data_4K5J # _model_server_result.job_id 2UHcaGhMnTtZQxUmJqVcng _model_server_result.datetime_utc '2024-11-23 03:05:35' _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 4k5j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":506}' # _entry.id 4K5J # _exptl.entry_id 4K5J _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 90 _cell.entry_id 4K5J _cell.length_a 57.813 _cell.length_b 106.289 _cell.length_c 156.72 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4K5J _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 PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,M,N,O,P,Q _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 O 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 A C VAL 344 A VAL 383 1_555 A N CAS 345 A CAS 384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale2 A C CAS 345 A CAS 384 1_555 A N MET 346 A MET 385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale3 B C VAL 344 B VAL 383 1_555 B N CAS 345 B CAS 384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale4 B C CAS 345 B CAS 384 1_555 B N MET 346 B MET 385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? metalc ? metalc1 A SG CYS 57 A CYS 96 1_555 I ZN ZN . A ZN 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.579 ? metalc ? metalc2 A SG CYS 62 A CYS 101 1_555 I ZN ZN . A ZN 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.552 ? metalc ? metalc3 A SG CYS 147 A CYS 186 1_555 C FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? metalc ? metalc4 I ZN ZN . A ZN 507 1_555 B SG CYS 57 B CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.518 ? metalc ? metalc5 I ZN ZN . A ZN 507 1_555 B SG CYS 62 B CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? metalc ? metalc6 B SG CYS 147 B CYS 186 1_555 J FE HEM . B HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? # _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 156 n n C1 C2 GOL sing 157 n n C1 H11 GOL sing 158 n n C1 H12 GOL sing 159 n n O1 HO1 GOL sing 160 n n C2 O2 GOL sing 161 n n C2 C3 GOL sing 162 n n C2 H2 GOL sing 163 n n O2 HO2 GOL sing 164 n n C3 O3 GOL sing 165 n n C3 H31 GOL sing 166 n n C3 H32 GOL sing 167 n n O3 HO3 GOL sing 168 n n # _atom_sites.entry_id 4K5J _atom_sites.fract_transf_matrix[1][1] 0.017297 _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] 0.009408 _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] 0.006381 _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 2 HEM A 1 501 500 HEM HEM . D 3 H4B A 1 502 600 H4B BH4 . E 4 Q14 A 1 503 800 Q14 Q14 . F 5 ACT A 1 504 860 ACT ACT . G 5 ACT A 1 505 861 ACT ACT . H 6 GOL A 1 506 880 GOL GOL . I 7 ZN A 1 507 900 ZN ZN . J 2 HEM B 1 501 500 HEM HEM . K 3 H4B B 1 502 600 H4B BH4 . L 4 Q14 B 1 503 800 Q14 Q14 . M 5 ACT B 1 504 860 ACT ACT . N 5 ACT B 1 505 861 ACT ACT . O 6 GOL B 1 506 880 GOL GOL . P 8 HOH A 1 601 1 HOH HOH . P 8 HOH A 2 602 2 HOH HOH . P 8 HOH A 3 603 5 HOH HOH . P 8 HOH A 4 604 6 HOH HOH . P 8 HOH A 5 605 8 HOH HOH . P 8 HOH A 6 606 10 HOH HOH . P 8 HOH A 7 607 11 HOH HOH . P 8 HOH A 8 608 12 HOH HOH . P 8 HOH A 9 609 13 HOH HOH . P 8 HOH A 10 610 14 HOH HOH . P 8 HOH A 11 611 15 HOH HOH . P 8 HOH A 12 612 16 HOH HOH . P 8 HOH A 