data_6ZFA # _model_server_result.job_id 380QvTR_5xoBXLbeVr5YOA _model_server_result.datetime_utc '2024-11-13 08:52:49' _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 6zfa # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":506}' # _entry.id 6ZFA # _exptl.entry_id 6ZFA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 147.172 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE _entity.pdbx_number_of_molecules 1 _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 6ZFA _cell.length_a 127.891 _cell.length_b 127.891 _cell.length_c 48.352 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6ZFA _symmetry.cell_setting ? _symmetry.Int_Tables_number 171 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 62' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id H _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 MAN _pdbx_entity_branch_link.comp_id_2 MAN _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O2 _pdbx_entity_branch_link.leaving_atom_id_2 HO2 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B MAN 1 A 1 MAN AiA 509 MAN 2 n B MAN 2 A 2 MAN AhA 508 MAN # 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 H O3 IFM . AAA IFM 506 1_555 I C1 GLC . AAA GLC 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale2 B O2 MAN . A MAN 1 1_555 B C1 MAN . A MAN 2 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.469 ? covale ? covale3 B O2 MAN . A MAN 1 1_555 B C1 MAN . A MAN 2 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.45 ? metalc ? metalc1 A OE1 GLU 77 AAA GLU 157 1_555 D MG MG . AAA MG 502 5_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc2 A OG1 THR 176 AAA THR 256 1_555 E W1 TEW . AAA TEW 503 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.539 ? metalc ? metalc3 D MG MG . AAA MG 502 1_555 J O HOH . AAA HOH 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc4 D MG MG . AAA MG 502 1_555 J O HOH . AAA HOH 611 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc5 D MG MG . AAA MG 502 1_555 J O HOH . AAA HOH 627 6_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? metalc ? metalc6 D MG MG . AAA MG 502 1_555 J O HOH . AAA HOH 681 6_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc7 D MG MG . AAA MG 502 1_555 J O HOH . AAA HOH 698 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? # _chem_comp.formula 'C6 H13 N O3' _chem_comp.formula_weight 147.172 _chem_comp.id IFM _chem_comp.mon_nstd_flag . _chem_comp.name 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Afegostat;isofagomine;(3R,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-3,4-DIOL # 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 O4 C4 IFM sing 209 n n O4 H4 IFM sing 210 n n C4 C3 IFM sing 211 n n C4 C5 IFM sing 212 n n C4 HA IFM sing 213 n n C3 O3 IFM sing 214 n n C3 C2 IFM sing 215 n n C3 H3 IFM sing 216 n n O3 HB IFM sing 217 n n C2 N IFM sing 218 n n C2 H2C1 IFM sing 219 n n C2 H2C2 IFM sing 220 n n N C1 IFM sing 221 n n N H IFM sing 222 n n C1 C5 IFM sing 223 n n C1 H1C1 IFM sing 224 n n C1 H1C2 IFM sing 225 n n C5 C6 IFM sing 226 