data_2D09 # _model_server_result.job_id 7iMugRqBVy4dKwJGWaK5Fg _model_server_result.datetime_utc '2024-11-15 16:23:56' _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 2d09 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":432}' # _entry.id 2D09 # _exptl.entry_id 2D09 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 206.152 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description FLAVIOLIN _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 2D09 _cell.length_a 55 _cell.length_b 70.935 _cell.length_c 102.95 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2D09 _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 ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 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 metalc ? metalc1 A SG CYS 353 A CYS 353 1_555 B FE HEM . A HEM 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? metalc ? metalc2 B FE HEM . A HEM 430 1_555 E O2 OXY . A OXY 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.897 ? metalc ? metalc3 B FE HEM . A HEM 430 1_555 E O1 OXY . A OXY 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.738 ? # _chem_comp.formula 'C10 H6 O5' _chem_comp.formula_weight 206.152 _chem_comp.id FLV _chem_comp.mon_nstd_flag . _chem_comp.name FLAVIOLIN _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 2,5,7-TRIHYDROXYNAPHTHOQUINONE # 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 OAB CAM FLV doub 83 n n CAM CAN FLV sing 84 n n CAM CAJ FLV sing 85 n n CAN CAH FLV sing 86 n y CAN CAO FLV doub 87 n y CAH CAI FLV doub 88 n y CAH HAH FLV sing 89 n n CAI OAC FLV sing 90 n n CAI CAF FLV sing 91 n y OAC HAC FLV sing 92 n n CAF CAK FLV doub 93 n y CAF HAF FLV sing 94 n n CAK OAE FLV sing 95 n n CAK CAO FLV sing 96 n y OAE HAE FLV sing 97 n n CAO CAL FLV sing 98 n n CAL OAA FLV doub 99 n n CAL CAG FLV sing 100 n n CAG CAJ FLV doub 101 n n CAG HAG FLV sing 102 n n CAJ OAD FLV sing 103 n n OAD HAD FLV sing 104 n n # _atom_sites.entry_id 2D09 _atom_sites.fract_transf_matrix[1][1] 0.018182 _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] 0.014097 _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] 0.009713 _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 HEM A 1 430 430 HEM HEM . C 3 FLV A 1 431 431 FLV FLV . D 3 FLV A 1 432 432 FLV FLV . E 4 OXY A 1 433 433 OXY OXY . 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 100 600 100 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 . F 5 HOH A 230 730 730 HOH HOH . F 5 HOH A 231 731 731 HOH HOH . F 5 HOH A 232 732 732 HOH HOH . F 5 HOH A 233 733 733 HOH HOH . F 5 HOH A 234 734 734 HOH HOH . F 5 HOH A 235 735 735 HOH HOH . F 5 HOH A 236 736 736 HOH HOH . F 5 HOH A 237 737 737 HOH HOH . F 5 HOH A 238 738 738 HOH HOH . F 5 HOH A 239 739 739 HOH HOH . F 5 HOH A 240 740 740 HOH HOH . F 5 HOH A 241 741 741 HOH HOH . F 5 HOH A 242 742 742 HOH HOH . F 5 HOH A 243 743 743 HOH HOH . F 5 HOH A 244 744 744 HOH HOH . F 5 HOH A 245 745 745 HOH HOH . F 5 HOH A 246 746 746 HOH HOH . F 5 HOH A 247 747 747 HOH HOH . F 5 HOH A 248 748 748 HOH HOH . F 5 HOH A 249 749 749 HOH HOH . F 5 HOH A 250 750 750 HOH HOH . F 5 HOH A 251 751 751 HOH HOH . F 5 HOH A 252 752 752 HOH HOH . F 5 HOH A 253 753 753 HOH HOH . F 5 HOH A 254 754 754 HOH HOH . F 5 HOH A 255 755 755 HOH HOH . F 5 HOH A 256 756 756 HOH HOH . F 5 HOH A 257 757 757 HOH HOH . F 5 HOH A 258 758 758 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 O OAB FLV . . . D 3 51.968 74.95 60.192 1 23.87 ? OAB FLV 432 A 1 HETATM 2 C CAM FLV . . . D 3 50.856 74.447 60.366 1 18.43 ? CAM FLV 432 A 1 HETATM 3 C CAN FLV . . . D 3 50.336 73.556 59.432 1 18.89 ? CAN FLV 432 A 1 HETATM 4 C CAH FLV . . . D 3 51.061 73.26 58.283 1 18.23 ? CAH FLV 432 A 1 HETATM 5 C CAI FLV . . . D 3 50.547 72.379 57.336 1 18.29 ? CAI FLV 432 A 1 HETATM 6 O OAC FLV . . . D 3 51.27 72.079 56.226 1 18.22 ? OAC FLV 432 A 1 HETATM 7 C CAF FLV . . . D 3 49.301 71.792 57.545 1 18.25 ? CAF FLV 432 A 1 HETATM 8 C CAK FLV . . . D 3 48.576 72.082 58.697 1 18.56 ? CAK FLV 432 A 1 HETATM 9 O OAE FLV . . . D 3 47.364 71.49 58.883 1 18.99 ? OAE FLV 432 A 1 HETATM 10 C CAO FLV . . . D 3 49.087 72.965 59.644 1 17.48 ? CAO FLV 432 A 1 HETATM 11 C CAL FLV . . . D 3 48.371 73.278 60.797 1 18.84 ? CAL FLV 432 A 1 HETATM 12 O OAA FLV . . . D 3 47.28 72.752 61.019 1 19.55 ? OAA FLV 432 A 1 HETATM 13 C CAG FLV . . . D 3 48.89 74.175 61.725 1 17.76 ? CAG FLV 432 A 1 HETATM 14 C CAJ FLV . . . D 3 50.135 74.763 61.511 1 19.92 ? CAJ FLV 432 A 1 HETATM 15 O OAD FLV . . . D 3 50.644 75.637 62.42 1 19.28 ? OAD FLV 432 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 15 #