13 613 19 HOH HOH . P 8 HOH A 14 614 21 HOH HOH . P 8 HOH A 15 615 23 HOH HOH . P 8 HOH A 16 616 24 HOH HOH . P 8 HOH A 17 617 25 HOH HOH . P 8 HOH A 18 618 26 HOH HOH . P 8 HOH A 19 619 27 HOH HOH . P 8 HOH A 20 620 28 HOH HOH . P 8 HOH A 21 621 29 HOH HOH . P 8 HOH A 22 622 32 HOH HOH . P 8 HOH A 23 623 33 HOH HOH . P 8 HOH A 24 624 34 HOH HOH . P 8 HOH A 25 625 35 HOH HOH . P 8 HOH A 26 626 38 HOH HOH . P 8 HOH A 27 627 40 HOH HOH . P 8 HOH A 28 628 45 HOH HOH . P 8 HOH A 29 629 47 HOH HOH . P 8 HOH A 30 630 48 HOH HOH . P 8 HOH A 31 631 49 HOH HOH . P 8 HOH A 32 632 53 HOH HOH . P 8 HOH A 33 633 60 HOH HOH . P 8 HOH A 34 634 61 HOH HOH . P 8 HOH A 35 635 64 HOH HOH . P 8 HOH A 36 636 66 HOH HOH . P 8 HOH A 37 637 67 HOH HOH . P 8 HOH A 38 638 68 HOH HOH . P 8 HOH A 39 639 70 HOH HOH . P 8 HOH A 40 640 71 HOH HOH . P 8 HOH A 41 641 73 HOH HOH . P 8 HOH A 42 642 78 HOH HOH . P 8 HOH A 43 643 79 HOH HOH . P 8 HOH A 44 644 81 HOH HOH . P 8 HOH A 45 645 82 HOH HOH . P 8 HOH A 46 646 84 HOH HOH . P 8 HOH A 47 647 85 HOH HOH . P 8 HOH A 48 648 87 HOH HOH . P 8 HOH A 49 649 88 HOH HOH . P 8 HOH A 50 650 89 HOH HOH . P 8 HOH A 51 651 90 HOH HOH . P 8 HOH A 52 652 92 HOH HOH . P 8 HOH A 53 653 93 HOH HOH . P 8 HOH A 54 654 94 HOH HOH . P 8 HOH A 55 655 95 HOH HOH . P 8 HOH A 56 656 97 HOH HOH . P 8 HOH A 57 657 98 HOH HOH . P 8 HOH A 58 658 99 HOH HOH . P 8 HOH A 59 659 100 HOH HOH . P 8 HOH A 60 660 101 HOH HOH . P 8 HOH A 61 661 102 HOH HOH . P 8 HOH A 62 662 106 HOH HOH . P 8 HOH A 63 663 107 HOH HOH . P 8 HOH A 64 664 108 HOH HOH . P 8 HOH A 65 665 109 HOH HOH . P 8 HOH A 66 666 110 HOH HOH . P 8 HOH A 67 667 111 HOH HOH . P 8 HOH A 68 668 126 HOH HOH . P 8 HOH A 69 669 127 HOH HOH . P 8 HOH A 70 670 128 HOH HOH . P 8 HOH A 71 671 129 HOH HOH . P 8 HOH A 72 672 130 HOH HOH . P 8 HOH A 73 673 132 HOH HOH . P 8 HOH A 74 674 133 HOH HOH . P 8 HOH A 75 675 134 HOH HOH . P 8 HOH A 76 676 135 HOH HOH . P 8 HOH A 77 677 136 HOH HOH . P 8 HOH A 78 678 137 HOH HOH . P 8 HOH A 79 679 138 HOH HOH . P 8 HOH A 80 680 139 HOH HOH . P 8 HOH A 81 681 140 HOH HOH . P 8 HOH A 82 682 141 HOH HOH . P 8 HOH A 83 683 142 HOH HOH . P 8 HOH A 84 684 143 HOH HOH . P 8 HOH A 85 685 144 HOH HOH . P 8 HOH A 86 686 145 HOH HOH . P 8 HOH A 87 687 146 HOH HOH . P 8 HOH A 88 688 147 HOH HOH . P 8 HOH A 89 689 148 HOH HOH . P 8 HOH A 90 690 149 HOH HOH . P 8 HOH A 91 691 150 HOH HOH . P 8 HOH A 92 692 151 HOH HOH . P 8 HOH A 93 693 152 HOH HOH . P 8 HOH A 94 694 153 HOH HOH . P 8 HOH A 95 695 154 HOH HOH . P 8 HOH A 96 696 155 HOH HOH . P 8 HOH A 97 697 156 HOH HOH . P 8 HOH A 98 698 157 HOH HOH . P 8 HOH A 99 699 159 HOH HOH . P 8 HOH A 100 700 160 HOH HOH . P 8 HOH A 101 701 161 HOH HOH . P 8 HOH A 102 702 184 HOH HOH . P 8 HOH A 103 703 188 HOH HOH . P 8 HOH A 104 704 189 HOH HOH . P 8 HOH A 105 705 190 HOH HOH . P 8 HOH A 106 706 191 HOH HOH . P 8 HOH A 107 707 192 HOH HOH . P 8 HOH A 108 708 193 HOH HOH . P 8 HOH A 109 709 194 HOH HOH . P 8 HOH A 110 710 195 HOH HOH . P 8 HOH A 111 711 196 HOH HOH . P 8 HOH A 112 712 197 HOH HOH . P 8 HOH A 113 713 199 HOH HOH . P 8 HOH A 114 714 200 HOH HOH . P 8 HOH A 115 715 202 HOH HOH . P 8 HOH A 116 716 203 