data_5YSP # _model_server_result.job_id LILUXfvuimtUlEVHgnxmyw _model_server_result.datetime_utc '2024-11-14 19:44:38' _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 5ysp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":302}' # _entry.id 5YSP # _exptl.entry_id 5YSP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 176.002 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'METHYLENEDIPHOSPHONIC ACID' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 105.05 _cell.angle_gamma 90 _cell.entry_id 5YSP _cell.length_a 46.673 _cell.length_b 63.009 _cell.length_c 89.884 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YSP _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_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,H 1 1 B,F,G,I 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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 D O2 MDN . A MDN 302 1_555 E MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc2 D O8 MDN . A MDN 302 1_555 E MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc3 E MG MG . A MG 303 1_555 H O HOH . A HOH 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? metalc ? metalc4 E MG MG . A MG 303 1_555 H O HOH . A HOH 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc5 E MG MG . A MG 303 1_555 H O HOH . A HOH 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.801 ? metalc ? metalc6 E MG MG . A MG 303 1_555 H O HOH . A HOH 443 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? # _chem_comp.formula 'C H6 O6 P2' _chem_comp.formula_weight 176.002 _chem_comp.id MDN _chem_comp.mon_nstd_flag . _chem_comp.name 'METHYLENEDIPHOSPHONIC ACID' _chem_comp.type non-polymer _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 O3 P1 MDN sing 242 n n O3 HO3 MDN sing 243 n n P1 O1 MDN doub 244 n n P1 O2 MDN sing 245 n n P1 C4 MDN sing 246 n n O2 HO2 MDN sing 247 n n C4 P5 MDN sing 248 n n C4 H41 MDN sing 249 n n C4 H42 MDN sing 250 n n P5 O6 MDN doub 251 n n P5 O7 MDN sing 252 n n P5 O8 MDN sing 253 n n O7 HO7 MDN sing 254 n n O8 HO8 MDN sing 255 n n # _atom_sites.entry_id 5YSP _atom_sites.fract_transf_matrix[1][1] 0.021426 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00576 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015871 _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] 0.01152 _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 INS A 1 301 301 INS INS . D 3 MDN A 1 302 302 MDN MDN . E 4 MG A 1 303 303 MG MG . F 2 INS B 1 301 301 INS INS . G 5 SO4 B 1 302 1 SO4 SO4 . H 6 HOH A 1 401 95 HOH HOH . H 6 HOH A 2 402 96 HOH HOH . H 6 HOH A 3 403 34 HOH HOH . H 6 HOH A 4 404 114 HOH HOH . H 6 HOH A 5 405 25 HOH HOH . H 6 HOH A 6 406 45 HOH HOH . H 6 HOH A 7 407 93 HOH HOH . H 6 HOH A 8 408 19 HOH HOH . H 6 HOH A 9 409 59 HOH HOH . H 6 HOH A 10 410 23 HOH HOH . H 6 HOH A 11 411 119 HOH HOH . H 6 HOH A 12 412 75 HOH HOH . H 6 HOH A 13 413 51 HOH HOH . H 6 HOH A 14 414 3 HOH HOH . H 6 HOH A 15 415 28 HOH HOH . H 6 HOH A 16 416 113 HOH HOH . H 6 HOH A 17 417 22 HOH HOH . H 6 HOH A 18 418 44 HOH HOH . H 6 HOH A 19 419 6 HOH HOH . H 6 HOH