data_7MD1 # _model_server_result.job_id IBeFZ1pOKDGZWfsBdlPVQQ _model_server_result.datetime_utc '2024-11-29 23:34:21' _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 7md1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":403}' # _entry.id 7MD1 # _exptl.entry_id 7MD1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 4 _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 7MD1 _cell.length_a 105.26 _cell.length_b 105.26 _cell.length_c 288.304 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7MD1 _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 _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 -1 105.26 105.26 0 3 'crystal symmetry operation' 10_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 105.26 105.26 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 ? 4 D N N ? 4 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 A N SER 1 H SER 1 1_555 C C4A PLP . H PLP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale2 A C THR 195 H THR 195 1_555 A N LLP 196 H LLP 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale3 A C LLP 196 H LLP 196 1_555 A N TYR 197 H TYR 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? metalc ? metalc1 A O ALA 77 H ALA 77 1_555 E NA NA . H NA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.873 ? metalc ? metalc2 D NA NA . H NA 403 1_555 H O HOH . H HOH 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.855 ? metalc ? metalc3 D NA NA . H NA 403 1_555 H O HOH . H HOH 528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.655 ? metalc ? metalc4 D NA NA . H NA 403 1_555 H O HOH . H HOH 655 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.632 ? metalc ? metalc5 D NA NA . H NA 403 1_555 H O HOH . H HOH 679 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.034 ? metalc ? metalc6 D NA NA . H NA 403 1_555 H O HOH . H HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.133 ? metalc ? metalc7 E NA NA . H NA 404 1_555 H O HOH . H HOH 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.694 ? metalc ? metalc8 E NA NA . H NA 404 1_555 H O HOH . H HOH 615 10_665 ? ? ? ? ? ? ? ? ? ? ? ? 2.689 ? metalc ? metalc9 E NA NA . H NA 404 1_555 H O HOH . H HOH 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.504 ? # _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 7MD1 _atom_sites.fract_transf_matrix[1][1] 0.0095 _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] 0.0095 _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] 0.003469 _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 EPE H 1 401 402 EPE EPE . C 3 PLP H 1 402 401 PLP PLP . D 4 NA H 1 403 1 NA NA . E 4 NA H 1 404 3 NA NA . F 5 GOL H 1 405 1 GOL GOL . G 5 GOL H 1 406 2 GOL GOL . H 6 HOH H 1 501 87 HOH HOH . H 6 HOH H 2 502 30 HOH HOH . H 6 HOH H 3 503 135 HOH HOH . H 6 HOH H 4 504 132 HOH HOH . H 6 HOH H 5 505 48 HOH HOH . H 6 HOH H 6 506 123 HOH HOH . H 6 HOH H 7 507 16 HOH HOH . H 6 HOH H 8 508 50 HOH HOH . H 6 HOH H 9 509 195 HOH HOH . H 6 HOH H 10 510 55 HOH HOH . H 6 HOH H 11 511 47 HOH HOH . H 6 HOH H 12 512 131 HOH HOH . H 6 HOH H 13 513 4 HOH HOH . H 