data_7MD8 # _model_server_result.job_id qlwLhdbFjY9opRvlUZA3xA _model_server_result.datetime_utc '2024-12-01 07:15:34' _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 7md8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":403}' # _entry.id 7MD8 # _exptl.entry_id 7MD8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM ION' _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 7MD8 _cell.length_a 106.107 _cell.length_b 106.107 _cell.length_c 287.636 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7MD8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 98 _symmetry.space_group_name_Hall 'I 4bw 2bw' _symmetry.space_group_name_H-M 'I 41 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,J,K _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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' 8_665 -y+1,-x+1,-z 0 -1 0 -1 0 0 0 0 -1 106.107 106.107 0 3 'crystal symmetry operation' 10_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 106.107 106.107 0 4 'crystal symmetry operation' 15_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 C N N ? 3 D 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 A N SER 1 H SER 1 1_555 B C4A PLP . H PLP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale2 A C THR 195 H THR 195 1_555 A N LLP 196 H LLP 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale3 A C LLP 196 H LLP 196 1_555 A N TYR 197 H TYR 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 A O HIS 9 H HIS 9 1_555 D NA NA . H NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc2 A O GLY 11 H GLY 11 1_555 D NA NA . H NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.538 ? metalc ? metalc3 C NA NA . H NA 402 1_555 K O HOH . H HOH 516 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.655 ? metalc ? metalc4 C NA NA . H NA 402 1_555 K O HOH . H HOH 548 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.697 ? metalc ? metalc5 C NA NA . H NA 402 1_555 K O HOH . H HOH 741 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.052 ? metalc ? metalc6 C NA NA . H NA 402 1_555 K O HOH . H HOH 756 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.77 ? metalc ? metalc7 C NA NA . H NA 402 1_555 K O HOH . H HOH 758 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.938 ? metalc ? metalc8 D NA NA . H NA 403 1_555 K O HOH . H HOH 562 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.616 ? metalc ? metalc9 D NA NA . H NA 403 1_555 K O HOH . H HOH 587 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.51 ? metalc ? metalc10 D NA NA . H NA 403 1_555 K O HOH . H HOH 633 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? metalc ? metalc11 D NA NA . H NA 403 1_555 K O HOH . H HOH 665 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.763 ? # _chem_comp.formula 'Na 1' _chem_comp.formula_weight 22.99 _chem_comp.id NA _chem_comp.mon_nstd_flag . _chem_comp.name 'SODIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 7MD8 _atom_sites.fract_transf_matrix[1][1] 0.009424 _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] 