data_4EBD # _model_server_result.job_id vjjEagieBnjq-tQ4qV-Hsg _model_server_result.datetime_utc '2024-11-22 16:20:57' _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 4ebd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":506}' # _entry.id 4EBD # _exptl.entry_id 4EBD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _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 4EBD _cell.length_a 97.776 _cell.length_b 97.776 _cell.length_c 202.739 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4EBD _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,K,L _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 ? 6 H N N ? 6 I 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 O3' DC 6 P DC 6 1_555 B P DOC 7 P DOC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.604 ? metalc ? metalc1 A OD2 ASP 34 A ASP 34 1_555 E CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.884 ? metalc ? metalc2 A OD1 ASP 34 A ASP 34 1_555 F CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.747 ? metalc ? metalc3 A O LEU 35 A LEU 35 1_555 F CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.766 ? metalc ? metalc4 A OE2 GLU 127 A GLU 127 1_555 E CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.903 ? metalc ? metalc5 A O LYS 237 A LYS 237 1_555 G CA CA . A CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.914 ? metalc ? metalc6 A O ILE 239 A ILE 239 1_555 G CA CA . A CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.191 ? metalc ? metalc7 A O ILE 242 A ILE 242 1_555 G CA CA . A CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.989 ? metalc ? metalc8 D OAF 0OJ . A 0OJ 501 1_555 F CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.706 ? metalc ? metalc9 D OAI 0OJ . A 0OJ 501 1_555 F CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.846 ? metalc ? metalc10 D OAC 0OJ . A 0OJ 501 1_555 F CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.122 ? metalc ? metalc11 D OAT 0OJ . A 0OJ 501 1_555 F CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.183 ? metalc ? metalc12 E CA CA . A CA 502 1_555 J O HOH . A HOH 651 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.989 ? metalc ? metalc13 E CA CA . A CA 502 1_555 J O HOH . A HOH 662 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.014 ? metalc ? metalc14 E CA CA . A CA 502 1_555 J O HOH . A HOH 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.028 ? metalc ? metalc15 F CA CA . A CA 503 1_555 J O HOH . A HOH 722 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.153 ? metalc ? metalc16 G CA CA . A CA 504 1_555 J O HOH . A HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.064 ? metalc ? metalc17 G CA CA . A CA 504 1_555 J O HOH . A HOH 708 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.013 ? metalc ? metalc18 G CA CA . A CA 504 1_555 B OP1 DC 6 P DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.896 ? hydrog WATSON-CRICK hydrog1 B N1 DA 1 P DA 1 1_555 C N3 DT 9 T DT 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N6 DA 1 P DA 1 1_555 C O4 DT 9 T DT 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B N1 DG 2 P DG 2 1_555 C N3 DC 8 T DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N2 DG 2 P DG 2 1_555 C O2 DC 8 T DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O6 DG 2 P DG 2 1_555 C N4 DC 8 T DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N1 DG 3 P DG 3 1_555 C N3 DC 7 T DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N2 DG 3 P DG 3 1_555 C O2 DC 7 T DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B