6 HOH H 14 514 1 HOH HOH . H 6 HOH H 15 515 10 HOH HOH . H 6 HOH H 16 516 90 HOH HOH . H 6 HOH H 17 517 74 HOH HOH . H 6 HOH H 18 518 68 HOH HOH . H 6 HOH H 19 519 15 HOH HOH . H 6 HOH H 20 520 86 HOH HOH . H 6 HOH H 21 521 129 HOH HOH . H 6 HOH H 22 522 134 HOH HOH . H 6 HOH H 23 523 43 HOH HOH . H 6 HOH H 24 524 66 HOH HOH . H 6 HOH H 25 525 110 HOH HOH . H 6 HOH H 26 526 20 HOH HOH . H 6 HOH H 27 527 19 HOH HOH . H 6 HOH H 28 528 11 HOH HOH . H 6 HOH H 29 529 3 HOH HOH . H 6 HOH H 30 530 62 HOH HOH . H 6 HOH H 31 531 23 HOH HOH . H 6 HOH H 32 532 39 HOH HOH . H 6 HOH H 33 533 137 HOH HOH . H 6 HOH H 34 534 6 HOH HOH . H 6 HOH H 35 535 51 HOH HOH . H 6 HOH H 36 536 65 HOH HOH . H 6 HOH H 37 537 24 HOH HOH . H 6 HOH H 38 538 34 HOH HOH . H 6 HOH H 39 539 70 HOH HOH . H 6 HOH H 40 540 161 HOH HOH . H 6 HOH H 41 541 29 HOH HOH . H 6 HOH H 42 542 77 HOH HOH . H 6 HOH H 43 543 206 HOH HOH . H 6 HOH H 44 544 7 HOH HOH . H 6 HOH H 45 545 102 HOH HOH . H 6 HOH H 46 546 33 HOH HOH . H 6 HOH H 47 547 104 HOH HOH . H 6 HOH H 48 548 124 HOH HOH . H 6 HOH H 49 549 64 HOH HOH . H 6 HOH H 50 550 45 HOH HOH . H 6 HOH H 51 551 141 HOH HOH . H 6 HOH H 52 552 203 HOH HOH . H 6 HOH H 53 553 130 HOH HOH . H 6 HOH H 54 554 35 HOH HOH . H 6 HOH H 55 555 14 HOH HOH . H 6 HOH H 56 556 2 HOH HOH . H 6 HOH H 57 557 54 HOH HOH . H 6 HOH H 58 558 42 HOH HOH . H 6 HOH H 59 559 79 HOH HOH . H 6 HOH H 60 560 92 HOH HOH . H 6 HOH H 61 561 179 HOH HOH . H 6 HOH H 62 562 8 HOH HOH . H 6 HOH H 63 563 38 HOH HOH . H 6 HOH H 64 564 107 HOH HOH . H 6 HOH H 65 565 201 HOH HOH . H 6 HOH H 66 566 31 HOH HOH . H 6 HOH H 67 567 18 HOH HOH . H 6 HOH H 68 568 151 HOH HOH . H 6 HOH H 69 569 125 HOH HOH . H 6 HOH H 70 570 84 HOH HOH . H 6 HOH H 71 571 101 HOH HOH . H 6 HOH H 72 572 159 HOH HOH . H 6 HOH H 73 573 21 HOH HOH . H 6 HOH H 74 574 91 HOH HOH . H 6 HOH H 75 575 113 HOH HOH . H 6 HOH H 76 576 147 HOH HOH . H 6 HOH H 77 577 166 HOH HOH . H 6 HOH H 78 578 112 HOH HOH . H 6 HOH H 79 579 22 HOH HOH . H 6 HOH H 80 580 58 HOH HOH . H 6 HOH H 81 581 72 HOH HOH . H 6 HOH H 82 582 60 HOH HOH . H 6 HOH H 83 583 162 HOH HOH . H 6 HOH H 84 584 37 HOH HOH . H 6 HOH H 85 585 5 HOH HOH . H 6 HOH H 86 586 78 HOH HOH . H 6 HOH H 87 587 36 HOH HOH . H 6 HOH H 88 588 17 HOH HOH . H 6 HOH H 89 589 57 HOH HOH . H 6 HOH H 90 590 106 HOH HOH . H 6 HOH H 91 591 9 HOH HOH . H 6 HOH H 92 592 171 HOH HOH . H 6 HOH H 93 593 111 HOH HOH . H 6 HOH H 94 594 25 HOH HOH . H 6 HOH H 95 595 13 HOH HOH . H 6 HOH H 96 596 185 HOH HOH . H 6 HOH H 97 597 94 HOH HOH . H 6 HOH H 98 598 98 HOH HOH . H 6 HOH H 99 599 12 HOH HOH . H 6 HOH H 100 600 41 HOH HOH . H 6 HOH H 101 601 139 HOH HOH . H 6 HOH H 102 602 100 HOH HOH . H 6 HOH H 103 603 117 HOH HOH . H 6 HOH H 104 604 69 HOH HOH . H 6 HOH H 105 605 140 HOH HOH . H 6 HOH H 106 606 59 HOH HOH . H 6 HOH H 107 607 108 HOH HOH . H 6 HOH H 108 608 28 HOH HOH . H 6 HOH H 109 609 176 HOH HOH . H 6 HOH H 110 610 44 HOH HOH . H 6 HOH H 111 611 89 HOH HOH . H 6 HOH H 112 612 177 HOH HOH . H 6 HOH H 113 613 96 HOH HOH . H 6 HOH H 114 614 114 HOH