data_6BXM # _model_server_result.job_id Op-cEraojALRO044LjLtGg _model_server_result.datetime_utc '2024-11-04 22:38:12' _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 6bxm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":403}' # _entry.id 6BXM # _exptl.entry_id 6BXM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 297.334 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-DEOXY-5'-METHYLTHIOADENOSINE" _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 90 _cell.angle_gamma 90 _cell.entry_id 6BXM _cell.length_a 61.887 _cell.length_b 64.08 _cell.length_c 158.368 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6BXM _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id G _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 A SG CYS 65 A CYS 61 1_555 C FE1 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc2 A SG CYS 163 A CYS 159 1_555 C FE2 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? metalc ? metalc3 A SG CYS 287 A CYS 283 1_555 C FE3 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.25 ? metalc ? metalc4 C FE4 SF4 . A SF4 401 1_555 D N SAM . A SAM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc5 B SG CYS 65 B CYS 61 1_555 E FE1 SF4 . B SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc6 B SG CYS 163 B CYS 159 1_555 E FE2 SF4 . B SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? metalc ? metalc7 B SG CYS 287 B CYS 283 1_555 E FE3 SF4 . B SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? metalc ? metalc8 E FE4 SF4 . B SF4 401 1_555 F N ABA . B ABA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.659 ? # _chem_comp.formula 'C11 H15 N5 O3 S' _chem_comp.formula_weight 297.334 _chem_comp.id MTA _chem_comp.mon_nstd_flag . _chem_comp.name "5'-DEOXY-5'-METHYLTHIOADENOSINE" _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 CS S5' MTA sing 252 n n CS HCS1 MTA sing 253 n n CS HCS2 MTA sing 254 n n CS HCS3 MTA sing 255 n n S5' C5' MTA sing 256 n n C5' C4' MTA sing 257 n n C5' "H5'1" MTA sing 258 n n C5' "H5'2" MTA sing 259 n n C4' O4' MTA sing 260 n n C4' C3' MTA sing 261 n n C4' H4' MTA sing 262 n n O4' C1' MTA sing 263 n n C2' O2' MTA sing 264 n n C2' C3' MTA sing 265 n n C2' C1' MTA sing 266 n n C2' H2' MTA sing 267 n n O2' HO2' MTA sing 268 n n C3' O3' MTA sing 269 n n C3' H3' MTA sing 270 n n O3' H3T MTA sing 271 n n C1' N9 MTA sing 272 n n C1' H1' MTA sing 273 n n N9 C8 MTA sing 274 n y N9 C4 MTA sing 275 n y C8 N7 MTA doub 276 n y C8 H8 MTA sing 277 n n N7 C5 MTA sing 278 n y C5 C6 MTA sing 279 n y C5 C4 MTA doub 280 n y C6 N6 MTA sing 281 n n C6 N1 MTA doub 282 n y N6 H61 MTA sing 283 n n N6 H62 MTA sing 284 n n N1 C2 MTA sing 285 n y C2 N3 MTA doub 286 n y C2 H2 MTA sing 287 n n N3 C4 MTA