data_1POY # _model_server_result.job_id unqqIhSAbJRF1RfmhXkb-g _model_server_result.datetime_utc '2024-12-26 10:12:44' _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 1poy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":400}' # _entry.id 1POY # _exptl.entry_id 1POY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 145.246 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SPERMIDINE _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 107.6 _cell.angle_gamma 90 _cell.entry_id 1POY _cell.length_a 145.3 _cell.length_b 69.1 _cell.length_c 72.5 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1POY _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_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,E,F,I,J 1 1 C,D,G,H,K,L 2 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 ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H N N # _chem_comp.formula 'C7 H19 N3' _chem_comp.formula_weight 145.246 _chem_comp.id SPD _chem_comp.mon_nstd_flag . _chem_comp.name SPERMIDINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE;PA(34) # 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 SPD sing 256 n n N1 HN11 SPD sing 257 n n N1 HN12 SPD sing 258 n n C2 C3 SPD sing 259 n n C2 H21 SPD sing 260 n n C2 H22 SPD sing 261 n n C3 C4 SPD sing 262 n n C3 H31 SPD sing 263 n n C3 H32 SPD sing 264 n n C4 C5 SPD sing 265 n n C4 H41 SPD sing 266 n n C4 H42 SPD sing 267 n n C5 N6 SPD sing 268 n n C5 H51 SPD sing 269 n n C5 H52 SPD sing 270 n n N6 C7 SPD sing 271 n n N6 HN6 SPD sing 272 n n C7 C8 SPD sing 273 n n C7 H71 SPD sing 274 n n C7 H72 SPD sing 275 n n C8 C9 SPD sing 276 n n C8 H81 SPD sing 277 n n C8 H82 SPD sing 278 n n C9 N10 SPD sing 279 n n C9 H91 SPD sing 280 n n C9 H92 SPD sing 281 n n N10 H101 SPD sing 282 n n N10 H102 SPD sing 283 n n # _atom_sites.entry_id 1POY _atom_sites.fract_transf_matrix[1][1] 0.006882 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002183 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014472 _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] 0.01447 _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 E 2 SPD 1 1 400 400 SPD SPD . F 2 SPD 2 1 400 400 SPD SPD . G 2 SPD 3 1 400 400 SPD SPD . H 2 SPD 4 1 400 400 SPD SPD . I 3 HOH 1 1 500 500 HOH HOH . I 3 HOH 1 2 501 501 HOH HOH . I 3 HOH 1 3 502 502 HOH HOH . I 3 HOH 1 4 503 503 HOH HOH . I 3 HOH 1 5 504 504 HOH HOH . I 3 HOH 1 6 505 505 HOH HOH . I 3 HOH 1 7 508 508 HOH HOH . I 3 HOH 1 8 509 509 HOH HOH . I 3 HOH 1 9 510 510 HOH HOH . I 3 HOH 1 10 511 511 HOH HOH . I 3 HOH 1 11 512 512 HOH HOH . I 3 HOH 1 12 513 513 HOH HOH . I 3 HOH 1 13 514 514 HOH HOH . I 3 HOH 1 14 517 517 HOH HOH . I 3 HOH 1 15 518 518 HOH HOH . I 3 HOH 1 16 519 519 HOH HOH . I 3 HOH 1 17 520 520 HOH HOH . I 3 HOH 1 18 523 523 HOH HOH . I 3 HOH 1 19 524 524 HOH HOH . I 3 HOH 1 20 526 526 HOH HOH . I 3 HOH 1 21 527 527 HOH HOH . I 3 HOH 1 22 529 529 HOH HOH . I 3 HOH 1 23 530 530 HOH HOH . I 3 HOH 1 24 534 534 HOH HOH . I 3 HOH 1 25 583 583 HOH HOH . I 3 HOH 1 26 584 584 HOH HOH . I 3 HOH 1 27 585 585 HOH HOH . I 3 HOH 1 28 586 586 HOH HOH . I 3 HOH 1 29 587 587 HOH HOH . I 3 HOH 1 30 588 588 HOH HOH . I 3 HOH 1 31 589 589 HOH HOH . I 3 HOH 1 32 590 590 HOH HOH . I 3 HOH 1 33 591 591 HOH HOH . I 3 HOH 1 34 592 592 HOH HOH . I 3 HOH 1 35 593 593 HOH HOH . I 3 HOH 1 36 594 594 HOH HOH . I 3 HOH 1 37 595 595 HOH HOH . I 3 HOH 1 38 596 596 HOH HOH . I 3 HOH 1 39 597 597 HOH HOH . I 3 HOH 1 40 599 599 HOH HOH . I 3 HOH 1 41 600 600 HOH HOH . I 3 HOH 1 42 601 601 HOH HOH . I 3 HOH 1 43 602 602 HOH HOH . I 3 HOH 1 44 604 604 HOH HOH . I 3 HOH 1 45 611 611 HOH HOH . I 3 HOH 1 46 612 612 HOH HOH . I 3 HOH 1 47 613 613 HOH HOH . I 3 HOH 1 48 615 615 HOH HOH . I 3 HOH 1 49 618 618 HOH HOH . I 3 HOH 1 50 619 619 HOH HOH . I 3 HOH 1 51 620 620 HOH HOH . I 3 HOH 1 52 625 625 HOH HOH . I 3 HOH 1 53 627 627 HOH HOH . I 3 HOH 1 54 629 629 HOH HOH . I 3 HOH 1 55 634 634 HOH HOH . I 3 HOH 1 56 636 636 HOH HOH . I 3 HOH 1 57 646 646 HOH HOH . I 3 HOH 1 58 647 647 HOH HOH . I 3 HOH 1 59 649 649 HOH HOH . J 3 HOH 2 1 506 506 HOH HOH . J 3 HOH 2 2 507 507 HOH HOH . J 3 HOH 2 3 515 515 HOH HOH . J 3 HOH 2 4 516 516 HOH HOH . J 3 HOH 2 5 521 521 HOH HOH . J 3 HOH 2 6 522 522 HOH HOH . J 3 HOH 2 7 525 525 HOH HOH . J 3 HOH 2 8 528 528 HOH HOH . J 3 HOH 2 9 531 531 HOH HOH . J 3 HOH 2 10 532 532 HOH HOH . J 3 HOH 2 11 533 533 HOH HOH . J 3 HOH 2 12 535 535 HOH HOH . J 3 HOH 2 13 536 536 HOH HOH . J 3 HOH 2 14 537 537 HOH HOH . J 3 HOH 2 15 538 538 HOH HOH . J 3 HOH 2 16 548 548 HOH HOH . J 3 HOH 2 17 598 598 HOH HOH . J 3 HOH 2 18 603 603 HOH HOH . J 3 HOH 2 19 605 605 HOH HOH . J 3 HOH 2 20 606 606 HOH HOH . J 3 HOH 2 21 607 607 HOH HOH . J 3 HOH 2 22 608 608 HOH HOH . J 3 HOH 2 23 609 609 HOH HOH . J 3 HOH 2 24 610 610 HOH HOH . J 3 HOH 2 25 614 614 HOH HOH . J 3 HOH 2 26 616 616 HOH HOH . J 3 HOH 2 27 617 617 HOH HOH . J 3 HOH 2 28 621 621 HOH HOH . J 3 HOH 2 29 622 622 HOH HOH . J 3 HOH 2 30 623 623 HOH HOH . J 3 HOH 2 31 624 624 HOH HOH . J 3 HOH 2 32 626 626 HOH HOH . J 3 HOH 2 33 628 628 HOH HOH . J 3 HOH 2 34 630 630 HOH HOH . J 3 HOH 2 35 631 631 HOH HOH . J 3 HOH 2 36 632 632 HOH HOH . J 3 HOH 2 37 633 633 