data_1D6S # _model_server_result.job_id xXxZgU8IJbRflWPlgO2Yqg _model_server_result.datetime_utc '2024-11-28 11:14:23' _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 1d6s # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 1D6S # _exptl.entry_id 1D6S _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 247.142 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "PYRIDOXAL-5'-PHOSPHATE" _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 90 _cell.entry_id 1D6S _cell.length_a 96.94 _cell.length_b 149.93 _cell.length_c 53.64 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1D6S _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # _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 _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 ? 3 D N N ? 3 E 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 C N MET . A MET 401 1_555 D C4A PLP . A PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.291 ? covale ? covale2 F N MET . B MET 402 1_555 E C4A PLP . B PLP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.296 ? # _chem_comp.formula 'C8 H10 N O6 P' _chem_comp.formula_weight 247.142 _chem_comp.id PLP _chem_comp.mon_nstd_flag . _chem_comp.name "PYRIDOXAL-5'-PHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'VITAMIN B6 Phosphate' # 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 N1 C2 PLP doub 260 n y N1 C6 PLP sing 261 n y C2 C2A PLP sing 262 n n C2 C3 PLP sing 263 n y C2A H2A1 PLP sing 264 n n C2A H2A2 PLP sing 265 n n C2A H2A3 PLP sing 266 n n C3 O3 PLP sing 267 n n C3 C4 PLP doub 268 n y O3 HO3 PLP sing 269 n n C4 C4A PLP sing 270 n n C4 C5 PLP sing 271 n y C4A O4A PLP doub 272 n n C4A H4A PLP sing 273 n n C5 C6 PLP doub 274 n y C5 C5A PLP sing 275 n n C6 H6 PLP sing 276 n n C5A O4P PLP sing 277 n n C5A H5A1 PLP sing 278 n n C5A H5A2 PLP sing 279 n n O4P P PLP sing 280 n n P O1P PLP doub 281 n n P O2P PLP sing 282 n n P O3P PLP sing 283 n n O2P HOP2 PLP sing 284 n n O3P HOP3 PLP sing 285 n n # _atom_sites.entry_id 1D6S _atom_sites.fract_transf_matrix[1][1] 0.010316 _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] 0.00667 _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] 0.018643 _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 MET A 1 401 1 MET MET . D 3 PLP A 1 501 1 PLP PLP . E 3 PLP B 1 502 2 PLP PLP . F 2 MET B 1 402 1 MET MET . G 4 HOH A 1 502 4 HOH HOH . G 4 HOH A 2 503 6 HOH HOH . G 4 HOH A 3 504 7 HOH HOH . G 4 HOH A 4 505 8 HOH HOH . G 4 HOH A 5 506 11 HOH HOH . G 4 HOH A 6 507 12 HOH HOH . G 4 HOH A 7 508 13 HOH HOH . G 4 HOH A 8 509 14 HOH HOH . G 4 HOH A 9 510 16 HOH HOH . G 4 HOH A 10 511 18 HOH HOH . G 4 HOH A 11 512 24 HOH HOH . G 4 HOH A 12 513 25 