data_3D38 # _model_server_result.job_id gH59wj4EDzH6BWPD3XMkrw _model_server_result.datetime_utc '2024-10-14 06:22:55' _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 3d38 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"X","auth_seq_id":705}' # _entry.id 3D38 # _exptl.entry_id 3D38 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 148.2 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description HEPTANE-1,2,3-TRIOL _entity.pdbx_number_of_molecules 3 _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 3D38 _cell.length_a 241.171 _cell.length_b 241.171 _cell.length_c 113.391 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3D38 _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details 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,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA _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 ? 7 P N N ? 7 Q N N ? 7 X 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 B C FME 1 H FME 1 1_555 B N TYR 2 H TYR 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? metalc ? metalc1 A SD MET 74 C MET 74 1_555 L FE HEC . C HEC 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc2 A NE2 HIS 91 C HIS 91 1_555 L FE HEC . C HEC 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? metalc ? metalc3 A SD MET 110 C MET 110 1_555 M FE HEC . C HEC 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc4 A NE2 HIS 124 C HIS 124 1_555 O FE HEC . C HEC 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.927 ? metalc ? metalc5 A NE2 HIS 136 C HIS 136 1_555 M FE HEC . C HEC 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.946 ? metalc ? metalc6 A SD MET 233 C MET 233 1_555 N FE HEC . C HEC 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? metalc ? metalc7 A NE2 HIS 248 C HIS 248 1_555 N FE HEC . C HEC 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.907 ? metalc ? metalc8 A NE2 HIS 309 C HIS 309 1_555 O FE HEC . C HEC 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? metalc ? metalc9 C NE2 HIS 153 L HIS 153 1_555 Z MG BCB . L BCB 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc10 C NE2 HIS 173 L HIS 173 1_555 Y MG BCB . L BCB 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? metalc ? metalc11 C NE2 HIS 190 L HIS 190 1_555 EA FE FE2 . M FE2 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc12 C NE2 HIS 230 L HIS 230 1_555 EA FE FE2 . M FE2 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc13 D NE2 HIS 180 M HIS 180 1_555 KA MG BCB . M BCB 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc14 D NE2 HIS 200 M HIS 200 1_555 LA MG BCB . M BCB 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? metalc ? metalc15 D NE2 HIS 217 M HIS 217 1_555 EA FE FE2 . M FE2 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? metalc ? metalc16 D OE1 GLU 232 M GLU 232 1_555 EA FE FE2 . M FE2 