data_5X03 # _model_server_result.job_id gDiD_n5C8xU9NfzviOzoTw _model_server_result.datetime_utc '2024-11-14 20:55:08' _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 5x03 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 5X03 # _exptl.entry_id 5X03 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 247.142 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "PYRIDOXAL-5'-PHOSPHATE" _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 5X03 _cell.length_a 118.497 _cell.length_b 118.497 _cell.length_c 75.862 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5X03 _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41' # _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 _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 ? 3 C N N ? 3 E 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 C C4A PLP . A PLP 501 1_555 D N ABU . A ABU 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.154 ? covale ? covale2 B NZ LYS 205 B LYS 312 1_555 E C4A PLP . B PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.906 ? # _chem_comp.formula 'C8 H10 N O6 P' _chem_comp.formula_weight 247.142 _chem_comp.id PLP _chem_comp.mon_nstd_flag . _chem_comp.name "PYRIDOXAL-5'-PHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'VITAMIN B6 Phosphate' # 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 N1 C2 PLP doub 275 n y N1 C6 PLP sing 276 n y C2 C2A PLP sing 277 n n C2 C3 PLP sing 278 n y C2A H2A1 PLP sing 279 n n C2A H2A2 PLP sing 280 n n C2A H2A3 PLP sing 281 n n C3 O3 PLP sing 282 n n C3 C4 PLP doub 283 n y O3 HO3 PLP sing 284 n n C4 C4A PLP sing 285 n n C4 C5 PLP sing 286 n y C4A O4A PLP doub 287 n n C4A H4A PLP sing 288 n n C5 C6 PLP doub 289 n y C5 C5A PLP sing 290 n n C6 H6 PLP sing 291 n n C5A O4P PLP sing 292 n n C5A H5A1 PLP sing 293 n n C5A H5A2 PLP sing 294 n n O4P P PLP sing 295 n n P O1P PLP doub 296 n n P O2P PLP sing 297 n n P O3P PLP sing 298 n n O2P HOP2 PLP sing 299 n n O3P HOP3 PLP sing 300 n n # _atom_sites.entry_id 5X03 _atom_sites.fract_transf_matrix[1][1] 0.008439 _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] 0.008439 _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] 0.013182 _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 PLP A 1 501 1 PLP PLP . D 4 ABU A 1 502 1 ABU ABU . E 3 PLP B 1 501 2 PLP PLP . F 5 HOH A 1 601 202 HOH HOH . F 5 HOH A 2 602 8 HOH HOH . F 5 HOH A 3 603 65 HOH HOH . F 5 HOH A 4 604 208 HOH HOH . F 5 HOH A 5 605 205 HOH HOH . F 5 HOH A 6 606 3 HOH HOH . F 5 HOH A 7 607 182 HOH HOH . F 5 HOH A 8 608 174 HOH HOH . F 5 HOH A 9 609 104 HOH HOH . F 5 HOH A 10 610 204 HOH HOH . F 5 HOH A 11 611 82 HOH HOH . F 5 HOH A 12 612 36 HOH HOH . F 5 HOH A 13 613 33 HOH HOH . F 5 HOH A 14 614 77 HOH HOH . F 5 HOH A 15 615 48 HOH HOH . F 5 HOH A 16 616 188 HOH HOH . F 5 HOH A 17 617 156 HOH HOH . F 5 HOH A 18 618 123 HOH HOH . F 5 HOH A 19 619 196 HOH HOH . F 5 HOH A 20 620 49 HOH HOH . F 5 HOH A 21 621 75 HOH HOH . F 5 HOH A 22 622 7 HOH HOH . F 5 HOH A 23 623 130 HOH HOH . F 5 HOH A 24 624 228 HOH HOH . F 5 HOH A 25 625 134 HOH HOH . F 5 HOH A 26 626 108 HOH HOH . F 5 HOH A 27 627 79 HOH HOH . F 5 HOH A 28 628 110 HOH HOH . F 5 HOH A 29 629 47 HOH HOH . F 5 HOH A 30 630 97 HOH HOH . F 5 HOH A 31 631 68 HOH HOH . F 5 HOH A 32 632 87 HOH HOH . F 5 HOH A 33 633 72 HOH HOH . F 5 HOH A 34 634 20 HOH HOH . F 5 HOH A 35 635 119 HOH HOH . F 5 HOH A 36 636 198 HOH HOH . F 5 HOH A 37 637 51 HOH HOH . F 5 HOH A 38 638 84 HOH HOH . F 5 HOH A 39 639 226 HOH HOH . F 5 HOH A 40 640 11 HOH HOH . F 5 HOH A 41 641 6 HOH HOH . F 5 HOH A 42 642 4 HOH HOH . F 5 HOH A 43 643 57 HOH HOH . F 5 HOH A 44 644 116 HOH HOH . F 5 HOH A 45 645 128 HOH HOH . F 5 HOH A 46 646 14 HOH HOH . F 5 HOH A 47 647 81 HOH HOH . F 5 HOH A 48 648 115 HOH HOH . F 5 HOH A 49 649 26 HOH HOH . F 5 HOH A 50 650 95 HOH HOH . F 5 HOH A 51 651 60 HOH HOH . F 5 HOH A 52 652 164 HOH HOH . F 5 HOH A 53 653 5 HOH HOH . F 5 HOH A 54 654 147 HOH HOH . F 5 HOH A 55 655 35 HOH HOH . F 5 HOH A 56 656 138 HOH HOH . F 5 HOH A 57 657 29 HOH HOH . F 5 HOH A 58 658 10 HOH HOH . F 5 HOH A 59 659 43 HOH HOH . F 5 HOH A 60 660 192 HOH HOH . F 5 HOH A 61 661 34 HOH HOH . F 5 HOH A 62 662 88 HOH HOH . F 5 HOH A 63 663 193 HOH HOH . F 5 HOH A 64 664 114 HOH HOH . F 5 HOH A 65 665 2 HOH HOH . F 5 HOH A 66 666 42 HOH HOH . F 5 HOH A 67 667 90 HOH HOH . F 5 HOH A 68 668 22 HOH HOH . F 5 HOH A 69 669 187 HOH HOH . F 5 HOH A 70 670 64 HOH HOH . F 5 HOH A 71 671 139 HOH HOH . F 5 HOH A 72 672 169 HOH HOH . F 5 HOH A 73 673 67 HOH HOH . F 5 HOH A 74 674 168 HOH HOH . F 5 HOH A 75 675 24 HOH HOH . F 5 HOH A 76 676 189 HOH HOH . F 5 HOH A 77 677 99 HOH HOH . F 5 HOH A 78 678 59 HOH HOH . F 5 HOH A 79 679 106 HOH HOH . F 5 HOH A 80 680 45 HOH HOH . F 5 HOH A 81 681 15 HOH HOH . F 5 HOH A 82 682 236 HOH HOH . F 5 HOH A 83 683 91 HOH HOH . F 5 HOH A 84 684 111 HOH HOH . F 5 HOH A 85 685 167 HOH HOH . F 5 HOH A 86 686 16 HOH HOH . F 5 HOH A 87 687 126 HOH HOH . F 5 HOH A 88 688 53 HOH HOH . F 5 HOH A 89 689 125 HOH HOH . F 5 HOH A 90 690 109 HOH HOH . F 5 HOH A 91 691 190 HOH HOH . F 5 HOH A 92 692 136 HOH HOH . F 5 HOH A 93 693 235 HOH HOH . F 5 HOH A 94 694 201 HOH HOH . F 5 HOH A 95 695 154 HOH HOH . F 5 HOH A 96 696 145 HOH HOH . F 5 HOH A 97 697 177 HOH HOH . F 5 HOH A 98 698 101 HOH HOH . F 5 HOH A 99 699 71 HOH HOH . F 5 HOH A 100 700 227 HOH HOH . F 5 HOH A 101 701 158 HOH HOH . F 5 HOH A 102 702 38 HOH HOH . F 5 HOH A 103 703 237 HOH HOH . F 5 HOH A 104 704 179 HOH HOH . F 5 HOH A 105 705 160 HOH HOH . F 5 HOH A 106 706 13 HOH HOH . F 5 HOH A 107 707 218 HOH HOH . F 5 HOH A 108 708 89 HOH HOH . F 5 HOH A 109 709 98 HOH HOH . F 5 HOH A 110 710 206 HOH HOH . F 5 HOH A 111 711 74 HOH HOH . F 5 HOH A 112 712 241 HOH HOH . F 5 HOH A 113 713 28 HOH HOH . F 5 HOH A 114 714 131 HOH HOH . F 5 HOH A 115 715 63 HOH HOH . F 5 HOH A 116 716 9 HOH HOH . F 5 HOH A 117 717 152 HOH HOH . F 5 HOH A 118 718 186 HOH HOH . F 5 HOH A 119 719 159 HOH HOH . F 5 HOH A 120 720 240 HOH HOH . F 5 HOH A 121 721 194 HOH HOH . F 5 HOH A 122 722 191 HOH HOH . F 5 HOH A 123 723 157 HOH HOH . F 5 HOH A 124 724 185 HOH HOH . F 5 HOH A 