HOH HOH . G 4 HOH A 13 514 29 HOH HOH . G 4 HOH A 14 515 30 HOH HOH . G 4 HOH A 15 516 33 HOH HOH . G 4 HOH A 16 517 38 HOH HOH . G 4 HOH A 17 518 39 HOH HOH . G 4 HOH A 18 519 40 HOH HOH . G 4 HOH A 19 520 41 HOH HOH . G 4 HOH A 20 521 42 HOH HOH . G 4 HOH A 21 522 44 HOH HOH . G 4 HOH A 22 523 51 HOH HOH . G 4 HOH A 23 524 56 HOH HOH . G 4 HOH A 24 525 59 HOH HOH . G 4 HOH A 25 526 60 HOH HOH . G 4 HOH A 26 527 62 HOH HOH . G 4 HOH A 27 528 64 HOH HOH . G 4 HOH A 28 529 66 HOH HOH . G 4 HOH A 29 530 68 HOH HOH . G 4 HOH A 30 531 69 HOH HOH . G 4 HOH A 31 532 71 HOH HOH . G 4 HOH A 32 533 72 HOH HOH . G 4 HOH A 33 534 73 HOH HOH . G 4 HOH A 34 535 77 HOH HOH . G 4 HOH A 35 536 78 HOH HOH . G 4 HOH A 36 537 80 HOH HOH . G 4 HOH A 37 538 84 HOH HOH . G 4 HOH A 38 539 88 HOH HOH . G 4 HOH A 39 540 89 HOH HOH . G 4 HOH A 40 541 91 HOH HOH . G 4 HOH A 41 542 92 HOH HOH . G 4 HOH A 42 543 94 HOH HOH . G 4 HOH A 43 544 95 HOH HOH . G 4 HOH A 44 545 96 HOH HOH . G 4 HOH A 45 546 104 HOH HOH . G 4 HOH A 46 547 105 HOH HOH . G 4 HOH A 47 548 107 HOH HOH . G 4 HOH A 48 549 108 HOH HOH . G 4 HOH A 49 550 109 HOH HOH . G 4 HOH A 50 551 113 HOH HOH . G 4 HOH A 51 552 115 HOH HOH . G 4 HOH A 52 553 117 HOH HOH . G 4 HOH A 53 554 118 HOH HOH . G 4 HOH A 54 555 119 HOH HOH . G 4 HOH A 55 556 120 HOH HOH . G 4 HOH A 56 557 122 HOH HOH . G 4 HOH A 57 558 125 HOH HOH . G 4 HOH A 58 559 127 HOH HOH . G 4 HOH A 59 560 128 HOH HOH . G 4 HOH A 60 561 129 HOH HOH . G 4 HOH A 61 562 131 HOH HOH . G 4 HOH A 62 563 133 HOH HOH . G 4 HOH A 63 564 134 HOH HOH . G 4 HOH A 64 565 137 HOH HOH . G 4 HOH A 65 566 140 HOH HOH . G 4 HOH A 66 567 141 HOH HOH . G 4 HOH A 67 568 142 HOH HOH . G 4 HOH A 68 569 145 HOH HOH . G 4 HOH A 69 570 147 HOH HOH . G 4 HOH A 70 571 150 HOH HOH . G 4 HOH A 71 572 156 HOH HOH . G 4 HOH A 72 573 164 HOH HOH . G 4 HOH A 73 574 167 HOH HOH . G 4 HOH A 74 575 171 HOH HOH . G 4 HOH A 75 576 179 HOH HOH . G 4 HOH A 76 577 180 HOH HOH . G 4 HOH A 77 578 181 HOH HOH . G 4 HOH A 78 579 182 HOH HOH . G 4 HOH A 79 580 183 HOH HOH . G 4 HOH A 80 581 184 HOH HOH . G 4 HOH A 81 582 185 HOH HOH . G 4 HOH A 82 583 186 HOH HOH . G 4 HOH A 83 584 187 HOH HOH . G 4 HOH A 84 585 188 HOH HOH . G 4 HOH A 85 586 190 HOH HOH . G 4 HOH A 86 587 193 HOH HOH . G 4 HOH A 87 588 194 HOH HOH . G 4 HOH A 88 589 197 HOH HOH . G 4 HOH A 89 590 200 HOH HOH . G 4 HOH A 90 591 201 HOH HOH . G 4 HOH A 91 592 202 HOH HOH . G 4 HOH A 92 593 203 HOH HOH . G 4 HOH A 93 594 205 HOH HOH . G 4 HOH A 94 595 208 HOH HOH . G 4 HOH A 95 596 211 HOH HOH . G 4 HOH A 96 597 213 HOH HOH . G 4 HOH A 97 598 219 HOH HOH . G 4 HOH A 98 599 222 HOH HOH . G 4 HOH A 99 600 225 HOH