data_2DKB
#
_model_server_result.job_id            ocilHS5dEU4BM4AHGkVT4A 
_model_server_result.datetime_utc      '2024-10-11 08:25:34' 
_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          2dkb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":435}' 
#
_entry.id    2DKB 
#
_exptl.entry_id    2DKB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              22.99 
_entity.id                          2 
_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         120 
_cell.entry_id            2DKB 
_cell.length_a            152.7 
_cell.length_b            152.7 
_cell.length_c            86.6 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2DKB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        181 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 64 2 2' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA,PQS tetrameric 4 software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F 1 1,2 
A,B,C,D,E,F 2 1,3,2,4 
#
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' 7_555 y,x,-z+1/3 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 28.866667 
3 'crystal symmetry operation' 4_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 76.35 132.242079 0 
4 'crystal symmetry operation' 10_665 -y+1,-x+1,-z+1/3 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 76.35 132.242079 28.866667 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 B N N 
? 2 C 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 NZ LYS 272 A LYS 272 1_555 D C4A PLP . A PLP 437 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.31 ? 
metalc ? metalc1 B NA NA . A NA 435 1_555 A O ALA 95 A ALA 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? 
metalc ? metalc2 B NA NA . A NA 435 1_555 A O PRO 99 A PRO 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? 
metalc ? metalc3 B NA NA . A NA 435 1_555 A O LEU 102 A LEU 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? 
metalc ? metalc4 B NA NA . A NA 435 1_555 F O HOH . A HOH 526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? 
metalc ? metalc5 B NA NA . A NA 435 1_555 A OG1 THR 98 A THR 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.564 ? 
metalc ? metalc6 B NA NA . A NA 435 1_555 A O THR 98 A THR 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.525 ? 
metalc ? metalc7 C NA NA . A NA 436 1_555 A O LEU 78 A LEU 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? 
metalc ? metalc8 C NA NA . A NA 436 1_555 F O HOH . A HOH 519 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? 
metalc ? metalc9 C NA NA . A NA 436 1_555 F O HOH . A HOH 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? 
metalc ? metalc10 C NA NA . A NA 436 1_555 A OD1 ASP 307 A ASP 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? 
metalc ? metalc11 A O VAL 305 A VAL 305 1_555 C NA NA . A NA 436 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.601 ? 
#
_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                     2DKB 
_atom_sites.fract_transf_matrix[1][1]    0.006549 
_atom_sites.fract_transf_matrix[1][2]    0.003781 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007562 
_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]    0.011547 
_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 NA A 1 435 435 NA NA . 
C 2 NA A 1 436 436 NA NA . 
D 3 PLP A 1 437 272 PLP PLP . 
E 4 MES A 1 434 434 MES MES . 
F 5 HOH A 1 501 501 HOH HOH . 
F 5 HOH A 2 502 502 HOH HOH . 
F 5 HOH A 3 503 503 HOH HOH . 
F 5 HOH A 4 504 504 HOH HOH . 
F 5 HOH A 5 505 505 HOH HOH . 
F 5 HOH A 6 506 506 HOH HOH . 
F 5 HOH A 7 507 507 HOH HOH . 
F 5 HOH A 8 508 508 HOH HOH . 
F 5 HOH A 9 509 509 HOH HOH . 
F 5 HOH A 10 510 510 HOH HOH . 
F 5 HOH A 11 511 511 HOH HOH . 
F 5 HOH A 12 512 512 HOH HOH . 
F 5 HOH A 13 513 513 HOH HOH . 
F 5 HOH A 14 514 514 HOH HOH . 
F 5 HOH A 15 515 515 HOH HOH . 
F 5 HOH A 16 516 516 HOH HOH . 
F 5 HOH A 17 517 517 HOH HOH . 
F 5 HOH A 18 518 518 HOH HOH . 
F 5 HOH A 19 519 519 HOH HOH . 
F 5 HOH A 20 520 520 HOH HOH . 
F 5 HOH A 21 521 521 HOH HOH . 
F 5 HOH A 22 522 522 HOH HOH . 
F 5 HOH A 23 523 523 HOH HOH . 
F 5 HOH A 24 524 524 HOH HOH . 
F 5 HOH A 25 525 525 HOH HOH . 