A 20 420 92 HOH HOH . H 6 HOH A 21 421 67 HOH HOH . H 6 HOH A 22 422 11 HOH HOH . H 6 HOH A 23 423 72 HOH HOH . H 6 HOH A 24 424 57 HOH HOH . H 6 HOH A 25 425 18 HOH HOH . H 6 HOH A 26 426 15 HOH HOH . H 6 HOH A 27 427 31 HOH HOH . H 6 HOH A 28 428 4 HOH HOH . H 6 HOH A 29 429 5 HOH HOH . H 6 HOH A 30 430 32 HOH HOH . H 6 HOH A 31 431 115 HOH HOH . H 6 HOH A 32 432 8 HOH HOH . H 6 HOH A 33 433 62 HOH HOH . H 6 HOH A 34 434 55 HOH HOH . H 6 HOH A 35 435 7 HOH HOH . H 6 HOH A 36 436 111 HOH HOH . H 6 HOH A 37 437 74 HOH HOH . H 6 HOH A 38 438 123 HOH HOH . H 6 HOH A 39 439 13 HOH HOH . H 6 HOH A 40 440 49 HOH HOH . H 6 HOH A 41 441 29 HOH HOH . H 6 HOH A 42 442 100 HOH HOH . H 6 HOH A 43 443 2 HOH HOH . H 6 HOH A 44 444 40 HOH HOH . H 6 HOH A 45 445 9 HOH HOH . H 6 HOH A 46 446 58 HOH HOH . H 6 HOH A 47 447 94 HOH HOH . H 6 HOH A 48 448 46 HOH HOH . H 6 HOH A 49 449 17 HOH HOH . H 6 HOH A 50 450 48 HOH HOH . H 6 HOH A 51 451 81 HOH HOH . H 6 HOH A 52 452 27 HOH HOH . H 6 HOH A 53 453 104 HOH HOH . H 6 HOH A 54 454 42 HOH HOH . H 6 HOH A 55 455 41 HOH HOH . H 6 HOH A 56 456 43 HOH HOH . H 6 HOH A 57 457 14 HOH HOH . H 6 HOH A 58 458 125 HOH HOH . H 6 HOH A 59 459 24 HOH HOH . H 6 HOH A 60 460 21 HOH HOH . H 6 HOH A 61 461 12 HOH HOH . H 6 HOH A 62 462 79 HOH HOH . H 6 HOH A 63 463 78 HOH HOH . H 6 HOH A 64 464 37 HOH HOH . H 6 HOH A 65 465 124 HOH HOH . H 6 HOH A 66 466 53 HOH HOH . H 6 HOH A 67 467 56 HOH HOH . H 6 HOH A 68 468 38 HOH HOH . H 6 HOH A 69 469 50 HOH HOH . H 6 HOH A 70 470 84 HOH HOH . H 6 HOH A 71 471 112 HOH HOH . H 6 HOH A 72 472 101 HOH HOH . H 6 HOH A 73 473 87 HOH HOH . H 6 HOH A 74 474 97 HOH HOH . H 6 HOH A 75 475 39 HOH HOH . H 6 HOH A 76 476 30 HOH HOH . H 6 HOH A 77 477 116 HOH HOH . H 6 HOH A 78 478 76 HOH HOH . H 6 HOH A 79 479 80 HOH HOH . H 6 HOH A 80 480 91 HOH HOH . H 6 HOH A 81 481 90 HOH HOH . I 6 HOH B 1 401 121 HOH HOH . I 6 HOH B 2 402 54 HOH HOH . I 6 HOH B 3 403 64 HOH HOH . I 6 HOH B 4 404 66 HOH HOH . I 6 HOH B 5 405 118 HOH HOH . I 6 HOH B 6 406 35 HOH HOH . I 6 HOH B 7 407 36 HOH HOH . I 6 HOH B 8 408 107 HOH HOH . I 6 HOH B 9 409 10 HOH HOH . I 6 HOH B 10 410 108 HOH HOH . I 6 HOH B 11 411 127 HOH HOH . I 6 HOH B 12 412 126 HOH HOH . I 6 HOH B 13 413 122 HOH HOH . I 6 HOH B 14 414 47 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 O O3 MDN . . . D 3 -3.06 8.466 29.914 1 31.71 ? O3 MDN 302 A 1 HETATM 2 P P1 MDN . . . D 3 -1.997 7.303 29.632 1 33.76 ? P1 MDN 302 A 1 HETATM 3 O O1 MDN . . . D 3 -2.467 6.412 28.538 1 33.22 ? O1 MDN 302 A 1 HETATM 4 O O2 MDN . . . D 3 -1.746 6.43 30.969 1 32.59 ? O2 MDN 302 A 1 HETATM 5 C C4 MDN . . . D 3 -0.499 8.186 29.11 1 31.18 ? C4 MDN 302 A 1 HETATM 6 P P5 MDN . . . D 3 1.013 7.185 28.953 1 30.82 ? P5 MDN 302 A 1 HETATM 7 O O6 MDN . . . D 3 1.468 7.153 27.535 1 30.61 ? O6 MDN 302 A 1 HETATM 8 O O7 MDN . . . D 3 2.076 8.016 29.818 1 29.89 ? O7 MDN 302 A 1 HETATM 9 O O8 MDN . . . D 3 0.891 5.714 29.554 1 28.09 ? O8 MDN 302 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 327 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 9 #