HOH . G 4 HOH A 100 601 229 HOH HOH . G 4 HOH A 101 602 230 HOH HOH . G 4 HOH A 102 603 231 HOH HOH . G 4 HOH A 103 604 232 HOH HOH . G 4 HOH A 104 605 236 HOH HOH . G 4 HOH A 105 606 237 HOH HOH . G 4 HOH A 106 607 243 HOH HOH . G 4 HOH A 107 608 244 HOH HOH . G 4 HOH A 108 609 245 HOH HOH . G 4 HOH A 109 610 247 HOH HOH . H 4 HOH B 1 503 2 HOH HOH . H 4 HOH B 2 504 3 HOH HOH . H 4 HOH B 3 505 5 HOH HOH . H 4 HOH B 4 506 9 HOH HOH . H 4 HOH B 5 507 10 HOH HOH . H 4 HOH B 6 508 15 HOH HOH . H 4 HOH B 7 509 17 HOH HOH . H 4 HOH B 8 510 19 HOH HOH . H 4 HOH B 9 511 20 HOH HOH . H 4 HOH B 10 512 21 HOH HOH . H 4 HOH B 11 513 22 HOH HOH . H 4 HOH B 12 514 23 HOH HOH . H 4 HOH B 13 515 26 HOH HOH . H 4 HOH B 14 516 27 HOH HOH . H 4 HOH B 15 517 28 HOH HOH . H 4 HOH B 16 518 32 HOH HOH . H 4 HOH B 17 519 34 HOH HOH . H 4 HOH B 18 520 35 HOH HOH . H 4 HOH B 19 521 36 HOH HOH . H 4 HOH B 20 522 37 HOH HOH . H 4 HOH B 21 523 43 HOH HOH . H 4 HOH B 22 524 45 HOH HOH . H 4 HOH B 23 525 46 HOH HOH . H 4 HOH B 24 526 47 HOH HOH . H 4 HOH B 25 527 48 HOH HOH . H 4 HOH B 26 528 53 HOH HOH . H 4 HOH B 27 529 54 HOH HOH . H 4 HOH B 28 530 55 HOH HOH . H 4 HOH B 29 531 57 HOH HOH . H 4 HOH B 30 532 58 HOH HOH . H 4 HOH B 31 533 61 HOH HOH . H 4 HOH B 32 534 63 HOH HOH . H 4 HOH B 33 535 65 HOH HOH . H 4 HOH B 34 536 67 HOH HOH . H 4 HOH B 35 537 70 HOH HOH . H 4 HOH B 36 538 74 HOH HOH . H 4 HOH B 37 539 75 HOH HOH . H 4 HOH B 38 540 76 HOH HOH . H 4 HOH B 39 541 79 HOH HOH . H 4 HOH B 40 542 81 HOH HOH . H 4 HOH B 41 543 82 HOH HOH . H 4 HOH B 42 544 83 HOH HOH . H 4 HOH B 43 545 85 HOH HOH . H 4 HOH B 44 546 87 HOH HOH . H 4 HOH B 45 547 90 HOH HOH . H 4 HOH B 46 548 93 HOH HOH . H 4 HOH B 47 549 97 HOH HOH . H 4 HOH B 48 550 98 HOH HOH . H 4 HOH B 49 551 99 HOH HOH . H 4 HOH B 50 552 101 HOH HOH . H 4 HOH B 51 553 103 HOH HOH . H 4 HOH B 52 554 106 HOH HOH . H 4 HOH B 53 555 110 HOH HOH . H 4 HOH B 54 556 111 HOH HOH . H 4 HOH B 55 557 112 HOH HOH . H 4 HOH B 56 558 114 HOH HOH . H 4 HOH B 57 559 116 HOH HOH . H 4 HOH B 58 560 121 HOH HOH . H 4 HOH B 59 561 123 HOH HOH . H 4 HOH B 60 562 124 HOH HOH . H 4 HOH B 61 563 126 HOH HOH . H 4 HOH B 62 564 130 HOH HOH . H 4 HOH B 63 565 132 HOH HOH . H 4 HOH B 64 566 135 HOH HOH . H 4 HOH B 65 567 136 HOH HOH . H 4 HOH B 66 568 138 HOH HOH . H 4 HOH B 67 569 139 HOH HOH . H 4 HOH B 68 570 143 HOH HOH . H 4 HOH B 69 571 144 HOH HOH . H 4 HOH B 70 572 146 HOH HOH . H 4 HOH B 71 573 148 HOH HOH . H 4 HOH B 72 574 149 HOH HOH . H 4 HOH B 73 575 151 HOH HOH . H 4 HOH B 74 576 152 HOH HOH . H 4 HOH B 75 577 154 HOH HOH . H 4 HOH B 76 578 155 HOH HOH . H 4 HOH B 77 579 157 HOH HOH . H 4 HOH B 78 580 158 