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.43 ? metalc ? metalc17 D OE2 GLU 232 M GLU 232 1_555 EA FE FE2 . M FE2 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc18 D NE2 HIS 264 M HIS 264 1_555 EA FE FE2 . M FE2 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? # _chem_comp.formula 'C7 H16 O3' _chem_comp.formula_weight 148.2 _chem_comp.id HTO _chem_comp.mon_nstd_flag . _chem_comp.name HEPTANE-1,2,3-TRIOL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 C1 O1 HTO sing 547 n n C1 C2 HTO sing 548 n n C1 H11 HTO sing 549 n n C1 H12 HTO sing 550 n n O1 HO1 HTO sing 551 n n C2 O2 HTO sing 552 n n C2 C3 HTO sing 553 n n C2 H2 HTO sing 554 n n O2 HO2 HTO sing 555 n n C3 O3 HTO sing 556 n n C3 C4 HTO sing 557 n n C3 H3 HTO sing 558 n n O3 HO3 HTO sing 559 n n C4 C5 HTO sing 560 n n C4 H41 HTO sing 561 n n C4 H42 HTO sing 562 n n C5 C6 HTO sing 563 n n C5 H51 HTO sing 564 n n C5 H52 HTO sing 565 n n C6 C7 HTO sing 566 n n C6 H61 HTO sing 567 n n C6 H62 HTO sing 568 n n C7 H71 HTO sing 569 n n C7 H72 HTO sing 570 n n C7 H73 HTO sing 571 n n # _atom_sites.entry_id 3D38 _atom_sites.fract_transf_matrix[1][1] 0.004146 _atom_sites.fract_transf_matrix[1][2] 0.002394 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004788 _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] 0.008819 _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 5 SO4 C 1 808 808 SO4 SO4 . F 5 SO4 C 1 809 809 SO4 SO4 . G 5 SO4 C 1 810 810 SO4 SO4 . H 5 SO4 C 1 811 811 SO4 SO4 . I 5 SO4 C 1 813 813 SO4 SO4 . J 5 SO4 C 1 814 814 SO4 SO4 . K 5 SO4 C 1 815 815 SO4 SO4 . L 6 HEC C 1 401 401 HEC HEC . M 6 HEC C 1 402 402 HEC HEC . N 6 HEC C 1 403 403 HEC HEC . O 6 HEC C 1 404 404 HEC HEC . P 7 HTO C 1 706 706 HTO HTO . Q 7 HTO C 1 707 707 HTO HTO . R 5 SO4 H 1 803 803 SO4 SO4 . S 5 SO4 H 1 806 806 SO4 SO4 . T 5 SO4 H 1 807 807 SO4 SO4 . U 5 SO4 H 1 812 812 SO4 SO4 . V 8 LDA H 1 701 701 LDA LDA . W 8 LDA H 1 703 703 LDA LDA . X 7 HTO H 1 705 705 HTO HTO . Y 9 BCB L 1 400 400 BCB BCB . Z 9 BCB L 1 401 401 BCB BCB . AA 10 BPB L 1 402 402 BPB BPB . BA 11 UQ1 L 1 502 502 UQ1 UQ1 . CA 11 UQ1 L 1 503 503 UQ1 UQ1 . DA 8 LDA L 1 702 702 LDA LDA . EA 12 FE2 M 1 500 500 FE2 FE2 . FA 5 SO4 M 1 801 801 SO4 SO4 . GA 5 SO4 M 1 802 802 SO4 SO4 . HA 5 SO4 M 1 804 804 SO4 SO4 . IA 5 SO4 M 1 805 805 SO4 SO4 . JA 13 MQ9 M 1 501 501 MQ9 MQ9 . KA 9 BCB M 1 400 400 BCB BCB . LA 9 BCB M 1 401 401 BCB BCB . MA 10 BPB M 1 402 402 BPB BPB . NA 14 NS5 M 1 600 600 NS5 NS5 . OA 8 LDA M 1 704 704 LDA LDA . PA 15 HOH C 1 816 503 HOH HOH . PA 15 HOH C 2 817 504 HOH HOH . PA 15 HOH C 3 818 505 HOH HOH . PA 15 HOH C 4 819 508 HOH HOH . PA 15 HOH C 5 820 512 HOH HOH . PA 15 HOH C 6 821 522 HOH HOH . PA 15 HOH C 7 822 527 HOH HOH . PA 15 HOH C 8 823 528 HOH HOH . PA 15 HOH C 9 824 529 HOH HOH . PA 15 HOH C 10 825 535 HOH HOH . PA 15 HOH C 11 826 538 HOH HOH . PA 15 HOH C 