0.009424 _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] 0.003477 _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 B 2 PLP H 1 401 401 PLP PLP . C 3 NA H 1 402 1 NA NA . D 3 NA H 1 403 3 NA NA . E 4 GOL H 1 404 4 GOL GOL . F 4 GOL H 1 405 5 GOL GOL . G 4 GOL H 1 406 6 GOL GOL . H 4 GOL H 1 407 8 GOL GOL . I 5 EPE H 1 408 1 EPE EPE . J 4 GOL H 1 409 2 GOL GOL . K 6 HOH H 1 501 317 HOH HOH . K 6 HOH H 2 502 530 HOH HOH . K 6 HOH H 3 503 88 HOH HOH . K 6 HOH H 4 504 172 HOH HOH . K 6 HOH H 5 505 71 HOH HOH . K 6 HOH H 6 506 66 HOH HOH . K 6 HOH H 7 507 28 HOH HOH . K 6 HOH H 8 508 25 HOH HOH . K 6 HOH H 9 509 38 HOH HOH . K 6 HOH H 10 510 8 HOH HOH . K 6 HOH H 11 511 523 HOH HOH . K 6 HOH H 12 512 16 HOH HOH . K 6 HOH H 13 513 54 HOH HOH . K 6 HOH H 14 514 315 HOH HOH . K 6 HOH H 15 515 26 HOH HOH . K 6 HOH H 16 516 57 HOH HOH . K 6 HOH H 17 517 118 HOH HOH . K 6 HOH H 18 518 99 HOH HOH . K 6 HOH H 19 519 53 HOH HOH . K 6 HOH H 20 520 41 HOH HOH . K 6 HOH H 21 521 84 HOH HOH . K 6 HOH H 22 522 40 HOH HOH . K 6 HOH H 23 523 64 HOH HOH . K 6 HOH H 24 524 86 HOH HOH . K 6 HOH H 25 525 70 HOH HOH . K 6 HOH H 26 526 189 HOH HOH . K 6 HOH H 27 527 108 HOH HOH . K 6 HOH H 28 528 437 HOH HOH . K 6 HOH H 29 529 62 HOH HOH . K 6 HOH H 30 530 478 HOH HOH . K 6 HOH H 31 531 12 HOH HOH . K 6 HOH H 32 532 31 HOH HOH . K 6 HOH H 33 533 194 HOH HOH . K 6 HOH H 34 534 32 HOH HOH . K 6 HOH H 35 535 133 HOH HOH . K 6 HOH H 36 536 58 HOH HOH . K 6 HOH H 37 537 67 HOH HOH . K 6 HOH H 38 538 11 HOH HOH . K 6 HOH H 39 539 36 HOH HOH . K 6 HOH H 40 540 200 HOH HOH . K 6 HOH H 41 541 9 HOH HOH . K 6 HOH H 42 542 30 HOH HOH . K 6 HOH H 43 543 56 HOH HOH . K 6 HOH H 44 544 43 HOH HOH . K 6 HOH H 45 545 65 HOH HOH . K 6 HOH H 46 546 77 HOH HOH . K 6 HOH H 47 547 76 HOH HOH . K 6 HOH H 48 548 15 HOH HOH . K 6 HOH H 49 549 517 HOH HOH . K 6 HOH H 50 550 61 HOH HOH . K 6 HOH H 51 551 1 HOH HOH . K 6 HOH H 52 552 3 HOH HOH . K 6 HOH H 53 553 7 HOH HOH . K 6 HOH H 54 554 136 HOH HOH . K 6 HOH H 55 555 19 HOH HOH . K 6 HOH H 56 556 154 HOH HOH . K 6 HOH H 57 557 361 HOH HOH . K 6 HOH H 58 558 93 HOH HOH . K 6 HOH H 59 559 528 HOH HOH . K 6 HOH H 60 560 23 HOH HOH . K 6 HOH H 61 561 117 HOH HOH . K 6 HOH H 62 562 74 HOH HOH . K 6 HOH H 63 563 4 HOH HOH . K 6 HOH H 64 564 63 HOH HOH . K 6 HOH H 65 565 73 HOH HOH . K 6 HOH H 66 566 169 HOH HOH . K 6 HOH H 67 567 17 HOH HOH . K 6 HOH H 68 568 78 HOH HOH . K 6 HOH H 69 569 166 HOH HOH . K 6 HOH H 70 570 149 HOH HOH . K 6 HOH H 71 571 135 HOH HOH . K 6 HOH H 72 572 22 HOH HOH . K 6 HOH H 73 573 100 HOH HOH . K 6 HOH H 74 574 46 HOH HOH . K 6 HOH H 75 575 60 HOH HOH . K 6 HOH H 76 576 98 HOH HOH . K 6 HOH H 77 577 80 HOH HOH . K 6 HOH H 78 578 18 HOH HOH . K 6 HOH H 79 579 360 HOH HOH . K 6 HOH H 80 580 94 HOH HOH . K 6 HOH H 81 581 33 HOH HOH . K 6 HOH H 82 582 171 HOH HOH . K 6 HOH H 83 583 199 HOH HOH . K 6 HOH H 84 584 529 HOH HOH . K 6 HOH H 85 585 249 HOH HOH . K 6 HOH H 86 586 320 HOH HOH . K 6 HOH H 87 587 120 HOH