sing 288 n y # _atom_sites.entry_id 6BXM _atom_sites.fract_transf_matrix[1][1] 0.016158 _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] 0.015605 _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] 0.006314 _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 SF4 A 1 401 324 SF4 SF4 . D 3 SAM A 1 402 600 SAM SAM . E 2 SF4 B 1 401 322 SF4 SF4 . F 4 ABA B 1 402 601 ABA AC3 . G 5 MTA B 1 403 602 MTA MTA . H 6 HOH A 1 501 51 HOH HOH . H 6 HOH A 2 502 25 HOH HOH . H 6 HOH A 3 503 57 HOH HOH . H 6 HOH A 4 504 76 HOH HOH . H 6 HOH A 5 505 9 HOH HOH . H 6 HOH A 6 506 54 HOH HOH . H 6 HOH A 7 507 60 HOH HOH . H 6 HOH A 8 508 65 HOH HOH . H 6 HOH A 9 509 15 HOH HOH . H 6 HOH A 10 510 91 HOH HOH . H 6 HOH A 11 511 7 HOH HOH . H 6 HOH A 12 512 23 HOH HOH . H 6 HOH A 13 513 1 HOH HOH . H 6 HOH A 14 514 59 HOH HOH . H 6 HOH A 15 515 74 HOH HOH . H 6 HOH A 16 516 87 HOH HOH . H 6 HOH A 17 517 20 HOH HOH . H 6 HOH A 18 518 32 HOH HOH . H 6 HOH A 19 519 189 HOH HOH . H 6 HOH A 20 520 95 HOH HOH . H 6 HOH A 21 521 13 HOH HOH . H 6 HOH A 22 522 24 HOH HOH . H 6 HOH A 23 523 47 HOH HOH . H 6 HOH A 24 524 43 HOH HOH . H 6 HOH A 25 525 10 HOH HOH . H 6 HOH A 26 526 22 HOH HOH . H 6 HOH A 27 527 8 HOH HOH . H 6 HOH A 28 528 16 HOH HOH . H 6 HOH A 29 529 173 HOH HOH . H 6 HOH A 30 530 27 HOH HOH . H 6 HOH A 31 531 38 HOH HOH . H 6 HOH A 32 532 4 HOH HOH . H 6 HOH A 33 533 29 HOH HOH . H 6 HOH A 34 534 6 HOH HOH . H 6 HOH A 35 535 40 HOH HOH . H 6 HOH A 36 536 45 HOH HOH . H 6 HOH A 37 537 5 HOH HOH . H 6 HOH A 38 538 85 HOH HOH . H 6 HOH A 39 539 19 HOH HOH . H 6 HOH A 40 540 3 HOH HOH . H 6 HOH A 41 541 31 HOH HOH . H 6 HOH A 42 542 92 HOH HOH . H 6 HOH A 43 543 14 HOH HOH . H 6 HOH A 44 544 49 HOH HOH . H 6 HOH A 45 545 70 HOH HOH . H 6 HOH A 46 546 78 HOH HOH . H 6 HOH A 47 547 36 HOH HOH . H 6 HOH A 48 548 61 HOH HOH . H 6 HOH A 49 549 17 HOH HOH . H 6 HOH A 50 550 63 HOH HOH . H 6 HOH A 51 551 53 HOH HOH . H 6 HOH A 52 552 35 HOH HOH . H 6 HOH A 53 553 18 HOH HOH . H 6 HOH A 54 554 37 HOH HOH . H 6 HOH A 55 555 93 HOH HOH . H 6 HOH A 56 556 58 HOH HOH . H 6 HOH A 57 557 81 HOH HOH . H 6 HOH A 58 558 79 HOH HOH . H 6 HOH A 59 559 33 HOH HOH . H 6 HOH A 60 560 102 HOH HOH . H 6 HOH A 61 561 55 HOH HOH . H 6 HOH A 62 562 2 HOH HOH . H 6 HOH A 63 563 11 HOH HOH . H 6 HOH A 64 564 44 HOH HOH . H 6 HOH A 65 565 83 HOH HOH . H 6 HOH A 66 566 50 HOH HOH . H 6 HOH A 67 567 52 HOH HOH . H 6 HOH A 68 568 86 HOH HOH . H 6 HOH A 69 569 88 HOH HOH . H 6 HOH A 70 570 56 HOH HOH . H 6 HOH A 71 571 26 HOH HOH . H 6 HOH A 72 572 48 HOH HOH . H 6 HOH A 73 573 67 HOH HOH . H 6 HOH A 74 574 21 HOH HOH . H 6 HOH A 75 575 90 HOH HOH . H 6 HOH A 76 576 30 HOH HOH . H 6 HOH A 77 577 82 HOH HOH . H 6 HOH A 78 578 73 HOH HOH . H 6 HOH A 79 579 94 HOH HOH . H 6 HOH A 80 580 39 HOH HOH . H 6 HOH A 81 581 34 HOH HOH . H 6 HOH A 82 582 80 HOH HOH . H 6 HOH A 83 583 64 HOH HOH . H 6 HOH A 84 584 69 HOH HOH . H 6 HOH A 85 585 12 HOH HOH . H 6 HOH A 86 586 71 HOH HOH . H 6 HOH A 87 587 28 HOH HOH . H 6 HOH A 88 588 46 HOH HOH . H 6 HOH A 89 589 41 HOH HOH . H 6 HOH A 90 590 42 HOH HOH . H 6 HOH A 91 591 200 HOH HOH . H 6 HOH A 92 592 89 HOH HOH . H 6 HOH A 93 593 151 HOH HOH . H 6 HOH A 94 594 62 HOH HOH . H 6 HOH A 95 595 72 HOH HOH . H 6 HOH A 96 596 68 HOH HOH . H 6 HOH A 97 597 84 HOH HOH . H 6 HOH A 98 598 66 HOH HOH . I 6 HOH B 1 501 186 HOH HOH . I 6 HOH B 2 502 187 HOH HOH . I 6 HOH B 3 503 159 HOH HOH . I 6 HOH B 4 504 122 HOH HOH . I 6 HOH B 5 505 199 HOH HOH . I 6 HOH B 6 506 127 HOH HOH . I 6 HOH B 7 507 165 HOH HOH . I 6 HOH B 8 508 174 HOH HOH . I 6 HOH B 9 509 125 HOH HOH . I 6 HOH B 10 510 106 HOH HOH . I 6 HOH B 11 511 109 HOH HOH . I 6 HOH B 12 512 119 HOH HOH . I 6 HOH B 13 513 107 HOH HOH . I 6 HOH B 14 514 196 HOH HOH . I 6 HOH B 15 515 112 HOH HOH . I 6 HOH B 16 516 124 HOH HOH . I 6 HOH B 17 517 103 HOH HOH . I 6 HOH B 18 518 97 HOH HOH . I 6 HOH B 19 519 96 HOH HOH . I 6 HOH B 20 520 123 HOH HOH . I 6 HOH B 21 521 132 HOH HOH . I 6 HOH B 22 522 120 HOH HOH . I 6 HOH B 23 523 133 HOH HOH . I 6 HOH B 24 524 134 HOH HOH . I 6 HOH B 25 525 160 HOH HOH . I 6 HOH B 26 526 149 HOH HOH . I 6 HOH B 27 527 115 HOH HOH . I 6 HOH B 28 528 142 HOH HOH . I 6 HOH B 29 529 198 HOH HOH . I 6 HOH B 30 530 99 HOH HOH . I 6 HOH B 31 531 116 HOH HOH . I 6 HOH B 32 532 138 HOH HOH . I 6 HOH B 33 533 131 HOH HOH . I 6 HOH B 34 534 118 HOH HOH . I 6 HOH B 35 535 152 HOH HOH . I 6 HOH B 36 536 183 HOH HOH . I 6 HOH B 37 537 104 HOH HOH . I 6 HOH B 38 538 126 HOH HOH . I 6 HOH B 39 539 136 HOH HOH . I 6 HOH B 40 540 150 HOH HOH . I 6 HOH B 41 541 139 HOH HOH . I 6 HOH B 42 542 108 HOH HOH . I 6 HOH B 43 543 128 HOH HOH . I 6 HOH B 44 544 101 HOH HOH . I 6 HOH B 45 545 137 HOH HOH . I 6 HOH B 46 546 100 HOH HOH . I 6 HOH B 47 547 98 HOH HOH . I 6 HOH B 48 548 114 HOH HOH . I 6 HOH B 49 549 179 HOH HOH . I 6 HOH B 50 550 184 HOH HOH . I 6 HOH B 51 551 157 HOH HOH . I 6 HOH B 52 552 169 HOH HOH . I 6 HOH B 53 553 143 HOH HOH . I 6 HOH B 54 554 195 HOH HOH . I 6 HOH B 55 555 181 HOH HOH . I 6 HOH B 56 556 185 HOH HOH . I 6 HOH B 57 557 171 HOH HOH . I 6 HOH B 58 558 175 HOH HOH . I 6 HOH B 59 559 111 HOH HOH . I 6 HOH B 60 560 154 HOH HOH . I 6 HOH B 61 561 113 HOH HOH . I 6 HOH B 62 562 190 HOH HOH . I 6 HOH B 63 563 129 HOH HOH . I 6 HOH B 64 564 110 HOH HOH . I 6 HOH B 65 565 194 HOH HOH . I 6 HOH B 66 566 145 HOH HOH . I 6 HOH B 67 567 135 HOH HOH . I 6 HOH B 68 568 