n n C5 H5 IFM sing 227 n n C6 O6 IFM sing 228 n n C6 H6C1 IFM sing 229 n n C6 H6C2 IFM sing 230 n n O6 H6 IFM sing 231 n n # _atom_sites.entry_id 6ZFA _atom_sites.fract_transf_matrix[1][1] 0.007819 _atom_sites.fract_transf_matrix[1][2] 0.004514 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009029 _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] 0.020682 _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 C 3 EPE AAA 1 501 501 EPE EPE . D 4 MG AAA 1 502 502 MG MG . E 5 TEW AAA 1 503 503 TEW TEW . F 5 TEW AAA 1 504 504 TEW TEW . G 5 TEW AAA 1 505 505 TEW TEW . H 6 IFM AAA 1 506 507 IFM IFM . I 7 GLC AAA 1 507 506 GLC GLC . J 8 HOH AAA 1 601 726 HOH HOH . J 8 HOH AAA 2 602 626 HOH HOH . J 8 HOH AAA 3 603 611 HOH HOH . J 8 HOH AAA 4 604 643 HOH HOH . J 8 HOH AAA 5 605 671 HOH HOH . J 8 HOH AAA 6 606 665 HOH HOH . J 8 HOH AAA 7 607 639 HOH HOH . J 8 HOH AAA 8 608 731 HOH HOH . J 8 HOH AAA 9 609 690 HOH HOH . J 8 HOH AAA 10 610 631 HOH HOH . J 8 HOH AAA 11 611 691 HOH HOH . J 8 HOH AAA 12 612 711 HOH HOH . J 8 HOH AAA 13 613 658 HOH HOH . J 8 HOH AAA 14 614 676 HOH HOH . J 8 HOH AAA 15 615 695 HOH HOH . J 8 HOH AAA 16 616 649 HOH HOH . J 8 HOH AAA 17 617 716 HOH HOH . J 8 HOH AAA 18 618 719 HOH HOH . J 8 HOH AAA 19 619 650 HOH HOH . J 8 HOH AAA 20 620 648 HOH HOH . J 8 HOH AAA 21 621 698 HOH HOH . J 8 HOH AAA 22 622 700 HOH HOH . J 8 HOH AAA 23 623 646 HOH HOH . J 8 HOH AAA 24 624 705 HOH HOH . J 8 HOH AAA 25 625 736 HOH HOH . J 8 HOH AAA 26 626 627 HOH HOH . J 8 HOH AAA 27 627 694 HOH HOH . J 8 HOH AAA 28 628 685 HOH HOH . J 8 HOH AAA 29 629 681 HOH HOH . J 8 HOH AAA 30 630 602 HOH HOH . J 8 HOH AAA 31 631 727 HOH HOH . J 8 HOH AAA 32 632 651 HOH HOH . J 8 HOH AAA 33 633 688 HOH HOH . J 8 HOH AAA 34 634 630 HOH HOH . J 8 HOH AAA 35 635 724 HOH HOH . J 8 HOH AAA 36 636 714 HOH HOH . J 8 HOH AAA 37 637 604 HOH HOH . J 8 HOH AAA 38 638 689 HOH HOH . J 8 HOH AAA 39 639 674 HOH HOH . J 8 HOH AAA 40 640 721 HOH HOH . J 8 HOH AAA 41 641 644 HOH HOH . J 8 HOH AAA 42 642 703 HOH HOH . J 8 HOH AAA 43 643 638 HOH HOH . J 8 HOH AAA 44 644 623 HOH HOH . J 8 HOH AAA 45 645 717 HOH HOH . J 8 HOH AAA 46 646 614 HOH HOH . J 8 HOH AAA 47 647 608 HOH HOH . J 8 HOH AAA 48 648 708 HOH HOH . J 8 HOH AAA 49 649 622 HOH HOH . J 8 HOH AAA 50 650 637 HOH HOH . J 8 HOH AAA 51 651 629 HOH HOH . J 8 HOH AAA 52 652 641 HOH HOH . J 8 HOH AAA 53 653 640 HOH HOH . J 8 HOH AAA 54 654 684 HOH HOH . J 8 HOH AAA 55 655 605 HOH HOH . J 8 HOH AAA 56 656 667 HOH HOH . J 8 HOH AAA 57 657 673 HOH HOH . J 8 HOH AAA 58 658 699 HOH HOH . J 8 HOH AAA 59 659 668 HOH HOH . J 8 HOH AAA 60 660 610 HOH HOH . J 8 HOH AAA 61 661 618 HOH HOH . J 8 HOH AAA 62 662 707 HOH HOH . J 8 HOH AAA 63 663 697 HOH HOH . J 8 HOH AAA 64 664 620 HOH HOH . J 8 HOH AAA 65 665 634 HOH HOH . J 8 HOH AAA 66 666 720 HOH HOH . J 8 HOH AAA 67 667 609 HOH HOH . J 8 HOH AAA 68 668 723 HOH HOH . J 8 HOH AAA 69 669 661 HOH HOH . J 8 HOH AAA 70 670 653 HOH HOH . J 8 HOH AAA 71 671 635 HOH HOH . J 8 HOH AAA 72 672 625 HOH HOH . J 8 HOH AAA 73 673 