F 5 HOH A 26 526 526 HOH HOH . 
F 5 HOH A 27 527 527 HOH HOH . 
F 5 HOH A 28 528 528 HOH HOH . 
F 5 HOH A 29 529 529 HOH HOH . 
F 5 HOH A 30 530 530 HOH HOH . 
F 5 HOH A 31 531 531 HOH HOH . 
F 5 HOH A 32 532 532 HOH HOH . 
F 5 HOH A 33 533 533 HOH HOH . 
F 5 HOH A 34 534 534 HOH HOH . 
F 5 HOH A 35 535 535 HOH HOH . 
F 5 HOH A 36 536 536 HOH HOH . 
F 5 HOH A 37 537 537 HOH HOH . 
F 5 HOH A 38 538 538 HOH HOH . 
F 5 HOH A 39 539 539 HOH HOH . 
F 5 HOH A 40 540 540 HOH HOH . 
F 5 HOH A 41 541 541 HOH HOH . 
F 5 HOH A 42 542 542 HOH HOH . 
F 5 HOH A 43 543 543 HOH HOH . 
F 5 HOH A 44 544 544 HOH HOH . 
F 5 HOH A 45 545 545 HOH HOH . 
F 5 HOH A 46 546 546 HOH HOH . 
F 5 HOH A 47 547 547 HOH HOH . 
F 5 HOH A 48 548 548 HOH HOH . 
F 5 HOH A 49 549 549 HOH HOH . 
F 5 HOH A 50 550 550 HOH HOH . 
F 5 HOH A 51 551 551 HOH HOH . 
F 5 HOH A 52 552 552 HOH HOH . 
F 5 HOH A 53 553 553 HOH HOH . 
F 5 HOH A 54 554 554 HOH HOH . 
F 5 HOH A 55 555 555 HOH HOH . 
F 5 HOH A 56 556 556 HOH HOH . 
F 5 HOH A 57 557 557 HOH HOH . 
F 5 HOH A 58 558 558 HOH HOH . 
F 5 HOH A 59 559 559 HOH HOH . 
F 5 HOH A 60 560 560 HOH HOH . 
F 5 HOH A 61 561 561 HOH HOH . 
F 5 HOH A 62 562 562 HOH HOH . 
F 5 HOH A 63 563 563 HOH HOH . 
F 5 HOH A 64 564 564 HOH HOH . 
F 5 HOH A 65 565 565 HOH HOH . 
F 5 HOH A 66 566 566 HOH HOH . 
F 5 HOH A 67 567 567 HOH HOH . 
F 5 HOH A 68 568 568 HOH HOH . 
F 5 HOH A 69 569 569 HOH HOH . 
F 5 HOH A 70 570 570 HOH HOH . 
F 5 HOH A 71 571 571 HOH HOH . 
F 5 HOH A 72 572 572 HOH HOH . 
F 5 HOH A 73 573 573 HOH HOH . 
F 5 HOH A 74 574 574 HOH HOH . 
F 5 HOH A 75 575 575 HOH HOH . 
F 5 HOH A 76 576 576 HOH HOH . 
F 5 HOH A 77 577 577 HOH HOH . 
F 5 HOH A 78 578 578 HOH HOH . 
F 5 HOH A 79 579 579 HOH HOH . 
F 5 HOH A 80 580 580 HOH HOH . 
F 5 HOH A 81 581 581 HOH HOH . 
F 5 HOH A 82 582 582 HOH HOH . 
F 5 HOH A 83 583 583 HOH HOH . 
F 5 HOH A 84 584 584 HOH HOH . 
F 5 HOH A 85 585 585 HOH HOH . 
F 5 HOH A 86 586 586 HOH HOH . 
F 5 HOH A 87 587 587 HOH HOH . 
F 5 HOH A 88 588 588 HOH HOH . 
F 5 HOH A 89 589 589 HOH HOH . 
F 5 HOH A 90 590 590 HOH HOH . 
F 5 HOH A 91 591 591 HOH HOH . 
F 5 HOH A 92 592 592 HOH HOH . 
F 5 HOH A 93 593 593 HOH HOH . 
F 5 HOH A 94 594 594 HOH HOH . 
F 5 HOH A 95 595 595 HOH HOH . 
F 5 HOH A 96 596 596 HOH HOH . 