O6 DG 3 P DG 3 1_555 C N4 DC 7 T DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N1 DA 4 P DA 4 1_555 C N3 DT 6 T DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N6 DA 4 P DA 4 1_555 C O4 DT 6 T DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N3 DC 5 P DC 5 1_555 C N1 DG 5 T DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N4 DC 5 P DC 5 1_555 C O6 DG 5 T DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B O2 DC 5 P DC 5 1_555 C N2 DG 5 T DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N3 DC 6 P DC 6 1_555 C N1 DG 4 T DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N4 DC 6 P DC 6 1_555 C O6 DG 4 T DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B O2 DC 6 P DC 6 1_555 C N2 DG 4 T DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N3 DOC 7 P DOC 7 1_555 C N1 DG 3 T DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N4 DOC 7 P DOC 7 1_555 C O6 DG 3 T DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B O2 DOC 7 P DOC 7 1_555 C N2 DG 3 T DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # 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 GOL sing 364 n n C1 C2 GOL sing 365 n n C1 H11 GOL sing 366 n n C1 H12 GOL sing 367 n n O1 HO1 GOL sing 368 n n C2 O2 GOL sing 369 n n C2 C3 GOL sing 370 n n C2 H2 GOL sing 371 n n O2 HO2 GOL sing 372 n n C3 O3 GOL sing 373 n n C3 H31 GOL sing 374 n n C3 H32 GOL sing 375 n n O3 HO3 GOL sing 376 n n # _atom_sites.entry_id 4EBD _atom_sites.fract_transf_matrix[1][1] 0.010227 _atom_sites.fract_transf_matrix[1][2] 0.005905 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01181 _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] 0.004932 _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 D 4 0OJ A 1 501 501 0OJ 0OJ . E 5 CA A 1 502 502 CA CA . F 5 CA A 1 503 503 CA CA . G 5 CA A 1 504 504 CA CA . H 6 GOL A 1 505 505 GOL GOL . I 6 GOL A 1 506 506 GOL GOL . J 7 HOH A 1 601 601 HOH HOH . J 7 HOH A 2 602 602 HOH HOH . J 7 HOH A 3 603 603 HOH HOH . J 7 HOH A 4 604 604 HOH HOH . J 7 HOH A 5 605 605 HOH HOH . J 7 HOH A 6 606 606 HOH HOH . J 7 HOH A 7 607 607 HOH HOH . J 7 HOH A 8 608 608 HOH HOH . J 7 HOH A 9 609 609 HOH HOH . J 7 HOH A 10 610 610 HOH HOH . J 7 HOH A 11 611 611 HOH HOH . J 7 HOH A 12 612 612 HOH HOH . J 7 HOH A 13 613 613 HOH HOH . J 7 HOH A 14 614 614 HOH HOH . J 7 HOH A 15 615 615 HOH HOH . J 7 HOH A 16 616 616 HOH HOH . J 7 HOH A 17 617 617 HOH HOH . J 7 HOH A 18 618 618 HOH HOH . J 7 HOH A 19 619 619 HOH HOH . J 7 HOH A 20 620 620 HOH HOH . J 7 HOH A 21 621 621 HOH HOH . J 7 HOH A 22 622 622 HOH HOH . J 7 HOH A 23 623 623 HOH HOH . J 7 HOH A 24 624 624 HOH HOH . J 7 HOH A 25 625 625 HOH HOH . J 7 HOH A 26 626 626 HOH HOH . J 7 HOH A 27 627 627 HOH HOH . J 7 HOH A 28 628 628 HOH HOH . J 7 HOH A 29 629 629 HOH HOH . J 7 HOH A 30 630 630 HOH HOH . J 7 HOH A 31 631 631 HOH HOH . J 7 HOH A 32 632 632 HOH HOH . J 7 HOH A 33 633 633 HOH HOH . J 7 HOH A 34 634 634 HOH HOH . J 7 HOH A 35 635 635 HOH HOH . J 7 HOH A 36 636 636 HOH HOH . J 7 HOH A 37 637 637 HOH HOH . J 7 HOH A 38 638 638 HOH HOH . J 7 HOH A 39 639 639 HOH HOH . J 7 HOH A 40 640 640 HOH HOH . J 7 HOH A 41 641 641 HOH HOH . J 7 HOH A 42 642 642 HOH HOH . J 7 HOH A 43 643 643 HOH HOH . J 7 HOH A 44 644 644 HOH HOH . J 7 HOH A 45 645 645 HOH HOH . J 7 HOH A 46 646 646 HOH HOH . J 7 HOH A 47 647 647 HOH HOH . J 7 HOH A 48 648 648 HOH HOH . J 7 HOH A 49 649 649 HOH HOH . J 7 HOH A 50 650 650 HOH HOH . J 7 HOH A 51 651 651 HOH HOH . J 7 HOH A 52 652 652 HOH HOH . J 