HOH . U 4 HOH D 14 514 104 HOH HOH . V 4 HOH E 1 501 105 HOH HOH . V 4 HOH E 2 502 76 HOH HOH . V 4 HOH E 3 503 21 HOH HOH . V 4 HOH E 4 504 139 HOH HOH . V 4 HOH E 5 505 151 HOH HOH . V 4 HOH E 6 506 84 HOH HOH . V 4 HOH E 7 507 140 HOH HOH . V 4 HOH E 8 508 148 HOH HOH . V 4 HOH E 9 509 146 HOH HOH . V 4 HOH E 10 510 147 HOH HOH . W 4 HOH F 1 501 3 HOH HOH . W 4 HOH F 2 502 117 HOH HOH . W 4 HOH F 3 503 38 HOH HOH . W 4 HOH F 4 504 80 HOH HOH . W 4 HOH F 5 505 23 HOH HOH . W 4 HOH F 6 506 40 HOH HOH . W 4 HOH F 7 507 33 HOH HOH . W 4 HOH F 8 508 113 HOH HOH . W 4 HOH F 9 509 100 HOH HOH . W 4 HOH F 10 510 78 HOH HOH . W 4 HOH F 11 511 99 HOH HOH . W 4 HOH F 12 512 39 HOH HOH . W 4 HOH F 13 513 31 HOH HOH . W 4 HOH F 14 514 121 HOH HOH . W 4 HOH F 15 515 34 HOH HOH . W 4 HOH F 16 516 97 HOH HOH . W 4 HOH F 17 517 120 HOH HOH . X 4 HOH G 1 501 4 HOH HOH . X 4 HOH G 2 502 61 HOH HOH . X 4 HOH G 3 503 98 HOH HOH . X 4 HOH G 4 504 52 HOH HOH . X 4 HOH G 5 505 150 HOH HOH . X 4 HOH G 6 506 43 HOH HOH . X 4 HOH G 7 507 1 HOH HOH . X 4 HOH G 8 508 51 HOH HOH . X 4 HOH G 9 509 9 HOH HOH . X 4 HOH G 10 510 2 HOH HOH . X 4 HOH G 11 511 81 HOH HOH . X 4 HOH G 12 512 70 HOH HOH . X 4 HOH G 13 513 49 HOH HOH . X 4 HOH G 14 514 85 HOH HOH . X 4 HOH G 15 515 71 HOH HOH . X 4 HOH G 16 516 86 HOH HOH . X 4 HOH G 17 517 5 HOH HOH . X 4 HOH G 18 518 96 HOH HOH . Y 4 HOH H 1 501 28 HOH HOH . Y 4 HOH H 2 502 83 HOH HOH . Y 4 HOH H 3 503 18 HOH HOH . Y 4 HOH H 4 504 55 HOH HOH . Y 4 HOH H 5 505 126 HOH HOH . Y 4 HOH H 6 506 66 HOH HOH . Y 4 HOH H 7 507 145 HOH HOH . Y 4 HOH H 8 508 65 HOH HOH . Y 4 HOH H 9 509 124 HOH HOH . Y 4 HOH H 10 510 35 HOH HOH . Y 4 HOH H 11 511 14 HOH HOH . Y 4 HOH H 12 512 24 HOH HOH . Y 4 HOH H 13 513 27 HOH HOH . Y 4 HOH H 14 514 53 HOH HOH . Y 4 HOH H 15 515 56 HOH HOH . Y 4 HOH H 16 516 13 HOH HOH . Y 4 HOH H 17 517 95 HOH HOH . Y 4 HOH H 18 518 90 HOH HOH . Y 4 HOH H 19 519 30 HOH HOH . Y 4 HOH H 20 520 106 HOH HOH . Y 4 HOH H 21 521 141 HOH HOH . Y 4 HOH H 22 522 29 HOH HOH . Y 4 HOH H 23 523 119 HOH HOH . Y 4 HOH H 24 524 118 HOH HOH . Y 4 HOH H 25 525 32 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 M6P . . . M 2 7.591 94.886 126.468 