data_6M3S # _model_server_result.job_id 6nSrY4-94vy0CINYCaB-gQ _model_server_result.datetime_utc '2024-12-26 16:48:08' _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 6m3s # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":402}' # _entry.id 6M3S # _exptl.entry_id 6M3S _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 231.194 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ISOCITRATE CALCIUM COMPLEX' _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 6M3S _cell.length_a 143.735 _cell.length_b 143.735 _cell.length_c 65.289 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6M3S _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall 'P 6c' _symmetry.space_group_name_H-M 'P 63' # _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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression B,F,G,H,I,K 1 1 A,C,D,E,J 1 2 # 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' 6_555 x-y,x,z+1/2 0.5 -0.866025 0 0.866025 0.5 0 0 0 1 0 0 32.6445 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 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 OD2 ASP 215 A ASP 207 1_555 G CA ICA . B ICA 402 5_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? metalc ? metalc2 A OD1 ASP 239 A ASP 231 1_555 D CA ICA . A ICA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc3 D CA ICA . A ICA 402 1_555 J O HOH . A HOH 549 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.519 ? metalc ? metalc4 D CA ICA . A ICA 402 6_555 B OD2 ASP 215 B ASP 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? metalc ? metalc5 B OD1 ASP 239 B ASP 231 1_555 G CA ICA . B ICA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc6 B OD1 ASP 243 B ASP 235 1_555 G CA ICA . B ICA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? metalc ? metalc7 G CA ICA . B ICA 402 1_555 K O HOH . B HOH 562 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.654 ? # _chem_comp.formula 'C6 H7 Ca O7' _chem_comp.formula_weight 231.194 _chem_comp.id ICA _chem_comp.mon_nstd_flag . _chem_comp.name 'ISOCITRATE CALCIUM COMPLEX' _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 C1 C2 ICA sing 165 n n C1 O1 ICA doub 166 n n C1 O2 ICA sing 167 n n C2 C3 ICA sing 168 n n C2 O7 ICA sing 169 n n C2 H2 ICA sing 170 n n C3 C4 ICA sing 171 n n C3 C6 ICA sing 172 n n C3 H3 ICA sing 173 n n C4 C5 ICA sing 174 n n C4 H41 ICA sing 175 n n C4 H42 ICA sing 176 n n C5 O3 ICA doub 177 n n C5 O4 ICA sing 178 n n C6 O5 ICA doub 179 n n C6 O6 ICA sing 180 n n O2 HO2 ICA sing 181 n n O4 HO4 ICA sing 182 n n O6 HO6 ICA sing 183 n n O7 CA ICA sing 184 n n # _atom_sites.entry_id 6M3S _atom_sites.fract_transf_matrix[1][1] 0.006957 _atom_sites.fract_transf_matrix[1][2] 0.004017 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008034 _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] 0.015317 _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 NAD A 1 401 401 NAD NAD . D 3 ICA A 1 402 501 ICA ICA . E 4 GOL A 1 403 601 GOL GOL . F 2 NAD B 1 401 401 NAD NAD . G 3 ICA B 1 402 501 ICA ICA . H 4 GOL B 1 403 601 GOL GOL . I 4 GOL B 1 404 701 GOL GOL . J 5 HOH A 1 501 145 HOH HOH . J 5 HOH A 2 502 79 HOH HOH . J 5 HOH A 3 503 194 HOH HOH . J 5 HOH A 4 504 155 HOH HOH . J 5 HOH A 5 505 1 HOH HOH . J 5 HOH A 6 506 94 HOH HOH . J 5 HOH A 7 507 86 HOH HOH . J 5 HOH A 8 508 137 HOH HOH . J 5 HOH A 9 509 2 HOH HOH . J 5 HOH A 10 510 122 HOH HOH . J 5 HOH A 11 511 100 HOH HOH . J 5 HOH A 12 512 11 HOH HOH . J 5 HOH A 13 513 29 HOH HOH . J 5 HOH A 14 514 60 HOH HOH . J 5 HOH A 15 515 92 HOH HOH . J 5 HOH A 16 516 14 HOH HOH . J 5 HOH A 17 517 9 HOH HOH . J 5 HOH A 18 518 49 HOH HOH . J 5 HOH A 19 519 191 HOH HOH . J 5 HOH A 20 520 146 HOH HOH . J 5 HOH A 21 521 103 HOH HOH . J 5 HOH A 22 522 131 HOH HOH . J 5 HOH A 23 523 6 HOH HOH . J 5 HOH A 24 524 88 HOH HOH . J 5 HOH A 25 525 4 HOH HOH . J 5 HOH A 26 526 59 HOH HOH . J 5 HOH A 27 527 52 HOH HOH . J 5 HOH A 28 528 128 HOH HOH . J 5 HOH A 29 529 184 HOH HOH . J 5 HOH A 30 530 53 HOH HOH . J 5 HOH A 31 531 114 HOH HOH . J 5 HOH A 32 532 33 HOH HOH . J 5 HOH A 33 533 43 HOH HOH . J 5 HOH A 34 534 98 HOH HOH . J 5 HOH A 35 535 78 HOH HOH . J 5 HOH A 36 536 36 HOH HOH . J 5 HOH A 37 537 134 HOH HOH . J 5 HOH A 38 538 67 HOH HOH . J 5 HOH A 39 539 34 HOH HOH . J 5 HOH A 40 540 21 HOH HOH . J 5 HOH A 41 541 70 HOH HOH . J 5 HOH A 42 542 72 HOH HOH . J 5 HOH A 43 543 69 HOH HOH . J 5 HOH A 44 544 57 HOH HOH . J 5 HOH A 45 545 63 HOH HOH . J 5 HOH A 46 546 164 HOH HOH . J 5 HOH A 47 547 133 HOH HOH . J 5 HOH A 48 548 32 HOH HOH . J 5 HOH A 49 549 216 HOH HOH . J 5 HOH A 50 550 144 HOH HOH . J 5 HOH A 51 551 193 HOH HOH . J 5 HOH A 52 552 208 HOH HOH . J 5 HOH A 53 553 112 HOH HOH . J 5 HOH A 54 554 176 HOH HOH . J 5 HOH A 55 555 124 HOH HOH . J 5 HOH A 56 556 104 HOH HOH . J 5 HOH A 57 557 189 HOH HOH . J 5 HOH A 58 558 23 HOH HOH . J 5 HOH A 59 559 168 HOH HOH . J 5 HOH A 60 560 76 HOH HOH . J 5 HOH A 61 561 96 HOH HOH . J 5 HOH A 62 562 17 HOH HOH . J 5 HOH A 63 563 188 HOH HOH . J 5 HOH A 64 564 71 HOH HOH . J 5 HOH A 65 565 173 HOH HOH . J 5 HOH A 66 566 75 HOH HOH . J 5 HOH A 67 567 157 HOH HOH . J 5 HOH A 68 568 54 HOH HOH . J 5 HOH A 69 569 211 HOH HOH . J 5 HOH A 70 570 22 HOH HOH . J 5 HOH A 71 571 142 HOH HOH . J 5 HOH A 72 572 55 HOH HOH . J 5 HOH A 73 573 111 HOH HOH . J 5 HOH A 74 574 50 HOH HOH . J 5 HOH A 75 575 74 HOH HOH . J 5 HOH A 76 576 201 HOH HOH . J 5 HOH A 77 577 45 HOH HOH . J 5 HOH A 78 578 212 HOH HOH . J 5 HOH A 79 579 210 HOH