data_5K08 # _model_server_result.job_id vUYen0xVnvTWgfBwrJ2j9w _model_server_result.datetime_utc '2024-11-13 07:13:43' _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 5k08 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":504}' # _entry.id 5K08 # _exptl.entry_id 5K08 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 250.186 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "3,3',3''-phosphanetriyltripropanoic acid" _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 90 _cell.entry_id 5K08 _cell.length_a 57.687 _cell.length_b 63.93 _cell.length_c 37.307 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5K08 _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 ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 4 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 metalc ? metalc1 A N CYS 1 A CYS 1 1_555 C PT ZPT . A ZPT 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? metalc ? metalc2 A SG CYS 1 A CYS 1 1_555 C PT ZPT . A ZPT 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? metalc ? metalc3 A NE2 HIS 138 A HIS 439 1_555 B PT ZPT . A ZPT 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? metalc ? metalc4 A SG CYS 140 A CYS 441 1_555 B PT ZPT . A ZPT 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? metalc ? metalc5 B PT ZPT . A ZPT 501 1_555 F O HOH . A HOH 716 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc6 C PT ZPT . A ZPT 502 1_555 F O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? metalc ? metalc7 C PT ZPT . A ZPT 502 1_555 F O HOH . A HOH 697 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? # _chem_comp.formula 'C9 H15 O6 P' _chem_comp.formula_weight 250.186 _chem_comp.id TCE _chem_comp.mon_nstd_flag . _chem_comp.name "3,3',3''-phosphanetriyltripropanoic acid" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '3-[bis(2-carboxyethyl)phosphanyl]propanoic acid' # 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 O16 C14 TCE doub 259 n n C14 O15 TCE sing 260 n n C14 C5 TCE sing 261 n n O15 HO15 TCE sing 262 n n C2 C5 TCE sing 263 n n C5 H5 TCE sing 264 n n C5 H5A TCE sing 265 n n C2 P TCE sing 266 n n C2 H2 TCE sing 267 n n C2 H2A TCE sing 268 n n C1 P TCE sing 269 n n P C3 TCE sing 270 n n C3 C6 TCE sing 271 n n C3 H3 TCE sing 272 n n C3 H3A TCE sing 273 n n C6 C8 TCE sing 274 n n C6 H6 TCE sing 275 n n C6 H6A TCE sing 276 n n O10 C8 TCE doub 277 n n C8 O9 TCE sing 278 n n O9 HO9 TCE sing 279 n n C4 C1 TCE sing 280 n n C1 H1 TCE sing 281 n n C1 H1A TCE sing 282 n n C11 C4 TCE sing 283 n n C4 H4 TCE sing 284 n n C4 H4A TCE sing 285 n n O13 C11 TCE doub 286 n n O12 C11 TCE sing 287 