7 HOH A 53 653 653 HOH HOH . J 7 HOH A 54 654 654 HOH HOH . J 7 HOH A 55 655 655 HOH HOH . J 7 HOH A 56 656 656 HOH HOH . J 7 HOH A 57 657 657 HOH HOH . J 7 HOH A 58 658 658 HOH HOH . J 7 HOH A 59 659 659 HOH HOH . J 7 HOH A 60 660 660 HOH HOH . J 7 HOH A 61 661 661 HOH HOH . J 7 HOH A 62 662 662 HOH HOH . J 7 HOH A 63 663 663 HOH HOH . J 7 HOH A 64 664 664 HOH HOH . J 7 HOH A 65 665 665 HOH HOH . J 7 HOH A 66 666 666 HOH HOH . J 7 HOH A 67 667 667 HOH HOH . J 7 HOH A 68 668 668 HOH HOH . J 7 HOH A 69 669 669 HOH HOH . J 7 HOH A 70 670 671 HOH HOH . J 7 HOH A 71 671 672 HOH HOH . J 7 HOH A 72 672 673 HOH HOH . J 7 HOH A 73 673 674 HOH HOH . J 7 HOH A 74 674 675 HOH HOH . J 7 HOH A 75 675 676 HOH HOH . J 7 HOH A 76 676 677 HOH HOH . J 7 HOH A 77 677 678 HOH HOH . J 7 HOH A 78 678 679 HOH HOH . J 7 HOH A 79 679 680 HOH HOH . J 7 HOH A 80 680 681 HOH HOH . J 7 HOH A 81 681 682 HOH HOH . J 7 HOH A 82 682 683 HOH HOH . J 7 HOH A 83 683 684 HOH HOH . J 7 HOH A 84 684 685 HOH HOH . J 7 HOH A 85 685 686 HOH HOH . J 7 HOH A 86 686 687 HOH HOH . J 7 HOH A 87 687 688 HOH HOH . J 7 HOH A 88 688 689 HOH HOH . J 7 HOH A 89 689 690 HOH HOH . J 7 HOH A 90 690 691 HOH HOH . J 7 HOH A 91 691 692 HOH HOH . J 7 HOH A 92 692 693 HOH HOH . J 7 HOH A 93 693 694 HOH HOH . J 7 HOH A 94 694 695 HOH HOH . J 7 HOH A 95 695 696 HOH HOH . J 7 HOH A 96 696 697 HOH HOH . J 7 HOH A 97 697 698 HOH HOH . J 7 HOH A 98 698 699 HOH HOH . J 7 HOH A 99 699 700 HOH HOH . J 7 HOH A 100 700 701 HOH HOH . J 7 HOH A 101 701 702 HOH HOH . J 7 HOH A 102 702 703 HOH HOH . J 7 HOH A 103 703 704 HOH HOH . J 7 HOH A 104 704 705 HOH HOH . J 7 HOH A 105 705 706 HOH HOH . J 7 HOH A 106 706 707 HOH HOH . J 7 HOH A 107 707 708 HOH HOH . J 7 HOH A 108 708 709 HOH HOH . J 7 HOH A 109 709 710 HOH HOH . J 7 HOH A 110 710 711 HOH HOH . J 7 HOH A 111 711 712 HOH HOH . J 7 HOH A 112 712 713 HOH HOH . J 7 HOH A 113 713 714 HOH HOH . J 7 HOH A 114 714 715 HOH HOH . J 7 HOH A 115 715 716 HOH HOH . J 7 HOH A 116 716 717 HOH HOH . J 7 HOH A 117 717 718 HOH HOH . J 7 HOH A 118 718 719 HOH HOH . J 7 HOH A 119 719 720 HOH HOH . J 7 HOH A 120 720 721 HOH HOH . J 7 HOH A 121 721 722 HOH HOH . J 7 HOH A 122 722 723 HOH HOH . K 7 HOH P 1 101 724 HOH HOH . K 7 HOH P 2 102 101 HOH HOH . K 7 HOH P 3 103 102 HOH HOH . K 7 HOH P 4 104 103 HOH HOH . K 7 HOH P 5 105 104 HOH HOH . K 7 HOH P 6 106 105 HOH HOH . K 7 HOH P 7 107 101 HOH HOH . L 7 HOH T 1 101 670 HOH HOH . L 7 HOH T 2 102 725 HOH HOH . L 7 HOH T 3 103 726 HOH HOH . L 7 HOH T 4 104 102 HOH HOH . L 7 HOH T 5 105 103 HOH HOH . L 7 HOH T 6 106 104 HOH HOH . L 7 HOH T 7 107 105 HOH HOH . L 7 HOH T 8 108 106 HOH HOH . L 7 HOH T 9 109 107 HOH HOH . L 7 HOH T 10 110 108 HOH HOH . L 7 HOH T 11 111 109 HOH HOH . L 7 HOH T 12 112 110 HOH HOH . L 7 HOH T 13 113 111 HOH HOH . L 7 HOH T 14 114 112 HOH HOH . L 7 HOH T 15 115 113 HOH HOH . L 7 HOH T 16 116 114 HOH HOH . L 7 HOH T 17 117 115 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 GOL . . . I 6 1.134 35.866 23.146 1 56.15 ? C1 GOL 506 A 1 HETATM 2 O O1 GOL . . . I 6 0.002 35.164 23.624 1 58.72 ? O1 GOL 506 A 1 HETATM 3 C C2 GOL . . . I 6 1.241 35.65 21.643 1 53.21 ? C2 GOL 506 A 1 HETATM 4 O O2 GOL . . . I 6 1.905 36.733 21.018 1 61.17 ? O2 GOL 506 A 1 HETATM 5 C C3 GOL . . . I 6 -0.135 35.351 21.044 1 56.17 ? C3 GOL 506 A 1 HETATM 6 O O3 GOL . . . I 6 -0.012 34.991 19.682 1 56.84 ? O3 GOL 506 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 265 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 6 #