HOH . J 5 HOH A 80 580 39 HOH HOH . J 5 HOH A 81 581 84 HOH HOH . J 5 HOH A 82 582 90 HOH HOH . J 5 HOH A 83 583 170 HOH HOH . J 5 HOH A 84 584 120 HOH HOH . J 5 HOH A 85 585 213 HOH HOH . J 5 HOH A 86 586 178 HOH HOH . J 5 HOH A 87 587 206 HOH HOH . J 5 HOH A 88 588 62 HOH HOH . J 5 HOH A 89 589 115 HOH HOH . J 5 HOH A 90 590 147 HOH HOH . J 5 HOH A 91 591 105 HOH HOH . J 5 HOH A 92 592 205 HOH HOH . J 5 HOH A 93 593 196 HOH HOH . J 5 HOH A 94 594 203 HOH HOH . J 5 HOH A 95 595 207 HOH HOH . J 5 HOH A 96 596 199 HOH HOH . J 5 HOH A 97 597 183 HOH HOH . J 5 HOH A 98 598 91 HOH HOH . J 5 HOH A 99 599 160 HOH HOH . J 5 HOH A 100 600 127 HOH HOH . J 5 HOH A 101 601 204 HOH HOH . J 5 HOH A 102 602 148 HOH HOH . J 5 HOH A 103 603 197 HOH HOH . J 5 HOH A 104 604 61 HOH HOH . J 5 HOH A 105 605 73 HOH HOH . J 5 HOH A 106 606 110 HOH HOH . J 5 HOH A 107 607 125 HOH HOH . J 5 HOH A 108 608 107 HOH HOH . J 5 HOH A 109 609 200 HOH HOH . J 5 HOH A 110 610 169 HOH HOH . K 5 HOH B 1 501 177 HOH HOH . K 5 HOH B 2 502 141 HOH HOH . K 5 HOH B 3 503 136 HOH HOH . K 5 HOH B 4 504 7 HOH HOH . K 5 HOH B 5 505 159 HOH HOH . K 5 HOH B 6 506 106 HOH HOH . K 5 HOH B 7 507 3 HOH HOH . K 5 HOH B 8 508 15 HOH HOH . K 5 HOH B 9 509 46 HOH HOH . K 5 HOH B 10 510 174 HOH HOH . K 5 HOH B 11 511 117 HOH HOH . K 5 HOH B 12 512 102 HOH HOH . K 5 HOH B 13 513 27 HOH HOH . K 5 HOH B 14 514 101 HOH HOH . K 5 HOH B 15 515 12 HOH HOH . K 5 HOH B 16 516 185 HOH HOH . K 5 HOH B 17 517 195 HOH HOH . K 5 HOH B 18 518 48 HOH HOH . K 5 HOH B 19 519 64 HOH HOH . K 5 HOH B 20 520 47 HOH HOH . K 5 HOH B 21 521 165 HOH HOH . K 5 HOH B 22 522 8 HOH HOH . K 5 HOH B 23 523 109 HOH HOH . K 5 HOH B 24 524 25 HOH HOH . K 5 HOH B 25 525 38 HOH HOH . K 5 HOH B 26 526 44 HOH HOH . K 5 HOH B 27 527 77 HOH HOH . K 5 HOH B 28 528 108 HOH HOH . K 5 HOH B 29 529 16 HOH HOH . K 5 HOH B 30 530 31 HOH HOH . K 5 HOH B 31 531 26 HOH HOH . K 5 HOH B 32 532 182 HOH HOH . K 5 HOH B 33 533 97 HOH HOH . K 5 HOH B 34 534 167 HOH HOH . K 5 HOH B 35 535 66 HOH HOH . K 5 HOH B 36 536 40 HOH HOH . K 5 HOH B 37 537 181 HOH HOH . K 5 HOH B 38 538 121 HOH HOH . K 5 HOH B 39 539 18 HOH HOH . K 5 HOH B 40 540 10 HOH HOH . K 5 HOH B 41 541 28 HOH HOH . K 5 HOH B 42 542 65 HOH HOH . K 5 HOH B 43 543 99 HOH HOH . K 5 HOH B 44 544 51 HOH HOH . K 5 HOH B 45 545 116 HOH HOH . K 5 HOH B 46 546 87 HOH HOH . K 5 HOH B 47 547 95 HOH HOH . K 5 HOH B 48 548 198 HOH HOH . K 5 HOH B 49 549 149 HOH HOH . K 5 HOH B 50 550 187 HOH HOH . K 5 HOH B 51 551 154 HOH HOH . K 5 HOH B 52 552 35 HOH HOH . K 5 HOH B 53 553 180 HOH HOH . K 5 HOH B 54 554 19 HOH HOH . K 5 HOH B 55 555 5 HOH HOH . K 5 HOH B 56 556 20 HOH HOH . K 5 HOH B 57 557 24 HOH HOH . K 5 HOH B 58 558 37 HOH HOH . K 5 HOH B 