n n O12 HO12 TCE sing 288 n n # _atom_sites.entry_id 5K08 _atom_sites.fract_transf_matrix[1][1] 0.017335 _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] 0.015642 _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] 0.026805 _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 B 2 ZPT A 1 501 1 ZPT PT . C 2 ZPT A 1 502 2 ZPT PT . D 3 SO4 A 1 503 1 SO4 SO4 . E 4 TCE A 1 504 1 TCE TCE . F 5 HOH A 1 601 26 HOH HOH . F 5 HOH A 2 602 45 HOH HOH . F 5 HOH A 3 603 2 HOH HOH . F 5 HOH A 4 604 129 HOH HOH . F 5 HOH A 5 605 128 HOH HOH . F 5 HOH A 6 606 79 HOH HOH . F 5 HOH A 7 607 46 HOH HOH . F 5 HOH A 8 608 101 HOH HOH . F 5 HOH A 9 609 132 HOH HOH . F 5 HOH A 10 610 21 HOH HOH . F 5 HOH A 11 611 117 HOH HOH . F 5 HOH A 12 612 68 HOH HOH . F 5 HOH A 13 613 83 HOH HOH . F 5 HOH A 14 614 104 HOH HOH . F 5 HOH A 15 615 18 HOH HOH . F 5 HOH A 16 616 78 HOH HOH . F 5 HOH A 17 617 47 HOH HOH . F 5 HOH A 18 618 8 HOH HOH . F 5 HOH A 19 619 38 HOH HOH . F 5 HOH A 20 620 9 HOH HOH . F 5 HOH A 21 621 67 HOH HOH . F 5 HOH A 22 622 36 HOH HOH . F 5 HOH A 23 623 40 HOH HOH . F 5 HOH A 24 624 10 HOH HOH . F 5 HOH A 25 625 71 HOH HOH . F 5 HOH A 26 626 39 HOH HOH . F 5 HOH A 27 627 44 HOH HOH . F 5 HOH A 28 628 65 HOH HOH . F 5 HOH A 29 629 59 HOH HOH . F 5 HOH A 30 630 61 HOH HOH . F 5 HOH A 31 631 43 HOH HOH . F 5 HOH A 32 632 54 HOH HOH . F 5 HOH A 33 633 35 HOH HOH . F 5 HOH A 34 634 72 HOH HOH . F 5 HOH A 35 635 53 HOH HOH . F 5 HOH A 36 636 64 HOH HOH . F 5 HOH A 37 637 22 HOH HOH . F 5 HOH A 38 638 82 HOH HOH . F 5 HOH A 39 639 90 HOH HOH . F 5 HOH A 40 640 110 HOH HOH . F 5 HOH A 41 641 30 HOH HOH . F 5 HOH A 42 642 48 HOH HOH . F 5 HOH A 43 643 85 HOH HOH . F 5 HOH A 44 644 29 HOH HOH . F 5 HOH A 45 645 37 HOH HOH . F 5 HOH A 46 646 20 HOH HOH . F 5 HOH A 47 647 105 HOH HOH . F 5 HOH A 48 648 19 HOH HOH . F 5 HOH A 49 649 12 HOH HOH . F 5 HOH A 50 650 69 HOH HOH . F 5 HOH A 51 651 76 HOH HOH . F 5 HOH A 52 652 34 HOH HOH . F 5 HOH A 53 653 94 HOH HOH . F 5 HOH A 54 654 88 HOH HOH . F 5 HOH A 55 655 13 HOH HOH . F 5 HOH A 56 656 6 HOH HOH . F 5 HOH A 57 657 96 HOH HOH . F 5 HOH A 58 658 41 HOH HOH . F 5 HOH A 59 659 16 HOH HOH . F 5 HOH A 60 660 91 HOH HOH . F 5 HOH A 61 661 32 HOH HOH . F 5 HOH A 62 662 4 HOH HOH . F 5 HOH A 63 663 109 HOH HOH . F 5 HOH A 64 664 73 HOH HOH . F 5 HOH A 65 665 7 HOH HOH . F 5 HOH A 66 666 52 HOH HOH . F 5 HOH A 67 667 86 HOH HOH . F 5 HOH A 68 668 15 HOH HOH . F 5 HOH A 69 669 24 HOH HOH . F 5 HOH A 70 670 31 HOH HOH . F 5 HOH A 71 671 50 HOH HOH . F 5 HOH A 72 672 60 HOH HOH . F 5 HOH A 73 673 58 HOH HOH . F 5 HOH A 74 674 