141 HOH HOH . I 6 HOH B 69 569 176 HOH HOH . I 6 HOH B 70 570 117 HOH HOH . I 6 HOH B 71 571 166 HOH HOH . I 6 HOH B 72 572 130 HOH HOH . I 6 HOH B 73 573 163 HOH HOH . I 6 HOH B 74 574 177 HOH HOH . I 6 HOH B 75 575 192 HOH HOH . I 6 HOH B 76 576 153 HOH HOH . I 6 HOH B 77 577 191 HOH HOH . I 6 HOH B 78 578 162 HOH HOH . I 6 HOH B 79 579 121 HOH HOH . I 6 HOH B 80 580 180 HOH HOH . I 6 HOH B 81 581 144 HOH HOH . I 6 HOH B 82 582 193 HOH HOH . I 6 HOH B 83 583 158 HOH HOH . I 6 HOH B 84 584 167 HOH HOH . I 6 HOH B 85 585 178 HOH HOH . I 6 HOH B 86 586 105 HOH HOH . I 6 HOH B 87 587 147 HOH HOH . I 6 HOH B 88 588 156 HOH HOH . I 6 HOH B 89 589 155 HOH HOH . I 6 HOH B 90 590 77 HOH HOH . I 6 HOH B 91 591 148 HOH HOH . I 6 HOH B 92 592 172 HOH HOH . I 6 HOH B 93 593 140 HOH HOH . I 6 HOH B 94 594 164 HOH HOH . I 6 HOH B 95 595 188 HOH HOH . I 6 HOH B 96 596 170 HOH HOH . I 6 HOH B 97 597 197 HOH HOH . I 6 HOH B 98 598 168 HOH HOH . I 6 HOH B 99 599 146 HOH HOH . I 6 HOH B 100 600 161 HOH HOH . I 6 HOH B 101 601 75 HOH HOH . I 6 HOH B 102 602 182 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 CS MTA . . . G 5 23.866 8.496 69.982 1 43.98 ? CS MTA 403 B 1 HETATM 2 S S5' MTA . . . G 5 23.595 9.484 68.541 1 63.47 ? S5' MTA 403 B 1 HETATM 3 C C5' MTA . . . G 5 23.817 11.166 69.071 1 44.63 ? C5' MTA 403 B 1 HETATM 4 C C4' MTA . . . G 5 22.921 11.547 70.257 1 38.77 ? C4' MTA 403 B 1 HETATM 5 O O4' MTA . . . G 5 23.485 11.086 71.501 1 30.51 ? O4' MTA 403 B 1 HETATM 6 C C2' MTA . . . G 5 22.527 13.206 71.905 1 32.45 ? C2' MTA 403 B 1 HETATM 7 O O2' MTA . . . G 5 21.132 13.058 72.151 1 43.05 ? O2' MTA 403 B 1 HETATM 8 C C3' MTA . . . G 5 22.746 13.052 70.421 1 32.86 ? C3' MTA 403 B 1 HETATM 9 O O3' MTA . . . G 5 21.571 13.511 69.76 1 42.57 ? O3' MTA 403 B 1 HETATM 10 C C1' MTA . . . G 5 23.246 12.023 72.53 1 25.29 ? C1' MTA 403 B 1 HETATM 11 N N9 MTA . . . G 5 24.575 12.447 73.012 1 24.01 ? N9 MTA 403 B 1 HETATM 12 C C8 MTA . . . G 5 25.733 12.363 72.336 1 19.85 ? C8 MTA 403 B 1 HETATM 13 N N7 MTA . . . G 5 26.772 12.837 73.072 1 16.85 ? N7 MTA 403 B 1 HETATM 14 C C5 MTA . . . G 5 26.259 13.224 74.246 1 24.46 ? C5 MTA 403 B 1 HETATM 15 C C6 MTA . . . G 5 26.8 13.821 75.474 1 19.95 ? C6 MTA 403 B 1 HETATM 16 N N6 MTA . . . G 5 28.13 14.084 75.553 1 21.33 ? N6 MTA 403 B 1 HETATM 17 N N1 MTA . . . G 5 25.928 14.068 76.476 1 23.71 ? N1 MTA 403 B 1 HETATM 18 C C2 MTA . . . G 5 24.613 13.813 76.379 1 23.36 ? C2 MTA 403 B 1 HETATM 19 N N3 MTA . . . G 5 24.061 13.277 75.282 1 26.51 ? N3 MTA 403 B 1 HETATM 20 C C4 MTA . . . G 5 24.82 12.965 74.21 1 22.95 ? C4 MTA 403 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 30 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 20 #