12 827 540 HOH HOH . PA 15 HOH C 13 828 542 HOH HOH . PA 15 HOH C 14 829 544 HOH HOH . PA 15 HOH C 15 830 545 HOH HOH . PA 15 HOH C 16 831 546 HOH HOH . PA 15 HOH C 17 832 547 HOH HOH . PA 15 HOH C 18 833 548 HOH HOH . PA 15 HOH C 19 834 563 HOH HOH . PA 15 HOH C 20 835 567 HOH HOH . PA 15 HOH C 21 836 578 HOH HOH . PA 15 HOH C 22 837 588 HOH HOH . PA 15 HOH C 23 838 597 HOH HOH . PA 15 HOH C 24 839 598 HOH HOH . PA 15 HOH C 25 840 602 HOH HOH . PA 15 HOH C 26 841 605 HOH HOH . PA 15 HOH C 27 842 615 HOH HOH . PA 15 HOH C 28 843 616 HOH HOH . PA 15 HOH C 29 844 618 HOH HOH . PA 15 HOH C 30 845 623 HOH HOH . PA 15 HOH C 31 846 628 HOH HOH . PA 15 HOH C 32 847 632 HOH HOH . PA 15 HOH C 33 848 634 HOH HOH . PA 15 HOH C 34 849 668 HOH HOH . PA 15 HOH C 35 850 669 HOH HOH . PA 15 HOH C 36 851 697 HOH HOH . PA 15 HOH C 37 852 708 HOH HOH . PA 15 HOH C 38 853 731 HOH HOH . PA 15 HOH C 39 854 738 HOH HOH . PA 15 HOH C 40 855 790 HOH HOH . PA 15 HOH C 41 856 814 HOH HOH . PA 15 HOH C 42 857 821 HOH HOH . PA 15 HOH C 43 858 825 HOH HOH . PA 15 HOH C 44 859 827 HOH HOH . PA 15 HOH C 45 860 901 HOH HOH . PA 15 HOH C 46 861 671 HOH HOH . PA 15 HOH C 47 862 701 HOH HOH . QA 15 HOH H 1 505 505 HOH HOH . QA 15 HOH H 2 511 511 HOH HOH . QA 15 HOH H 3 512 512 HOH HOH . QA 15 HOH H 4 518 518 HOH HOH . QA 15 HOH H 5 526 526 HOH HOH . QA 15 HOH H 6 541 541 HOH HOH . QA 15 HOH H 7 542 542 HOH HOH . QA 15 HOH H 8 555 555 HOH HOH . QA 15 HOH H 9 562 562 HOH HOH . QA 15 HOH H 10 568 568 HOH HOH . QA 15 HOH H 11 574 574 HOH HOH . QA 15 HOH H 12 581 581 HOH HOH . QA 15 HOH H 13 587 587 HOH HOH . QA 15 HOH H 14 605 605 HOH HOH . QA 15 HOH H 15 623 623 HOH HOH . QA 15 HOH H 16 628 628 HOH HOH . QA 15 HOH H 17 637 637 HOH HOH . QA 15 HOH H 18 641 641 HOH HOH . QA 15 HOH H 19 642 642 HOH HOH . QA 15 HOH H 20 656 656 HOH HOH . QA 15 HOH H 21 658 658 HOH HOH . QA 15 HOH H 22 661 661 HOH HOH . QA 15 HOH H 23 901 901 HOH HOH . QA 15 HOH H 24 902 902 HOH HOH . QA 15 HOH H 25 903 903 HOH HOH . QA 15 HOH H 26 904 904 HOH HOH . QA 15 HOH H 27 905 905 HOH HOH . QA 15 HOH H 28 906 906 HOH HOH . RA 15 HOH L 1 513 513 HOH HOH . RA 15 HOH L 2 571 571 HOH HOH . RA 15 HOH L 3 573 573 HOH HOH . RA 15 HOH L 4 580 580 HOH HOH . RA 15 HOH L 5 599 599 HOH HOH . RA 15 HOH L 6 602 602 HOH HOH . RA 15 HOH L 7 603 603 HOH HOH . RA 15 HOH L 8 604 604 HOH HOH . RA 15 HOH L 9 605 605 HOH HOH . RA 15 HOH L 10 606 606 HOH HOH . RA 15 HOH L 11 607 607 HOH HOH . RA 15 HOH L 12 608 608 HOH HOH . RA 15 HOH L 13 609 609 HOH HOH . RA 15 HOH L 14 610 610 HOH HOH . RA 15 HOH L 15 611 611 HOH HOH . RA 15 HOH L 16 612 612 HOH HOH . RA 15 HOH L 17 614 614 HOH HOH . RA 15 HOH L 18 615 615 HOH HOH . RA 15 HOH L 19 616 616 HOH HOH . RA 15 HOH L 20 618 618 HOH HOH . RA 15 HOH L 21 619 619 HOH HOH . RA 15 HOH L 22 622 622 HOH HOH . RA 15 HOH L 23 625 625 HOH HOH . RA 15 HOH L 24 