59 559 192 HOH HOH . K 5 HOH B 60 560 82 HOH HOH . K 5 HOH B 61 561 41 HOH HOH . K 5 HOH B 62 562 68 HOH HOH . K 5 HOH B 63 563 80 HOH HOH . K 5 HOH B 64 564 93 HOH HOH . K 5 HOH B 65 565 139 HOH HOH . K 5 HOH B 66 566 30 HOH HOH . K 5 HOH B 67 567 158 HOH HOH . K 5 HOH B 68 568 119 HOH HOH . K 5 HOH B 69 569 129 HOH HOH . K 5 HOH B 70 570 130 HOH HOH . K 5 HOH B 71 571 13 HOH HOH . K 5 HOH B 72 572 89 HOH HOH . K 5 HOH B 73 573 152 HOH HOH . K 5 HOH B 74 574 190 HOH HOH . K 5 HOH B 75 575 85 HOH HOH . K 5 HOH B 76 576 179 HOH HOH . K 5 HOH B 77 577 162 HOH HOH . K 5 HOH B 78 578 215 HOH HOH . K 5 HOH B 79 579 81 HOH HOH . K 5 HOH B 80 580 156 HOH HOH . K 5 HOH B 81 581 42 HOH HOH . K 5 HOH B 82 582 161 HOH HOH . K 5 HOH B 83 583 166 HOH HOH . K 5 HOH B 84 584 135 HOH HOH . K 5 HOH B 85 585 172 HOH HOH . K 5 HOH B 86 586 163 HOH HOH . K 5 HOH B 87 587 126 HOH HOH . K 5 HOH B 88 588 150 HOH HOH . K 5 HOH B 89 589 209 HOH HOH . K 5 HOH B 90 590 123 HOH HOH . K 5 HOH B 91 591 58 HOH HOH . K 5 HOH B 92 592 175 HOH HOH . K 5 HOH B 93 593 153 HOH HOH . K 5 HOH B 94 594 214 HOH HOH . K 5 HOH B 95 595 138 HOH HOH . K 5 HOH B 96 596 56 HOH HOH . K 5 HOH B 97 597 143 HOH HOH . K 5 HOH B 98 598 186 HOH HOH . K 5 HOH B 99 599 132 HOH HOH . K 5 HOH B 100 600 118 HOH HOH . K 5 HOH B 101 601 113 HOH HOH . K 5 HOH B 102 602 171 HOH HOH . K 5 HOH B 103 603 83 HOH HOH . K 5 HOH B 104 604 202 HOH HOH . K 5 HOH B 105 605 140 HOH HOH . K 5 HOH B 106 606 151 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 ICA . . . G 3 47.792 -13.519 -9.526 1 60.28 ? C1 ICA 402 B 1 HETATM 2 C C2 ICA . . . G 3 47.541 -12.988 -10.943 1 60.15 ? C2 ICA 402 B 1 HETATM 3 C C3 ICA . . . G 3 46.057 -12.888 -11.282 1 58.57 ? C3 ICA 402 B 1 HETATM 4 C C4 ICA . . . G 3 45.884 -12.602 -12.774 1 55.09 ? C4 ICA 402 B 1 HETATM 5 C C5 ICA . . . G 3 44.872 -13.499 -13.452 1 51.24 ? C5 ICA 402 B 1 HETATM 6 C C6 ICA . . . G 3 45.564 -11.806 -10.364 1 62.73 ? C6 ICA 402 B 1 HETATM 7 O O1 ICA . . . G 3 48.971 -13.56 -9.039 1 54.5 ? O1 ICA 402 B 1 HETATM 8 O O2 ICA . . . G 3 46.812 -13.922 -8.862 1 61.7 ? O2 ICA 402 B 1 HETATM 9 O O3 ICA . . . G 3 45.152 -13.816 -14.568 1 48.49 ? O3 ICA 402 B 1 HETATM 10 O O4 ICA . . . G 3 43.801 -13.901 -12.976 1 52.56 ? O4 ICA 402 B 1 HETATM 11 O O5 ICA . . . G 3 45.419 -12.128 -9.161 1 54.17 ? O5 ICA 402 B 1 HETATM 12 O O6 ICA . . . G 3 45.391 -10.637 -10.783 1 73.84 ? O6 ICA 402 B 1 HETATM 13 O O7 ICA . . . G 3 48.259 -11.737 -11.18 1 59.2 ? O7 ICA 402 B 1 HETATM 14 CA CA ICA . . . G 3 50.249 -11.423 -9.964 1 53.48 ? CA ICA 402 B 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 32 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 333 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 14 #