0.85 61.79 ? C1 M6P 401 D 1 HETATM 2 C C2 M6P . . . M 2 7.785 93.553 127.139 0.85 50.89 ? C2 M6P 401 D 1 HETATM 3 C C3 M6P . . . M 2 8.266 92.52 126.164 0.85 60.37 ? C3 M6P 401 D 1 HETATM 4 C C4 M6P . . . M 2 7.461 92.529 124.898 0.85 61.02 ? C4 M6P 401 D 1 HETATM 5 C C5 M6P . . . M 2 7.332 93.917 124.35 0.85 56.63 ? C5 M6P 401 D 1 HETATM 6 C C6 M6P . . . M 2 6.475 93.873 123.115 0.85 50.74 ? C6 M6P 401 D 1 HETATM 7 O O1 M6P . . . M 2 8.834 95.429 126.045 0.85 55.46 ? O1 M6P 401 D 1 HETATM 8 O O2 M6P . . . M 2 6.531 93.123 127.619 0.85 58.15 ? O2 M6P 401 D 1 HETATM 9 O O3 M6P . . . M 2 8.102 91.223 126.705 0.85 68.11 ? O3 M6P 401 D 1 HETATM 10 O O4 M6P . . . M 2 8.111 91.706 123.955 0.85 56.89 ? O4 M6P 401 D 1 HETATM 11 O O5 M6P . . . M 2 6.74 94.706 125.354 0.85 58.11 ? O5 M6P 401 D 1 HETATM 12 O O6 M6P . . . M 2 5.143 93.685 123.504 0.85 55.5 ? O6 M6P 401 D 1 HETATM 13 P P M6P . . . M 2 4.136 93.16 122.458 0.85 52.1 ? P M6P 401 D 1 HETATM 14 O O1P M6P . . . M 2 3.846 94.345 121.672 0.85 46.58 ? O1P M6P 401 D 1 HETATM 15 O O2P M6P . . . M 2 3.047 92.664 123.284 0.85 58.34 ? O2P M6P 401 D 1 HETATM 16 O O3P M6P . . . M 2 4.907 92.122 121.777 0.85 54.62 ? O3P M6P 401 D 1 HETATM 17 H H1 M6P . . . M 2 7.117 95.569 127.186 0.85 74.25 ? H1 M6P 401 D 1 HETATM 18 H H2 M6P . . . M 2 8.507 93.652 127.963 0.85 61.16 ? H2 M6P 401 D 1 HETATM 19 H H3 M6P . . . M 2 9.323 92.706 125.926 0.85 72.54 ? H3 M6P 401 D 1 HETATM 20 H H4 M6P . . . M 2 6.457 92.136 125.111 0.85 73.32 ? H4 M6P 401 D 1 HETATM 21 H H5 M6P . . . M 2 8.329 94.302 124.092 0.85 68.05 ? H5 M6P 401 D 1 HETATM 22 H H61 M6P . . . M 2 6.794 93.053 122.469 0.85 60.99 ? H61 M6P 401 D 1 HETATM 23 H H62 M6P . . . M 2 6.573 94.808 122.56 0.85 60.99 ? H62 M6P 401 D 1 HETATM 24 H HO1 M6P . . . M 2 9.48 95.353 126.761 0.85 66.64 ? HO1 M6P 401 D 1 HETATM 25 H HO2 M6P . . . M 2 6.581 92.988 128.575 0.85 69.87 ? HO2 M6P 401 D 1 HETATM 26 H HO3 M6P . . . M 2 8.321 90.564 126.032 0.85 81.83 ? HO3 M6P 401 D 1 HETATM 27 H HO4 M6P . . . M 2 8.891 91.305 124.363 0.85 68.37 ? HO4 M6P 401 D 1 # _model_server_stats.io_time_ms 154 _model_server_stats.parse_time_ms 30 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 27 #