626 626 HOH HOH . RA 15 HOH L 25 629 629 HOH HOH . RA 15 HOH L 26 630 630 HOH HOH . RA 15 HOH L 27 633 633 HOH HOH . RA 15 HOH L 28 638 638 HOH HOH . RA 15 HOH L 29 643 643 HOH HOH . RA 15 HOH L 30 646 646 HOH HOH . RA 15 HOH L 31 648 648 HOH HOH . RA 15 HOH L 32 662 662 HOH HOH . RA 15 HOH L 33 666 666 HOH HOH . RA 15 HOH L 34 684 684 HOH HOH . RA 15 HOH L 35 695 695 HOH HOH . RA 15 HOH L 36 703 703 HOH HOH . RA 15 HOH L 37 704 704 HOH HOH . RA 15 HOH L 38 901 901 HOH HOH . SA 15 HOH M 1 806 509 HOH HOH . SA 15 HOH M 2 807 510 HOH HOH . SA 15 HOH M 3 808 642 HOH HOH . SA 15 HOH M 4 809 601 HOH HOH . SA 15 HOH M 5 810 623 HOH HOH . SA 15 HOH M 6 811 644 HOH HOH . SA 15 HOH M 7 812 654 HOH HOH . SA 15 HOH M 8 813 668 HOH HOH . SA 15 HOH M 9 814 701 HOH HOH . SA 15 HOH M 10 815 702 HOH HOH . SA 15 HOH M 11 816 708 HOH HOH . SA 15 HOH M 12 817 711 HOH HOH . SA 15 HOH M 13 818 712 HOH HOH . SA 15 HOH M 14 819 713 HOH HOH . SA 15 HOH M 15 820 714 HOH HOH . SA 15 HOH M 16 821 715 HOH HOH . SA 15 HOH M 17 822 716 HOH HOH . SA 15 HOH M 18 823 720 HOH HOH . SA 15 HOH M 19 824 721 HOH HOH . SA 15 HOH M 20 825 722 HOH HOH . SA 15 HOH M 21 826 723 HOH HOH . SA 15 HOH M 22 827 724 HOH HOH . SA 15 HOH M 23 828 725 HOH HOH . SA 15 HOH M 24 829 727 HOH HOH . SA 15 HOH M 25 830 746 HOH HOH . SA 15 HOH M 26 831 747 HOH HOH . SA 15 HOH M 27 832 754 HOH HOH . SA 15 HOH M 28 833 755 HOH HOH . SA 15 HOH M 29 834 756 HOH HOH . SA 15 HOH M 30 835 757 HOH HOH . SA 15 HOH M 31 836 772 HOH HOH . SA 15 HOH M 32 837 774 HOH HOH . SA 15 HOH M 33 838 783 HOH HOH . SA 15 HOH M 34 839 802 HOH HOH . SA 15 HOH M 35 840 810 HOH HOH . SA 15 HOH M 36 841 819 HOH HOH . SA 15 HOH M 37 842 829 HOH HOH . SA 15 HOH M 38 843 834 HOH HOH . SA 15 HOH M 39 844 845 HOH HOH . SA 15 HOH M 40 845 848 HOH HOH . SA 15 HOH M 41 846 901 HOH HOH . SA 15 HOH M 42 847 902 HOH HOH . SA 15 HOH M 43 848 903 HOH HOH . SA 15 HOH M 44 849 904 HOH HOH . SA 15 HOH M 45 850 905 HOH HOH . SA 15 HOH M 46 851 906 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 C C1 HTO . . . X 7 -60.248 93.475 107.366 0.5 58.16 ? C1 HTO 705 H 1 HETATM 2 O O1 HTO . . . X 7 -60.876 94.474 106.572 0.5 56.56 ? O1 HTO 705 H 1 HETATM 3 C C2 HTO . . . X 7 -61.171 92.273 107.38 0.5 60.16 ? C2 HTO 705 H 1 HETATM 4 O O2 HTO . . . X 7 -60.388 91.067 107.413 0.5 61.04 ? O2 HTO 705 H 1 HETATM 5 C C3 HTO . . . X 7 -62.158 92.358 108.562 0.5 60.52 ? C3 HTO 705 H 1 HETATM 6 O O3 HTO . . . X 7 -61.496 92.96 109.683 0.5 58.7 ? O3 HTO 705 H 1 HETATM 7 C C4 HTO . . . X 7 -62.769 90.989 108.959 0.5 61.46 ? C4 HTO 705 H 1 HETATM 8 C C5 HTO . . . X 7 -64.163 90.729 108.33 0.5 60.97 ? C5 HTO 705 H 1 HETATM 9 C C6 HTO . . . X 7 -64.903 89.545 108.98 0.5 59.46 ? C6 HTO 705 H 1 HETATM 10 C C7 HTO . . . X 7 -66.193 89.97 109.665 0.5 57.5 ? C7 HTO 705 H 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 10 #