647 HOH HOH . J 8 HOH AAA 74 674 652 HOH HOH . J 8 HOH AAA 75 675 616 HOH HOH . J 8 HOH AAA 76 676 633 HOH HOH . J 8 HOH AAA 77 677 704 HOH HOH . J 8 HOH AAA 78 678 734 HOH HOH . J 8 HOH AAA 79 679 683 HOH HOH . J 8 HOH AAA 80 680 666 HOH HOH . J 8 HOH AAA 81 681 693 HOH HOH . J 8 HOH AAA 82 682 619 HOH HOH . J 8 HOH AAA 83 683 678 HOH HOH . J 8 HOH AAA 84 684 696 HOH HOH . J 8 HOH AAA 85 685 603 HOH HOH . J 8 HOH AAA 86 686 617 HOH HOH . J 8 HOH AAA 87 687 725 HOH HOH . J 8 HOH AAA 88 688 722 HOH HOH . J 8 HOH AAA 89 689 735 HOH HOH . J 8 HOH AAA 90 690 679 HOH HOH . J 8 HOH AAA 91 691 636 HOH HOH . J 8 HOH AAA 92 692 702 HOH HOH . J 8 HOH AAA 93 693 675 HOH HOH . J 8 HOH AAA 94 694 642 HOH HOH . J 8 HOH AAA 95 695 718 HOH HOH . J 8 HOH AAA 96 696 656 HOH HOH . J 8 HOH AAA 97 697 612 HOH HOH . J 8 HOH AAA 98 698 692 HOH HOH . J 8 HOH AAA 99 699 607 HOH HOH . J 8 HOH AAA 100 700 615 HOH HOH . J 8 HOH AAA 101 701 659 HOH HOH . J 8 HOH AAA 102 702 606 HOH HOH . J 8 HOH AAA 103 703 621 HOH HOH . J 8 HOH AAA 104 704 657 HOH HOH . J 8 HOH AAA 105 705 706 HOH HOH . J 8 HOH AAA 106 706 682 HOH HOH . J 8 HOH AAA 107 707 732 HOH HOH . J 8 HOH AAA 108 708 713 HOH HOH . J 8 HOH AAA 109 709 729 HOH HOH . J 8 HOH AAA 110 710 709 HOH HOH . J 8 HOH AAA 111 711 680 HOH HOH . J 8 HOH AAA 112 712 715 HOH HOH . J 8 HOH AAA 113 713 655 HOH HOH . J 8 HOH AAA 114 714 645 HOH HOH . J 8 HOH AAA 115 715 728 HOH HOH . J 8 HOH AAA 116 716 632 HOH HOH . J 8 HOH AAA 117 717 664 HOH HOH . J 8 HOH AAA 118 718 670 HOH HOH . J 8 HOH AAA 119 719 701 HOH HOH . J 8 HOH AAA 120 720 686 HOH HOH . J 8 HOH AAA 121 721 663 HOH HOH . J 8 HOH AAA 122 722 712 HOH HOH . J 8 HOH AAA 123 723 624 HOH HOH . J 8 HOH AAA 124 724 613 HOH HOH . J 8 HOH AAA 125 725 662 HOH HOH . J 8 HOH AAA 126 726 660 HOH HOH . J 8 HOH AAA 127 727 628 HOH HOH . J 8 HOH AAA 128 728 654 HOH HOH . J 8 HOH AAA 129 729 669 HOH HOH . J 8 HOH AAA 130 730 733 HOH HOH . J 8 HOH AAA 131 731 601 HOH HOH . J 8 HOH AAA 132 732 710 HOH HOH . J 8 HOH AAA 133 733 677 HOH HOH . J 8 HOH AAA 134 734 730 HOH HOH . J 8 HOH AAA 135 735 687 HOH HOH . J 8 HOH AAA 136 736 672 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 O4 IFM . . . H 6 49.374 21.488 -8.019 1 16.52 ? O4 IFM 506 AAA 1 HETATM 2 C C4 IFM . . . H 6 49.162 20.106 -7.736 1 16.18 ? C4 IFM 506 AAA 1 HETATM 3 C C3 IFM . . . H 6 50.547 19.482 -7.448 1 15.72 ? C3 IFM 506 AAA 1 HETATM 4 O O3 IFM . . . H 6 51.348 19.588 -8.626 1 16.03 ? O3 IFM 506 AAA 1 HETATM 5 C C2 IFM . . . H 6 50.418 18.019 -6.997 1 15.94 ? C2 IFM 506 AAA 1 HETATM 6 N N IFM . . . H 6 49.435 17.94 -5.943 1 16.36 ? N IFM 506 AAA 1 HETATM 7 C C1 IFM . . . H 6 48.113 18.473 -6.158 1 15.88 ? C1 IFM 506 AAA 1 HETATM 8 C C5 IFM . . . H 6 48.204 19.938 -6.546 1 16.05 ? C5 IFM 506 AAA 1 HETATM 9 C C6 IFM . . . H 6 46.784 20.458 -6.749 1 16.3 ? C6 IFM 506 AAA 1 HETATM 10 O O6 IFM . . . H 6 46.11 19.857 -7.868 1 16.09 ? O6 IFM 506 AAA 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 332 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 10 #