HOH HOH . Q 8 HOH B 1 601 3 HOH HOH . Q 8 HOH B 2 602 4 HOH HOH . Q 8 HOH B 3 603 7 HOH HOH . Q 8 HOH B 4 604 9 HOH HOH . Q 8 HOH B 5 605 17 HOH HOH . Q 8 HOH B 6 606 18 HOH HOH . Q 8 HOH B 7 607 20 HOH HOH . Q 8 HOH B 8 608 22 HOH HOH . Q 8 HOH B 9 609 30 HOH HOH . Q 8 HOH B 10 610 31 HOH HOH . Q 8 HOH B 11 611 36 HOH HOH . Q 8 HOH B 12 612 37 HOH HOH . Q 8 HOH B 13 613 39 HOH HOH . Q 8 HOH B 14 614 41 HOH HOH . Q 8 HOH B 15 615 42 HOH HOH . Q 8 HOH B 16 616 43 HOH HOH . Q 8 HOH B 17 617 44 HOH HOH . Q 8 HOH B 18 618 46 HOH HOH . Q 8 HOH B 19 619 50 HOH HOH . Q 8 HOH B 20 620 51 HOH HOH . Q 8 HOH B 21 621 52 HOH HOH . Q 8 HOH B 22 622 54 HOH HOH . Q 8 HOH B 23 623 55 HOH HOH . Q 8 HOH B 24 624 56 HOH HOH . Q 8 HOH B 25 625 57 HOH HOH . Q 8 HOH B 26 626 58 HOH HOH . Q 8 HOH B 27 627 59 HOH HOH . Q 8 HOH B 28 628 62 HOH HOH . Q 8 HOH B 29 629 63 HOH HOH . Q 8 HOH B 30 630 65 HOH HOH . Q 8 HOH B 31 631 69 HOH HOH . Q 8 HOH B 32 632 72 HOH HOH . Q 8 HOH B 33 633 74 HOH HOH . Q 8 HOH B 34 634 75 HOH HOH . Q 8 HOH B 35 635 76 HOH HOH . Q 8 HOH B 36 636 77 HOH HOH . Q 8 HOH B 37 637 80 HOH HOH . Q 8 HOH B 38 638 83 HOH HOH . Q 8 HOH B 39 639 86 HOH HOH . Q 8 HOH B 40 640 91 HOH HOH . Q 8 HOH B 41 641 96 HOH HOH . Q 8 HOH B 42 642 103 HOH HOH . Q 8 HOH B 43 643 104 HOH HOH . Q 8 HOH B 44 644 105 HOH HOH . Q 8 HOH B 45 645 112 HOH HOH . Q 8 HOH B 46 646 113 HOH HOH . Q 8 HOH B 47 647 114 HOH HOH . Q 8 HOH B 48 648 115 HOH HOH . Q 8 HOH B 49 649 116 HOH HOH . Q 8 HOH B 50 650 117 HOH HOH . Q 8 HOH B 51 651 118 HOH HOH . Q 8 HOH B 52 652 119 HOH HOH . Q 8 HOH B 53 653 120 HOH HOH . Q 8 HOH B 54 654 121 HOH HOH . Q 8 HOH B 55 655 122 HOH HOH . Q 8 HOH B 56 656 123 HOH HOH . Q 8 HOH B 57 657 124 HOH HOH . Q 8 HOH B 58 658 125 HOH HOH . Q 8 HOH B 59 659 131 HOH HOH . Q 8 HOH B 60 660 158 HOH HOH . Q 8 HOH B 61 661 162 HOH HOH . Q 8 HOH B 62 662 163 HOH HOH . Q 8 HOH B 63 663 164 HOH HOH . Q 8 HOH B 64 664 165 HOH HOH . Q 8 HOH B 65 665 166 HOH HOH . Q 8 HOH B 66 666 167 HOH HOH . Q 8 HOH B 67 667 168 HOH HOH . Q 8 HOH B 68 668 169 HOH HOH . Q 8 HOH B 69 669 170 HOH HOH . Q 8 HOH B 70 670 171 HOH HOH . Q 8 HOH B 71 671 172 HOH HOH . Q 8 HOH B 72 672 173 HOH HOH . Q 8 HOH B 73 673 174 HOH HOH . Q 8 HOH B 74 674 175 HOH HOH . Q 8 HOH B 75 675 176 HOH HOH . Q 8 HOH B 76 676 177 HOH HOH . Q 8 HOH B 77 677 178 HOH HOH . Q 8 HOH B 78 678 179 HOH HOH . Q 8 HOH B 79 679 180 HOH HOH . Q 8 HOH B 80 680 181 HOH HOH . Q 8 HOH B 81 681 182 HOH HOH . Q 8 HOH B 82 682 183 HOH HOH . Q 8 HOH B 83 683 185 HOH HOH . Q 8 HOH B 84 684 186 HOH HOH . Q 8 HOH B 85 685 187 HOH HOH . Q 8 HOH B 86 686 198 HOH HOH . Q 8 HOH B 87 687 201 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 . . . H 6 13.543 17.576 42.367 1 78.51 ? C1 GOL 506 A 1 HETATM 2 O O1 GOL . . . H 6 13.882 16.266 41.881 1 77.29 ? O1 GOL 506 A 1 HETATM 3 C C2 GOL . . . H 6 12.319 17.319 43.235 1 79.97 ? C2 GOL 506 A 1 HETATM 4 O O2 GOL . . . H 6 11.26 16.946 42.339 1 67.17 ? O2 GOL 506 A 1 HETATM 5 C C3 GOL . . . H 6 11.934 18.499 44.154 1 77.33 ? C3 GOL 506 A 1 HETATM 6 O O3 GOL . . . H 6 11.508 18.041 45.474 1 56.98 ? O3 GOL 506 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 6 #