HOH HOH . J 3 HOH 2 38 635 635 HOH HOH . J 3 HOH 2 39 637 637 HOH HOH . J 3 HOH 2 40 638 638 HOH HOH . J 3 HOH 2 41 639 639 HOH HOH . J 3 HOH 2 42 640 640 HOH HOH . J 3 HOH 2 43 641 641 HOH HOH . J 3 HOH 2 44 642 642 HOH HOH . J 3 HOH 2 45 643 643 HOH HOH . J 3 HOH 2 46 644 644 HOH HOH . J 3 HOH 2 47 645 645 HOH HOH . J 3 HOH 2 48 648 648 HOH HOH . J 3 HOH 2 49 650 650 HOH HOH . J 3 HOH 2 50 651 651 HOH HOH . J 3 HOH 2 51 652 652 HOH HOH . J 3 HOH 2 52 653 653 HOH HOH . J 3 HOH 2 53 654 654 HOH HOH . K 3 HOH 3 1 550 550 HOH HOH . K 3 HOH 3 2 551 551 HOH HOH . K 3 HOH 3 3 553 553 HOH HOH . K 3 HOH 3 4 556 556 HOH HOH . K 3 HOH 3 5 557 557 HOH HOH . K 3 HOH 3 6 558 558 HOH HOH . K 3 HOH 3 7 559 559 HOH HOH . K 3 HOH 3 8 560 560 HOH HOH . K 3 HOH 3 9 563 563 HOH HOH . K 3 HOH 3 10 564 564 HOH HOH . K 3 HOH 3 11 565 565 HOH HOH . K 3 HOH 3 12 566 566 HOH HOH . K 3 HOH 3 13 567 567 HOH HOH . K 3 HOH 3 14 568 568 HOH HOH . K 3 HOH 3 15 569 569 HOH HOH . K 3 HOH 3 16 570 570 HOH HOH . K 3 HOH 3 17 571 571 HOH HOH . K 3 HOH 3 18 572 572 HOH HOH . K 3 HOH 3 19 575 575 HOH HOH . K 3 HOH 3 20 576 576 HOH HOH . K 3 HOH 3 21 577 577 HOH HOH . K 3 HOH 3 22 578 578 HOH HOH . K 3 HOH 3 23 579 579 HOH HOH . K 3 HOH 3 24 580 580 HOH HOH . K 3 HOH 3 25 581 581 HOH HOH . K 3 HOH 3 26 582 582 HOH HOH . K 3 HOH 3 27 666 666 HOH HOH . K 3 HOH 3 28 673 673 HOH HOH . K 3 HOH 3 29 676 676 HOH HOH . K 3 HOH 3 30 679 679 HOH HOH . K 3 HOH 3 31 680 680 HOH HOH . K 3 HOH 3 32 681 681 HOH HOH . K 3 HOH 3 33 682 682 HOH HOH . K 3 HOH 3 34 684 684 HOH HOH . K 3 HOH 3 35 685 685 HOH HOH . K 3 HOH 3 36 686 686 HOH HOH . K 3 HOH 3 37 687 687 HOH HOH . K 3 HOH 3 38 688 688 HOH HOH . K 3 HOH 3 39 689 689 HOH HOH . K 3 HOH 3 40 690 690 HOH HOH . K 3 HOH 3 41 693 693 HOH HOH . K 3 HOH 3 42 697 697 HOH HOH . K 3 HOH 3 43 698 698 HOH HOH . K 3 HOH 3 44 699 699 HOH HOH . K 3 HOH 3 45 700 700 HOH HOH . K 3 HOH 3 46 701 701 HOH HOH . K 3 HOH 3 47 702 702 HOH HOH . K 3 HOH 3 48 704 704 HOH HOH . K 3 HOH 3 49 705 705 HOH HOH . K 3 HOH 3 50 706 706 HOH HOH . K 3 HOH 3 51 707 707 HOH HOH . K 3 HOH 3 52 715 715 HOH HOH . K 3 HOH 3 53 716 716 HOH HOH . K 3 HOH 3 54 717 717 HOH HOH . K 3 HOH 3 55 718 718 HOH HOH . K 3 HOH 3 56 719 719 HOH HOH . K 3 HOH 3 57 720 720 HOH HOH . K 3 HOH 3 58 721 721 HOH HOH . K 3 HOH 3 59 722 722 HOH HOH . K 3 HOH 3 60 723 723 HOH HOH . K 3 HOH 3 61 724 724 HOH HOH . K 3 HOH 3 62 725 725 HOH HOH . K 3 HOH 3 63 726 726 HOH HOH . K 3 HOH 3 64 728 728 HOH HOH . K 3 HOH 3 65 729 729 HOH HOH . K 3 HOH 3 66 730 730 HOH HOH . K 3 HOH 3 67 731 731 HOH HOH . K 3 HOH 3 