HOH HOH . H 4 HOH B 79 581 159 HOH HOH . H 4 HOH B 80 582 161 HOH HOH . H 4 HOH B 81 583 162 HOH HOH . H 4 HOH B 82 584 163 HOH HOH . H 4 HOH B 83 585 165 HOH HOH . H 4 HOH B 84 586 166 HOH HOH . H 4 HOH B 85 587 168 HOH HOH . H 4 HOH B 86 588 169 HOH HOH . H 4 HOH B 87 589 172 HOH HOH . H 4 HOH B 88 590 173 HOH HOH . H 4 HOH B 89 591 174 HOH HOH . H 4 HOH B 90 592 176 HOH HOH . H 4 HOH B 91 593 177 HOH HOH . H 4 HOH B 92 594 178 HOH HOH . H 4 HOH B 93 595 189 HOH HOH . H 4 HOH B 94 596 191 HOH HOH . H 4 HOH B 95 597 192 HOH HOH . H 4 HOH B 96 598 195 HOH HOH . H 4 HOH B 97 599 196 HOH HOH . H 4 HOH B 98 600 198 HOH HOH . H 4 HOH B 99 601 199 HOH HOH . H 4 HOH B 100 602 204 HOH HOH . H 4 HOH B 101 603 206 HOH HOH . H 4 HOH B 102 604 207 HOH HOH . H 4 HOH B 103 605 210 HOH HOH . H 4 HOH B 104 606 212 HOH HOH . H 4 HOH B 105 607 214 HOH HOH . H 4 HOH B 106 608 216 HOH HOH . H 4 HOH B 107 609 217 HOH HOH . H 4 HOH B 108 610 218 HOH HOH . H 4 HOH B 109 611 220 HOH HOH . H 4 HOH B 110 612 221 HOH HOH . H 4 HOH B 111 613 223 HOH HOH . H 4 HOH B 112 614 224 HOH HOH . H 4 HOH B 113 615 226 HOH HOH . H 4 HOH B 114 616 227 HOH HOH . H 4 HOH B 115 617 228 HOH HOH . H 4 HOH B 116 618 233 HOH HOH . H 4 HOH B 117 619 234 HOH HOH . H 4 HOH B 118 620 235 HOH HOH . H 4 HOH B 119 621 238 HOH HOH . H 4 HOH B 120 622 239 HOH HOH . H 4 HOH B 121 623 240 HOH HOH . H 4 HOH B 122 624 241 HOH HOH . H 4 HOH B 123 625 242 HOH HOH . H 4 HOH B 124 626 246 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 N N1 PLP . . . D 3 35.88 26.289 15.932 1 21.07 ? N1 PLP 501 A 1 HETATM 2 C C2 PLP . . . D 3 37.141 26.634 15.511 1 21.9 ? C2 PLP 501 A 1 HETATM 3 C C2A PLP . . . D 3 37.336 27.353 14.188 1 14.17 ? C2A PLP 501 A 1 HETATM 4 C C3 PLP . . . D 3 38.233 26.278 16.251 1 27.07 ? C3 PLP 501 A 1 HETATM 5 O O3 PLP . . . D 3 39.474 26.694 15.85 1 28.58 ? O3 PLP 501 A 1 HETATM 6 C C4 PLP . . . D 3 38.072 25.539 17.42 1 29.44 ? C4 PLP 501 A 1 HETATM 7 C C4A PLP . . . D 3 39.304 25.028 18.191 1 29.77 ? C4A PLP 501 A 1 HETATM 8 C C5 PLP . . . D 3 36.806 25.189 17.834 1 24.25 ? C5 PLP 501 A 1 HETATM 9 C C6 PLP . . . D 3 35.716 25.573 17.096 1 23.42 ? C6 PLP 501 A 1 HETATM 10 C C5A PLP . . . D 3 36.615 24.265 19.014 1 21.95 ? C5A PLP 501 A 1 HETATM 11 O O4P PLP . . . D 3 36.657 24.963 20.256 1 22.41 ? O4P PLP 501 A 1 HETATM 12 P P PLP . . . D 3 37.093 24.134 21.549 1 24.18 ? P PLP 501 A 1 HETATM 13 O O1P PLP . . . D 3 36.851 24.916 22.776 1 17.65 ? O1P PLP 501 A 1 HETATM 14 O O2P PLP . . . D 3 36.034 22.922 21.521 1 24.79 ? O2P PLP 501 A 1 HETATM 15 O O3P PLP . . . D 3 38.433 23.563 21.279 1 33.32 ? O3P PLP 501 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 15 #