97 HOH HOH . F 5 HOH A 75 675 100 HOH HOH . F 5 HOH A 76 676 113 HOH HOH . F 5 HOH A 77 677 33 HOH HOH . F 5 HOH A 78 678 23 HOH HOH . F 5 HOH A 79 679 28 HOH HOH . F 5 HOH A 80 680 70 HOH HOH . F 5 HOH A 81 681 25 HOH HOH . F 5 HOH A 82 682 14 HOH HOH . F 5 HOH A 83 683 62 HOH HOH . F 5 HOH A 84 684 63 HOH HOH . F 5 HOH A 85 685 124 HOH HOH . F 5 HOH A 86 686 107 HOH HOH . F 5 HOH A 87 687 57 HOH HOH . F 5 HOH A 88 688 74 HOH HOH . F 5 HOH A 89 689 122 HOH HOH . F 5 HOH A 90 690 17 HOH HOH . F 5 HOH A 91 691 127 HOH HOH . F 5 HOH A 92 692 103 HOH HOH . F 5 HOH A 93 693 93 HOH HOH . F 5 HOH A 94 694 125 HOH HOH . F 5 HOH A 95 695 134 HOH HOH . F 5 HOH A 96 696 42 HOH HOH . F 5 HOH A 97 697 3 HOH HOH . F 5 HOH A 98 698 106 HOH HOH . F 5 HOH A 99 699 77 HOH HOH . F 5 HOH A 100 700 95 HOH HOH . F 5 HOH A 101 701 116 HOH HOH . F 5 HOH A 102 702 111 HOH HOH . F 5 HOH A 103 703 27 HOH HOH . F 5 HOH A 104 704 5 HOH HOH . F 5 HOH A 105 705 131 HOH HOH . F 5 HOH A 106 706 56 HOH HOH . F 5 HOH A 107 707 55 HOH HOH . F 5 HOH A 108 708 66 HOH HOH . F 5 HOH A 109 709 11 HOH HOH . F 5 HOH A 110 710 84 HOH HOH . F 5 HOH A 111 711 126 HOH HOH . F 5 HOH A 112 712 118 HOH HOH . F 5 HOH A 113 713 98 HOH HOH . F 5 HOH A 114 714 114 HOH HOH . F 5 HOH A 115 715 102 HOH HOH . F 5 HOH A 116 716 1 HOH HOH . F 5 HOH A 117 717 51 HOH HOH . F 5 HOH A 118 718 75 HOH HOH . F 5 HOH A 119 719 92 HOH HOH . F 5 HOH A 120 720 120 HOH HOH . F 5 HOH A 121 721 89 HOH HOH . F 5 HOH A 122 722 121 HOH HOH . F 5 HOH A 123 723 108 HOH HOH . F 5 HOH A 124 724 81 HOH HOH . F 5 HOH A 125 725 49 HOH HOH . F 5 HOH A 126 726 112 HOH HOH . F 5 HOH A 127 727 87 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 P P TCE . . . E 4 -2.863 4.085 -4.138 1 65.04 ? P TCE 504 A 1 HETATM 2 C C3 TCE . . . E 4 -1.999 3.569 -5.658 1 69.42 ? C3 TCE 504 A 1 HETATM 3 C C6 TCE . . . E 4 -2.552 2.365 -6.341 1 71.81 ? C6 TCE 504 A 1 HETATM 4 C C8 TCE . . . E 4 -1.8 1.802 -7.497 1 71.43 ? C8 TCE 504 A 1 HETATM 5 O O10 TCE . . . E 4 -1.053 2.549 -8.182 1 73.03 ? O10 TCE 504 A 1 HETATM 6 O O9 TCE . . . E 4 -1.919 0.581 -7.787 1 67.7 ? O9 TCE 504 A 1 HETATM 7 C C1 TCE . . . E 4 -3.648 2.611 -3.402 1 68.05 ? C1 TCE 504 A 1 HETATM 8 C C4 TCE . . . E 4 -3.634 2.478 -1.919 1 66.17 ? C4 TCE 504 A 1 HETATM 9 C C11 TCE . . . E 4 -4.312 3.548 -1.132 1 71.94 ? C11 TCE 504 A 1 HETATM 10 O O12 TCE . . . E 4 -3.638 4.445 -0.559 1 70.91 ? O12 TCE 504 A 1 HETATM 11 O O13 TCE . . . E 4 -5.566 3.552 -1.044 1 78.97 ? O13 TCE 504 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 239 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 11 #