HOH . K 6 HOH H 88 588 168 HOH HOH . K 6 HOH H 89 589 538 HOH HOH . K 6 HOH H 90 590 47 HOH HOH . K 6 HOH H 91 591 29 HOH HOH . K 6 HOH H 92 592 140 HOH HOH . K 6 HOH H 93 593 55 HOH HOH . K 6 HOH H 94 594 374 HOH HOH . K 6 HOH H 95 595 21 HOH HOH . K 6 HOH H 96 596 52 HOH HOH . K 6 HOH H 97 597 85 HOH HOH . K 6 HOH H 98 598 176 HOH HOH . K 6 HOH H 99 599 243 HOH HOH . K 6 HOH H 100 600 195 HOH HOH . K 6 HOH H 101 601 130 HOH HOH . K 6 HOH H 102 602 14 HOH HOH . K 6 HOH H 103 603 104 HOH HOH . K 6 HOH H 104 604 6 HOH HOH . K 6 HOH H 105 605 37 HOH HOH . K 6 HOH H 106 606 39 HOH HOH . K 6 HOH H 107 607 124 HOH HOH . K 6 HOH H 108 608 72 HOH HOH . K 6 HOH H 109 609 20 HOH HOH . K 6 HOH H 110 610 87 HOH HOH . K 6 HOH H 111 611 177 HOH HOH . K 6 HOH H 112 612 5 HOH HOH . K 6 HOH H 113 613 59 HOH HOH . K 6 HOH H 114 614 27 HOH HOH . K 6 HOH H 115 615 239 HOH HOH . K 6 HOH H 116 616 2 HOH HOH . K 6 HOH H 117 617 92 HOH HOH . K 6 HOH H 118 618 35 HOH HOH . K 6 HOH H 119 619 123 HOH HOH . K 6 HOH H 120 620 45 HOH HOH . K 6 HOH H 121 621 534 HOH HOH . K 6 HOH H 122 622 260 HOH HOH . K 6 HOH H 123 623 501 HOH HOH . K 6 HOH H 124 624 234 HOH HOH . K 6 HOH H 125 625 69 HOH HOH . K 6 HOH H 126 626 543 HOH HOH . K 6 HOH H 127 627 227 HOH HOH . K 6 HOH H 128 628 129 HOH HOH . K 6 HOH H 129 629 75 HOH HOH . K 6 HOH H 130 630 143 HOH HOH . K 6 HOH H 131 631 451 HOH HOH . K 6 HOH H 132 632 183 HOH HOH . K 6 HOH H 133 633 540 HOH HOH . K 6 HOH H 134 634 96 HOH HOH . K 6 HOH H 135 635 119 HOH HOH . K 6 HOH H 136 636 213 HOH HOH . K 6 HOH H 137 637 50 HOH HOH . K 6 HOH H 138 638 515 HOH HOH . K 6 HOH H 139 639 163 HOH HOH . K 6 HOH H 140 640 219 HOH HOH . K 6 HOH H 141 641 10 HOH HOH . K 6 HOH H 142 642 49 HOH HOH . K 6 HOH H 143 643 79 HOH HOH . K 6 HOH H 144 644 479 HOH HOH . K 6 HOH H 145 645 160 HOH HOH . K 6 HOH H 146 646 82 HOH HOH . K 6 HOH H 147 647 535 HOH HOH . K 6 HOH H 148 648 132 HOH HOH . K 6 HOH H 149 649 13 HOH HOH . K 6 HOH H 150 650 545 HOH HOH . K 6 HOH H 151 651 106 HOH HOH . K 6 HOH H 152 652 232 HOH HOH . K 6 HOH H 153 653 157 HOH HOH . K 6 HOH H 154 654 68 HOH HOH . K 6 HOH H 155 655 469 HOH HOH . K 6 HOH H 156 656 287 HOH HOH . K 6 HOH H 157 657 182 HOH HOH . K 6 HOH H 158 658 128 HOH HOH . K 6 HOH H 159 659 509 HOH HOH . K 6 HOH H 160 660 90 HOH HOH . K 6 HOH H 161 661 197 HOH HOH . K 6 HOH H 162 662 231 HOH HOH . K 6 HOH H 163 663 105 HOH HOH . K 6 HOH H 164 664 438 HOH HOH . K 6 HOH H 165 665 258 HOH HOH . K 6 HOH H 166 666 519 HOH HOH . K 6 HOH H 167 667 240 HOH HOH . K 6 HOH H 168 668 24 HOH HOH . K 6 HOH H 169 669 161 HOH HOH . K 6 HOH H 170 670 218 HOH HOH . K 6 HOH H 171 671 165 HOH HOH . K 6 HOH H 172 672 181 HOH HOH . K 6 HOH H 173 673 113 HOH HOH . K 6 HOH H 174 674 184 HOH HOH . K 6 HOH H 175 675 162 HOH HOH . K 6 HOH H 176 676 284 HOH HOH . K 6 HOH H 177 677 420 HOH HOH . K 6 HOH H 178 678 244 HOH HOH . K 6 HOH H 179 679 110 HOH HOH . K 6 HOH H 180 680 191 HOH HOH . K 6 HOH H 181 681 347 HOH HOH . K 6 HOH H 182 682 328 HOH HOH . K 6 HOH H 