data_3H3K # _model_server_result.job_id 1RE5Ow8KTCI6aaqCqOFwDw _model_server_result.datetime_utc '2024-11-25 22:19:41' _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 3h3k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":540}' # _entry.id 3H3K # _exptl.entry_id 3H3K _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 118.174 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (4S)-2-METHYL-2,4-PENTANEDIOL _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 3H3K _cell.length_a 85.09 _cell.length_b 129.3 _cell.length_c 49.13 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3H3K _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _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 _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 F N N ? 6 G N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 BGC GLC C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BGC BGC C1 O1 . O4 HO4 . sing 3 ? 2 4 3 BGC BGC C1 O1 . O4 HO4 . 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 GLC 1 B 1 GLC X 604 GLC 2 n B BGC 2 B 2 BGC X 603 GLC 2 n B BGC 3 B 3 BGC X 602 GLC 2 n B BGC 4 B 4 BGC X 601 GLC # 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 O4 GLC . B GLC 1 1_555 B C1 BGC . B BGC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale2 B O4 BGC . B BGC 2 1_555 B C1 BGC . B BGC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale3 B O4 BGC . B BGC 3 1_555 B C1 BGC . B BGC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? metalc ? metalc1 A SG CYS 104 A CYS 104 1_555 E ZN ZN . A ZN 539 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc2 A SG CYS 121 A CYS 121 1_555 E ZN ZN . A ZN 539 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? metalc ? metalc3 A ND1 HIS 122 A HIS 122 1_555 E ZN ZN . A ZN 539 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc4 A NE2 HIS 142 A HIS 142 1_555 E ZN ZN . A ZN 539 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc5 A OD2 ASP 302 A ASP 302 1_555 D CA CA . A CA 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc6 A O GLU 304 A GLU 304 1_555 D CA CA . A CA 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc7 A OD1 ASP 307 A ASP 307 1_555 D CA CA . A CA 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.55 ? metalc ? metalc8 A OD2 ASP 307 A ASP 307 1_555 D CA CA . A CA 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.555 ? metalc ? metalc9 A OE1 GLU 308 A GLU 308 1_555 D CA CA . A CA 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.636 ? metalc ? metalc10 A OE2 GLU 308 A GLU 308 1_555 D CA CA . A CA 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc11 A O ALA 344 A ALA 344 1_555 D CA CA . A CA 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? metalc ? metalc12 D CA CA . A CA 538 1_555 H O HOH . A HOH 594 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? # _chem_comp.formula 'C6 H14 O2' _chem_comp.formula_weight 118.174 _chem_comp.id MPD _chem_comp.mon_nstd_flag . _chem_comp.name (4S)-2-METHYL-2,4-PENTANEDIOL _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 C2 MPD sing 285 n n C1 H11 MPD sing 286 n n C1 H12 MPD sing 287 n n C1 H13 MPD sing 288 n n C2 O2 MPD sing 289 n n C2 CM MPD sing 290 n n C2 C3 MPD sing 291 n n O2 HO2 MPD sing 292 n n CM HM1 MPD sing 293 n n CM HM2 MPD sing 294 n n CM HM3 MPD sing 