F 5 HOH A 97 597 597 HOH HOH . 
F 5 HOH A 98 598 598 HOH HOH . 
F 5 HOH A 99 599 599 HOH HOH . 
F 5 HOH A 100 600 600 HOH HOH . 
F 5 HOH A 101 601 601 HOH HOH . 
F 5 HOH A 102 602 602 HOH HOH . 
F 5 HOH A 103 603 603 HOH HOH . 
F 5 HOH A 104 604 604 HOH HOH . 
F 5 HOH A 105 605 605 HOH HOH . 
F 5 HOH A 106 606 606 HOH HOH . 
F 5 HOH A 107 607 607 HOH HOH . 
F 5 HOH A 108 608 608 HOH HOH . 
F 5 HOH A 109 609 609 HOH HOH . 
F 5 HOH A 110 610 610 HOH HOH . 
F 5 HOH A 111 611 611 HOH HOH . 
F 5 HOH A 112 612 612 HOH HOH . 
F 5 HOH A 113 613 613 HOH HOH . 
F 5 HOH A 114 614 614 HOH HOH . 
F 5 HOH A 115 615 615 HOH HOH . 
F 5 HOH A 116 616 616 HOH HOH . 
F 5 HOH A 117 617 617 HOH HOH . 
F 5 HOH A 118 618 618 HOH HOH . 
F 5 HOH A 119 619 619 HOH HOH . 
F 5 HOH A 120 620 620 HOH HOH . 
F 5 HOH A 121 621 621 HOH HOH . 
F 5 HOH A 122 622 622 HOH HOH . 
F 5 HOH A 123 623 623 HOH HOH . 
F 5 HOH A 124 624 624 HOH HOH . 
F 5 HOH A 125 625 625 HOH HOH . 
F 5 HOH A 126 626 626 HOH HOH . 
F 5 HOH A 127 627 627 HOH HOH . 
F 5 HOH A 128 628 628 HOH HOH . 
F 5 HOH A 129 629 629 HOH HOH . 
F 5 HOH A 130 630 630 HOH HOH . 
F 5 HOH A 131 631 631 HOH HOH . 
F 5 HOH A 132 632 632 HOH HOH . 
F 5 HOH A 133 633 633 HOH HOH . 
F 5 HOH A 134 634 634 HOH HOH . 
F 5 HOH A 135 635 635 HOH HOH . 
F 5 HOH A 136 636 636 HOH HOH . 
F 5 HOH A 137 637 637 HOH HOH . 
F 5 HOH A 138 638 638 HOH HOH . 
F 5 HOH A 139 639 639 HOH HOH . 
F 5 HOH A 140 640 640 HOH HOH . 
F 5 HOH A 141 641 641 HOH HOH . 
F 5 HOH A 142 642 642 HOH HOH . 
F 5 HOH A 143 643 643 HOH HOH . 
F 5 HOH A 144 644 644 HOH HOH . 
F 5 HOH A 145 645 645 HOH HOH . 
F 5 HOH A 146 646 646 HOH HOH . 
F 5 HOH A 147 647 647 HOH HOH . 
F 5 HOH A 148 648 648 HOH HOH . 
F 5 HOH A 149 649 649 HOH HOH . 
F 5 HOH A 150 650 650 HOH HOH . 
F 5 HOH A 151 651 651 HOH HOH . 
F 5 HOH A 152 652 652 HOH HOH . 
F 5 HOH A 153 653 653 HOH HOH . 
F 5 HOH A 154 654 654 HOH HOH . 
F 5 HOH A 155 655 655 HOH HOH . 
F 5 HOH A 156 656 656 HOH HOH . 
F 5 HOH A 157 657 657 HOH HOH . 
F 5 HOH A 158 658 658 HOH HOH . 
F 5 HOH A 159 659 659 HOH HOH . 
F 5 HOH A 160 660 660 HOH HOH . 
F 5 HOH A 161 661 661 HOH HOH . 
F 5 HOH A 162 662 662 HOH HOH . 
F 5 HOH A 163 663 663 HOH HOH . 
F 5 HOH A 164 664 664 HOH HOH . 
F 5 HOH A 165 665 665 HOH HOH . 
F 5 HOH A 166 666 666 HOH HOH . 