183 683 34 HOH HOH . K 6 HOH H 184 684 283 HOH HOH . K 6 HOH H 185 685 144 HOH HOH . K 6 HOH H 186 686 522 HOH HOH . K 6 HOH H 187 687 146 HOH HOH . K 6 HOH H 188 688 223 HOH HOH . K 6 HOH H 189 689 42 HOH HOH . K 6 HOH H 190 690 474 HOH HOH . K 6 HOH H 191 691 89 HOH HOH . K 6 HOH H 192 692 521 HOH HOH . K 6 HOH H 193 693 470 HOH HOH . K 6 HOH H 194 694 286 HOH HOH . K 6 HOH H 195 695 525 HOH HOH . K 6 HOH H 196 696 419 HOH HOH . K 6 HOH H 197 697 224 HOH HOH . K 6 HOH H 198 698 188 HOH HOH . K 6 HOH H 199 699 541 HOH HOH . K 6 HOH H 200 700 461 HOH HOH . K 6 HOH H 201 701 187 HOH HOH . K 6 HOH H 202 702 314 HOH HOH . K 6 HOH H 203 703 526 HOH HOH . K 6 HOH H 204 704 134 HOH HOH . K 6 HOH H 205 705 222 HOH HOH . K 6 HOH H 206 706 102 HOH HOH . K 6 HOH H 207 707 345 HOH HOH . K 6 HOH H 208 708 516 HOH HOH . K 6 HOH H 209 709 294 HOH HOH . K 6 HOH H 210 710 302 HOH HOH . K 6 HOH H 211 711 546 HOH HOH . K 6 HOH H 212 712 121 HOH HOH . K 6 HOH H 213 713 262 HOH HOH . K 6 HOH H 214 714 441 HOH HOH . K 6 HOH H 215 715 295 HOH HOH . K 6 HOH H 216 716 476 HOH HOH . K 6 HOH H 217 717 424 HOH HOH . K 6 HOH H 218 718 235 HOH HOH . K 6 HOH H 219 719 103 HOH HOH . K 6 HOH H 220 720 380 HOH HOH . K 6 HOH H 221 721 111 HOH HOH . K 6 HOH H 222 722 332 HOH HOH . K 6 HOH H 223 723 536 HOH HOH . K 6 HOH H 224 724 494 HOH HOH . K 6 HOH H 225 725 532 HOH HOH . K 6 HOH H 226 726 205 HOH HOH . K 6 HOH H 227 727 300 HOH HOH . K 6 HOH H 228 728 539 HOH HOH . K 6 HOH H 229 729 147 HOH HOH . K 6 HOH H 230 730 486 HOH HOH . K 6 HOH H 231 731 432 HOH HOH . K 6 HOH H 232 732 248 HOH HOH . K 6 HOH H 233 733 496 HOH HOH . K 6 HOH H 234 734 518 HOH HOH . K 6 HOH H 235 735 127 HOH HOH . K 6 HOH H 236 736 259 HOH HOH . K 6 HOH H 237 737 51 HOH HOH . K 6 HOH H 238 738 150 HOH HOH . K 6 HOH H 239 739 520 HOH HOH . K 6 HOH H 240 740 513 HOH HOH . K 6 HOH H 241 741 148 HOH HOH . K 6 HOH H 242 742 115 HOH HOH . K 6 HOH H 243 743 527 HOH HOH . K 6 HOH H 244 744 158 HOH HOH . K 6 HOH H 245 745 456 HOH HOH . K 6 HOH H 246 746 275 HOH HOH . K 6 HOH H 247 747 533 HOH HOH . K 6 HOH H 248 748 151 HOH HOH . K 6 HOH H 249 749 97 HOH HOH . K 6 HOH H 250 750 467 HOH HOH . K 6 HOH H 251 751 245 HOH HOH . K 6 HOH H 252 752 350 HOH HOH . K 6 HOH H 253 753 220 HOH HOH . K 6 HOH H 254 754 537 HOH HOH . K 6 HOH H 255 755 423 HOH HOH . K 6 HOH H 256 756 531 HOH HOH . K 6 HOH H 257 757 204 HOH HOH . K 6 HOH H 258 758 368 HOH HOH . K 6 HOH H 259 759 544 HOH HOH . K 6 HOH H 260 760 524 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol NA _atom_site.label_atom_id NA _atom_site.label_comp_id NA _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id D _atom_site.label_entity_id 3 _atom_site.Cartn_x 53.608 _atom_site.Cartn_y 30.771 _atom_site.Cartn_z -3.745 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 52.55 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 403 _atom_site.auth_asym_id H _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 233 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 1 #