295 n n C3 C4 MPD sing 296 n n C3 H31 MPD sing 297 n n C3 H32 MPD sing 298 n n C4 O4 MPD sing 299 n n C4 C5 MPD sing 300 n n C4 H4 MPD sing 301 n n O4 HO4 MPD sing 302 n n C5 H51 MPD sing 303 n n C5 H52 MPD sing 304 n n C5 H53 MPD sing 305 n n # _atom_sites.entry_id 3H3K _atom_sites.fract_transf_matrix[1][1] 0.011752 _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] 0.007734 _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] 0.020354 _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 BGC A 1 605 605 BGC GLC . D 4 CA A 1 538 1 CA CA . E 5 ZN A 1 539 2 ZN ZN . F 6 MPD A 1 540 540 MPD MPD . G 6 MPD A 1 541 541 MPD MPD . H 7 HOH A 1 542 1 HOH HOH . H 7 HOH A 2 543 2 HOH HOH . H 7 HOH A 3 544 3 HOH HOH . H 7 HOH A 4 545 4 HOH HOH . H 7 HOH A 5 546 5 HOH HOH . H 7 HOH A 6 547 6 HOH HOH . H 7 HOH A 7 548 7 HOH HOH . H 7 HOH A 8 549 8 HOH HOH . H 7 HOH A 9 550 9 HOH HOH . H 7 HOH A 10 551 10 HOH HOH . H 7 HOH A 11 552 11 HOH HOH . H 7 HOH A 12 553 12 HOH HOH . H 7 HOH A 13 554 13 HOH HOH . H 7 HOH A 14 555 14 HOH HOH . H 7 HOH A 15 556 15 HOH HOH . H 7 HOH A 16 557 16 HOH HOH . H 7 HOH A 17 558 17 HOH HOH . H 7 HOH A 18 559 18 HOH HOH . H 7 HOH A 19 560 19 HOH HOH . H 7 HOH A 20 561 20 HOH HOH . H 7 HOH A 21 562 21 HOH HOH . H 7 HOH A 22 563 22 HOH HOH . H 7 HOH A 23 564 23 HOH HOH . H 7 HOH A 24 565 24 HOH HOH . H 7 HOH A 25 566 25 HOH HOH . H 7 HOH A 26 567 26 HOH HOH . H 7 HOH A 27 568 27 HOH HOH . H 7 HOH A 28 569 28 HOH HOH . H 7 HOH A 29 570 29 HOH HOH . H 7 HOH A 30 571 30 HOH HOH . H 7 HOH A 31 572 31 HOH HOH . H 7 HOH A 32 573 32 HOH HOH . H 7 HOH A 33 574 33 HOH HOH . H 7 HOH A 34 575 34 HOH HOH . H 7 HOH A 35 576 35 HOH HOH . H 7 HOH A 36 577 36 HOH HOH . H 7 HOH A 37 578 37 HOH HOH . H 7 HOH A 38 579 38 HOH HOH . H 7 HOH A 39 580 39 HOH HOH . H 7 HOH A 40 581 40 HOH HOH . H 7 HOH A 41 582 41 HOH HOH . H 7 HOH A 42 583 42 HOH HOH . H 7 HOH A 43 584 43 HOH HOH . H 7 HOH A 44 585 44 HOH HOH . H 7 HOH A 45 586 45 HOH HOH . H 7 HOH A 46 587 46 HOH HOH . H 7 HOH A 47 588 47 HOH HOH . H 7 HOH A 48 589 48 HOH HOH . H 7 HOH A 49 590 49 HOH HOH . H 7 HOH A 50 591 50 HOH HOH . H 7 HOH A 51 592 51 HOH HOH . H 7 HOH A 52 593 52 HOH HOH . H 7 HOH A 53 594 53 HOH HOH . H 7 HOH A 54 595 54 HOH HOH . H 7 HOH A 55 596 55 HOH HOH . H 7 HOH A 56 597 56 HOH HOH . H 7 HOH A 57 598 57 HOH HOH . H 7 HOH A 58 599 58 HOH HOH . H 7 HOH A 59 600 59 HOH HOH . H 7 HOH A 60 606 60 HOH HOH . H 7 HOH A 61 607 61 HOH HOH . H 7 HOH A 62 608 62 HOH HOH . H 7 HOH A 63 609 63 HOH HOH . H 7 HOH A 64 610 64 HOH HOH . H 7 HOH A 65 611 65 HOH HOH . H 7 HOH A 66 612 66 HOH HOH . H 7 HOH A 67 613 67 HOH HOH . H 7 HOH A 68 614 68 HOH HOH . H 7 HOH A 69 615 69 HOH HOH . H 7 HOH A 70 616 70 HOH HOH . H 7 HOH A 71 617 71 HOH HOH . H 7 HOH A 72 618 72 HOH HOH . H 7 HOH A 73 619 73 HOH HOH . H 7 HOH A 74 620 74 HOH HOH . H 7 HOH A 75 621 75 HOH HOH . H 7 HOH A 76 622 76 HOH HOH . H 7 HOH A 77 623 77 HOH HOH . H 7 HOH A 78 624 78 HOH HOH . H 7 HOH A 79 625 79 HOH HOH . H 7 HOH A 80 626 80 HOH HOH . H 7 HOH A 81 627 81 HOH HOH . H 7 HOH A 82 628 82 HOH HOH . H 7 HOH A 83 629 83 HOH HOH . H 7 HOH A 84 630 84 HOH HOH . H 7 HOH A 85 631 85 HOH HOH . H 7 HOH A 86 632 86 HOH HOH . H 7 HOH A 87 633 87 HOH HOH . H 7 HOH A 88 634 88 HOH HOH . H 7 HOH A 89 635 89 