F 5 HOH A 167 667 667 HOH HOH . 
F 5 HOH A 168 668 668 HOH HOH . 
F 5 HOH A 169 669 669 HOH HOH . 
F 5 HOH A 170 670 670 HOH HOH . 
F 5 HOH A 171 671 671 HOH HOH . 
F 5 HOH A 172 672 672 HOH HOH . 
F 5 HOH A 173 673 673 HOH HOH . 
F 5 HOH A 174 674 674 HOH HOH . 
F 5 HOH A 175 675 675 HOH HOH . 
F 5 HOH A 176 676 676 HOH HOH . 
F 5 HOH A 177 677 677 HOH HOH . 
F 5 HOH A 178 678 678 HOH HOH . 
F 5 HOH A 179 679 679 HOH HOH . 
F 5 HOH A 180 680 680 HOH HOH . 
F 5 HOH A 181 681 681 HOH HOH . 
F 5 HOH A 182 682 682 HOH HOH . 
F 5 HOH A 183 683 683 HOH HOH . 
F 5 HOH A 184 684 684 HOH HOH . 
F 5 HOH A 185 685 685 HOH HOH . 
F 5 HOH A 186 686 686 HOH HOH . 
F 5 HOH A 187 687 687 HOH HOH . 
F 5 HOH A 188 688 688 HOH HOH . 
F 5 HOH A 189 689 689 HOH HOH . 
F 5 HOH A 190 690 690 HOH HOH . 
F 5 HOH A 191 691 691 HOH HOH . 
F 5 HOH A 192 692 692 HOH HOH . 
F 5 HOH A 193 693 693 HOH HOH . 
F 5 HOH A 194 694 694 HOH HOH . 
F 5 HOH A 195 695 695 HOH HOH . 
F 5 HOH A 196 696 696 HOH HOH . 
F 5 HOH A 197 697 697 HOH HOH . 
F 5 HOH A 198 698 698 HOH HOH . 
F 5 HOH A 199 699 699 HOH HOH . 
F 5 HOH A 200 700 700 HOH HOH . 
F 5 HOH A 201 701 701 HOH HOH . 
F 5 HOH A 202 702 702 HOH HOH . 
F 5 HOH A 203 703 703 HOH HOH . 
F 5 HOH A 204 704 704 HOH HOH . 
F 5 HOH A 205 705 705 HOH HOH . 
F 5 HOH A 206 706 706 HOH HOH . 
F 5 HOH A 207 707 707 HOH HOH . 
F 5 HOH A 208 708 708 HOH HOH . 
F 5 HOH A 209 709 709 HOH HOH . 
F 5 HOH A 210 710 710 HOH HOH . 
F 5 HOH A 211 711 711 HOH HOH . 
F 5 HOH A 212 712 712 HOH HOH . 
F 5 HOH A 213 713 713 HOH HOH . 
F 5 HOH A 214 714 714 HOH HOH . 
F 5 HOH A 215 715 715 HOH HOH . 
F 5 HOH A 216 716 716 HOH HOH . 
F 5 HOH A 217 717 717 HOH HOH . 
F 5 HOH A 218 718 718 HOH HOH . 
F 5 HOH A 219 719 719 HOH HOH . 
F 5 HOH A 220 720 720 HOH HOH . 
F 5 HOH A 221 721 721 HOH HOH . 
F 5 HOH A 222 722 722 HOH HOH . 
F 5 HOH A 223 723 723 HOH HOH . 
F 5 HOH A 224 724 724 HOH HOH . 
F 5 HOH A 225 725 725 HOH HOH . 
F 5 HOH A 226 726 726 HOH HOH . 
F 5 HOH A 227 727 727 HOH HOH . 
F 5 HOH A 228 728 728 HOH HOH . 
F 5 HOH A 229 729 729 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         B 
_atom_site.label_entity_id       2 
_atom_site.Cartn_x               12.298 
_atom_site.Cartn_y               49.26 
_atom_site.Cartn_z               -5.781 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        31.11 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          NA 
_atom_site.auth_comp_id          NA 
_atom_site.auth_seq_id           435 
_atom_site.auth_asym_id          A 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           299 
_model_server_stats.encode_time_ms          17 
_model_server_stats.element_count           1 
#