HOH . H 6 HOH H 115 615 128 HOH HOH . H 6 HOH H 116 616 204 HOH HOH . H 6 HOH H 117 617 73 HOH HOH . H 6 HOH H 118 618 169 HOH HOH . H 6 HOH H 119 619 46 HOH HOH . H 6 HOH H 120 620 27 HOH HOH . H 6 HOH H 121 621 67 HOH HOH . H 6 HOH H 122 622 63 HOH HOH . H 6 HOH H 123 623 122 HOH HOH . H 6 HOH H 124 624 109 HOH HOH . H 6 HOH H 125 625 178 HOH HOH . H 6 HOH H 126 626 61 HOH HOH . H 6 HOH H 127 627 32 HOH HOH . H 6 HOH H 128 628 181 HOH HOH . H 6 HOH H 129 629 52 HOH HOH . H 6 HOH H 130 630 168 HOH HOH . H 6 HOH H 131 631 144 HOH HOH . H 6 HOH H 132 632 148 HOH HOH . H 6 HOH H 133 633 53 HOH HOH . H 6 HOH H 134 634 85 HOH HOH . H 6 HOH H 135 635 40 HOH HOH . H 6 HOH H 136 636 115 HOH HOH . H 6 HOH H 137 637 97 HOH HOH . H 6 HOH H 138 638 49 HOH HOH . H 6 HOH H 139 639 143 HOH HOH . H 6 HOH H 140 640 81 HOH HOH . H 6 HOH H 141 641 188 HOH HOH . H 6 HOH H 142 642 120 HOH HOH . H 6 HOH H 143 643 80 HOH HOH . H 6 HOH H 144 644 149 HOH HOH . H 6 HOH H 145 645 99 HOH HOH . H 6 HOH H 146 646 142 HOH HOH . H 6 HOH H 147 647 26 HOH HOH . H 6 HOH H 148 648 83 HOH HOH . H 6 HOH H 149 649 56 HOH HOH . H 6 HOH H 150 650 76 HOH HOH . H 6 HOH H 151 651 121 HOH HOH . H 6 HOH H 152 652 82 HOH HOH . H 6 HOH H 153 653 172 HOH HOH . H 6 HOH H 154 654 95 HOH HOH . H 6 HOH H 155 655 175 HOH HOH . H 6 HOH H 156 656 138 HOH HOH . H 6 HOH H 157 657 119 HOH HOH . H 6 HOH H 158 658 196 HOH HOH . H 6 HOH H 159 659 105 HOH HOH . H 6 HOH H 160 660 133 HOH HOH . H 6 HOH H 161 661 190 HOH HOH . H 6 HOH H 162 662 191 HOH HOH . H 6 HOH H 163 663 194 HOH HOH . H 6 HOH H 164 664 193 HOH HOH . H 6 HOH H 165 665 164 HOH HOH . H 6 HOH H 166 666 202 HOH HOH . H 6 HOH H 167 667 93 HOH HOH . H 6 HOH H 168 668 184 HOH HOH . H 6 HOH H 169 669 183 HOH HOH . H 6 HOH H 170 670 160 HOH HOH . H 6 HOH H 171 671 163 HOH HOH . H 6 HOH H 172 672 187 HOH HOH . H 6 HOH H 173 673 198 HOH HOH . H 6 HOH H 174 674 103 HOH HOH . H 6 HOH H 175 675 158 HOH HOH . H 6 HOH H 176 676 182 HOH HOH . H 6 HOH H 177 677 146 HOH HOH . H 6 HOH H 178 678 167 HOH HOH . H 6 HOH H 179 679 174 HOH HOH . H 6 HOH H 180 680 156 HOH HOH . H 6 HOH H 181 681 189 HOH HOH . H 6 HOH H 182 682 205 HOH HOH . H 6 HOH H 183 683 154 HOH HOH . H 6 HOH H 184 684 180 HOH HOH . H 6 HOH H 185 685 88 HOH HOH . H 6 HOH H 186 686 150 HOH HOH . H 6 HOH H 187 687 118 HOH HOH . H 6 HOH H 188 688 75 HOH HOH . H 6 HOH H 189 689 153 HOH HOH . H 6 HOH H 190 690 155 HOH HOH . H 6 HOH H 191 691 197 HOH HOH . H 6 HOH H 192 692 165 HOH HOH . H 6 HOH H 193 693 170 HOH HOH . H 6 HOH H 194 694 186 HOH HOH . H 6 HOH H 195 695 136 HOH HOH . H 6 HOH H 196 696 157 HOH HOH . H 6 HOH H 197 697 127 HOH HOH . H 6 HOH H 198 698 126 HOH HOH . H 6 HOH H 199 699 152 HOH HOH . H 6 HOH H 200 700 192 HOH HOH . H 6 HOH H 201 701 173 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 4 _atom_site.Cartn_x 49.353 _atom_site.Cartn_y 26.812 _atom_site.Cartn_z -27.337 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 69.61 _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 53 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 1 #