HOH HOH . H 7 HOH A 90 636 90 HOH HOH . H 7 HOH A 91 637 91 HOH HOH . H 7 HOH A 92 638 92 HOH HOH . H 7 HOH A 93 639 93 HOH HOH . H 7 HOH A 94 640 94 HOH HOH . H 7 HOH A 95 641 95 HOH HOH . H 7 HOH A 96 642 96 HOH HOH . H 7 HOH A 97 643 97 HOH HOH . H 7 HOH A 98 644 98 HOH HOH . H 7 HOH A 99 645 99 HOH HOH . H 7 HOH A 100 646 100 HOH HOH . H 7 HOH A 101 647 101 HOH HOH . H 7 HOH A 102 648 102 HOH HOH . H 7 HOH A 103 649 103 HOH HOH . H 7 HOH A 104 650 104 HOH HOH . H 7 HOH A 105 651 105 HOH HOH . H 7 HOH A 106 652 106 HOH HOH . H 7 HOH A 107 653 107 HOH HOH . H 7 HOH A 108 654 108 HOH HOH . H 7 HOH A 109 655 109 HOH HOH . H 7 HOH A 110 656 110 HOH HOH . H 7 HOH A 111 657 111 HOH HOH . H 7 HOH A 112 658 112 HOH HOH . H 7 HOH A 113 659 113 HOH HOH . H 7 HOH A 114 660 114 HOH HOH . H 7 HOH A 115 661 115 HOH HOH . H 7 HOH A 116 662 116 HOH HOH . H 7 HOH A 117 663 117 HOH HOH . H 7 HOH A 118 664 118 HOH HOH . H 7 HOH A 119 665 119 HOH HOH . H 7 HOH A 120 666 120 HOH HOH . H 7 HOH A 121 667 121 HOH HOH . H 7 HOH A 122 668 122 HOH HOH . H 7 HOH A 123 669 123 HOH HOH . H 7 HOH A 124 670 124 HOH HOH . H 7 HOH A 125 671 125 HOH HOH . H 7 HOH A 126 672 126 HOH HOH . H 7 HOH A 127 673 127 HOH HOH . H 7 HOH A 128 674 128 HOH HOH . H 7 HOH A 129 675 129 HOH HOH . H 7 HOH A 130 676 130 HOH HOH . H 7 HOH A 131 677 131 HOH HOH . H 7 HOH A 132 678 132 HOH HOH . H 7 HOH A 133 679 133 HOH HOH . H 7 HOH A 134 680 134 HOH HOH . H 7 HOH A 135 681 135 HOH HOH . H 7 HOH A 136 682 136 HOH HOH . H 7 HOH A 137 683 137 HOH HOH . H 7 HOH A 138 684 138 HOH HOH . H 7 HOH A 139 685 139 HOH HOH . H 7 HOH A 140 686 140 HOH HOH . H 7 HOH A 141 687 141 HOH HOH . H 7 HOH A 142 688 142 HOH HOH . H 7 HOH A 143 689 143 HOH HOH . H 7 HOH A 144 690 144 HOH HOH . H 7 HOH A 145 691 145 HOH HOH . H 7 HOH A 146 692 146 HOH HOH . H 7 HOH A 147 693 147 HOH HOH . H 7 HOH A 148 694 148 HOH HOH . H 7 HOH A 149 695 149 HOH HOH . H 7 HOH A 150 696 150 HOH HOH . H 7 HOH A 151 697 151 HOH HOH . H 7 HOH A 152 698 152 HOH HOH . H 7 HOH A 153 699 153 HOH HOH . H 7 HOH A 154 700 154 HOH HOH . H 7 HOH A 155 701 155 HOH HOH . H 7 HOH A 156 702 156 HOH HOH . H 7 HOH A 157 703 157 HOH HOH . H 7 HOH A 158 704 158 HOH HOH . H 7 HOH A 159 705 159 HOH HOH . H 7 HOH A 160 706 160 HOH HOH . H 7 HOH A 161 707 161 HOH HOH . H 7 HOH A 162 708 162 HOH HOH . H 7 HOH A 163 709 163 HOH HOH . H 7 HOH A 164 710 164 HOH HOH . H 7 HOH A 165 711 165 HOH HOH . H 7 HOH A 166 712 166 HOH HOH . H 7 HOH A 167 713 167 HOH HOH . H 7 HOH A 168 714 168 HOH HOH . H 7 HOH A 169 715 169 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 MPD . . . F 6 -43.535 31.765 -11.497 1 55.94 ? C1 MPD 540 A 1 HETATM 2 C C2 MPD . . . F 6 -42.137 32.011 -10.936 1 55.79 ? C2 MPD 540 A 1 HETATM 3 O O2 MPD . . . F 6 -42.053 31.384 -9.625 1 55.8 ? O2 MPD 540 A 1 HETATM 4 C CM MPD . . . F 6 -41.109 31.351 -11.847 1 55.55 ? CM MPD 540 A 1 HETATM 5 C C3 MPD . . . F 6 -41.804 33.503 -10.824 1 55.76 ? C3 MPD 540 A 1 HETATM 6 C C4 MPD . . . F 6 -42.957 34.401 -10.361 1 55.61 ? C4 MPD 540 A 1 HETATM 7 O O4 MPD . . . F 6 -43.333 34.125 -9.026 1 55.29 ? O4 MPD 540 A 1 HETATM 8 C C5 MPD . . . F 6 -42.559 35.869 -10.465 1 55.58 ? C5 MPD 540 A 1 # _model_server_stats.io_time_ms 46 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 8 #