68 732 732 HOH HOH . K 3 HOH 3 69 733 733 HOH HOH . K 3 HOH 3 70 734 734 HOH HOH . K 3 HOH 3 71 735 735 HOH HOH . L 3 HOH 4 1 539 539 HOH HOH . L 3 HOH 4 2 540 540 HOH HOH . L 3 HOH 4 3 541 541 HOH HOH . L 3 HOH 4 4 542 542 HOH HOH . L 3 HOH 4 5 543 543 HOH HOH . L 3 HOH 4 6 544 544 HOH HOH . L 3 HOH 4 7 545 545 HOH HOH . L 3 HOH 4 8 546 546 HOH HOH . L 3 HOH 4 9 547 547 HOH HOH . L 3 HOH 4 10 549 549 HOH HOH . L 3 HOH 4 11 552 552 HOH HOH . L 3 HOH 4 12 554 554 HOH HOH . L 3 HOH 4 13 555 555 HOH HOH . L 3 HOH 4 14 561 561 HOH HOH . L 3 HOH 4 15 562 562 HOH HOH . L 3 HOH 4 16 573 573 HOH HOH . L 3 HOH 4 17 574 574 HOH HOH . L 3 HOH 4 18 655 655 HOH HOH . L 3 HOH 4 19 656 656 HOH HOH . L 3 HOH 4 20 657 657 HOH HOH . L 3 HOH 4 21 658 658 HOH HOH . L 3 HOH 4 22 659 659 HOH HOH . L 3 HOH 4 23 660 660 HOH HOH . L 3 HOH 4 24 661 661 HOH HOH . L 3 HOH 4 25 662 662 HOH HOH . L 3 HOH 4 26 663 663 HOH HOH . L 3 HOH 4 27 664 664 HOH HOH . L 3 HOH 4 28 665 665 HOH HOH . L 3 HOH 4 29 667 667 HOH HOH . L 3 HOH 4 30 668 668 HOH HOH . L 3 HOH 4 31 669 669 HOH HOH . L 3 HOH 4 32 670 670 HOH HOH . L 3 HOH 4 33 671 671 HOH HOH . L 3 HOH 4 34 672 672 HOH HOH . L 3 HOH 4 35 674 674 HOH HOH . L 3 HOH 4 36 675 675 HOH HOH . L 3 HOH 4 37 677 677 HOH HOH . L 3 HOH 4 38 678 678 HOH HOH . L 3 HOH 4 39 683 683 HOH HOH . L 3 HOH 4 40 691 691 HOH HOH . L 3 HOH 4 41 692 692 HOH HOH . L 3 HOH 4 42 694 694 HOH HOH . L 3 HOH 4 43 695 695 HOH HOH . L 3 HOH 4 44 696 696 HOH HOH . L 3 HOH 4 45 703 703 HOH HOH . L 3 HOH 4 46 708 708 HOH HOH . L 3 HOH 4 47 709 709 HOH HOH . L 3 HOH 4 48 710 710 HOH HOH . L 3 HOH 4 49 712 712 HOH HOH . L 3 HOH 4 50 713 713 HOH HOH . L 3 HOH 4 51 714 714 HOH HOH . L 3 HOH 4 52 727 727 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 SPD . . . H 2 -53.343 0.544 13.243 1 22.87 ? N1 SPD 400 4 1 HETATM 2 C C2 SPD . . . H 2 -52.281 -0.485 13.261 1 26.17 ? C2 SPD 400 4 1 HETATM 3 C C3 SPD . . . H 2 -51.423 -0.576 12.01 1 22.36 ? C3 SPD 400 4 1 HETATM 4 C C4 SPD . . . H 2 -50.61 -1.861 12.076 1 22.41 ? C4 SPD 400 4 1 HETATM 5 C C5 SPD . . . H 2 -49.096 -1.632 12.074 1 21.15 ? C5 SPD 400 4 1 HETATM 6 N N6 SPD . . . H 2 -48.58 -2.945 11.589 1 21.65 ? N6 SPD 400 4 1 HETATM 7 C C7 SPD . . . H 2 -47.42 -3.324 12.239 1 20.56 ? C7 SPD 400 4 1 HETATM 8 C C8 SPD . . . H 2 -46.079 -2.973 11.612 1 20.88 ? C8 SPD 400 4 1 HETATM 9 C C9 SPD . . . H 2 -45.009 -2.72 12.704 1 14.88 ? C9 SPD 400 4 1 HETATM 10 N N10 SPD . . . H 2 -43.833 -2.019 12.167 1 14.64 ? N10 SPD 400 4 1 # _model_server_stats.io_time_ms 37 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 10 #