125 725 200 HOH HOH . F 5 HOH A 126 726 238 HOH HOH . F 5 HOH A 127 727 120 HOH HOH . F 5 HOH A 128 728 239 HOH HOH . F 5 HOH A 129 729 121 HOH HOH . F 5 HOH A 130 730 170 HOH HOH . F 5 HOH A 131 731 102 HOH HOH . F 5 HOH A 132 732 242 HOH HOH . F 5 HOH A 133 733 220 HOH HOH . F 5 HOH A 134 734 173 HOH HOH . F 5 HOH A 135 735 112 HOH HOH . F 5 HOH A 136 736 217 HOH HOH . F 5 HOH A 137 737 184 HOH HOH . F 5 HOH A 138 738 207 HOH HOH . F 5 HOH A 139 739 209 HOH HOH . F 5 HOH A 140 740 195 HOH HOH . G 5 HOH B 1 601 183 HOH HOH . G 5 HOH B 2 602 171 HOH HOH . G 5 HOH B 3 603 76 HOH HOH . G 5 HOH B 4 604 203 HOH HOH . G 5 HOH B 5 605 39 HOH HOH . G 5 HOH B 6 606 61 HOH HOH . G 5 HOH B 7 607 1 HOH HOH . G 5 HOH B 8 608 27 HOH HOH . G 5 HOH B 9 609 175 HOH HOH . G 5 HOH B 10 610 153 HOH HOH . G 5 HOH B 11 611 166 HOH HOH . G 5 HOH B 12 612 244 HOH HOH . G 5 HOH B 13 613 69 HOH HOH . G 5 HOH B 14 614 215 HOH HOH . G 5 HOH B 15 615 52 HOH HOH . G 5 HOH B 16 616 80 HOH HOH . G 5 HOH B 17 617 94 HOH HOH . G 5 HOH B 18 618 58 HOH HOH . G 5 HOH B 19 619 172 HOH HOH . G 5 HOH B 20 620 19 HOH HOH . G 5 HOH B 21 621 105 HOH HOH . G 5 HOH B 22 622 30 HOH HOH . G 5 HOH B 23 623 78 HOH HOH . G 5 HOH B 24 624 107 HOH HOH . G 5 HOH B 25 625 46 HOH HOH . G 5 HOH B 26 626 224 HOH HOH . G 5 HOH B 27 627 143 HOH HOH . G 5 HOH B 28 628 176 HOH HOH . G 5 HOH B 29 629 162 HOH HOH . G 5 HOH B 30 630 17 HOH HOH . G 5 HOH B 31 631 234 HOH HOH . G 5 HOH B 32 632 103 HOH HOH . G 5 HOH B 33 633 93 HOH HOH . G 5 HOH B 34 634 129 HOH HOH . G 5 HOH B 35 635 225 HOH HOH . G 5 HOH B 36 636 141 HOH HOH . G 5 HOH B 37 637 12 HOH HOH . G 5 HOH B 38 638 197 HOH HOH . G 5 HOH B 39 639 37 HOH HOH . G 5 HOH B 40 640 73 HOH HOH . G 5 HOH B 41 641 151 HOH HOH . G 5 HOH B 42 642 66 HOH HOH . G 5 HOH B 43 643 132 HOH HOH . G 5 HOH B 44 644 55 HOH HOH . G 5 HOH B 45 645 230 HOH HOH . G 5 HOH B 46 646 32 HOH HOH . G 5 HOH B 47 647 40 HOH HOH . G 5 HOH B 48 648 137 HOH HOH . G 5 HOH B 49 649 31 HOH HOH . G 5 HOH B 50 650 140 HOH HOH . G 5 HOH B 51 651 117 HOH HOH . G 5 HOH B 52 652 44 HOH HOH . G 5 HOH B 53 653 62 HOH HOH . G 5 HOH B 54 654 248 HOH HOH . G 5 HOH B 55 655 165 HOH HOH . G 5 HOH B 56 656 180 HOH HOH . G 5 HOH B 57 657 163 HOH HOH . G 5 HOH B 58 658 124 HOH HOH . G 5 HOH B 59 659 23 HOH HOH . G 5 HOH B 60 660 56 HOH HOH . G 5 HOH B 61 661 213 HOH HOH . G 5 HOH B 62 662 18 HOH HOH . G 5 HOH B 63 663 25 HOH HOH . G 5 HOH B 64 664 70 HOH HOH . G 5 HOH B 65 665 181 HOH HOH . G 5 HOH B 66 666 243 HOH HOH . G 5 HOH B 67 667 41 HOH HOH . G 5 HOH B 68 668 54 HOH HOH . G 5 HOH B 69 669 146 HOH HOH . G 5 HOH B 70 670 96 HOH HOH . G 5 HOH B 71 671 223 HOH HOH . G 5 HOH B 72 672 231 HOH HOH . G 5 HOH B 73 673 85 HOH HOH . G 5 HOH B 74 674 229 HOH HOH . G 5 HOH B 75 675 92 HOH HOH . G 5 HOH B 76 676 142 HOH HOH . G 5 HOH B 77 677 100 HOH HOH . G 5 HOH B 78 678 148 HOH HOH . G 5 HOH B 79 679 50 HOH HOH . G 5 HOH B 80 680 118 HOH HOH . G 5 HOH B 81 681 150 HOH HOH . G 5 HOH B 82 682 216 HOH HOH . G 5 HOH B 83 683 86 HOH HOH . G 5 HOH B 84 684 21 HOH HOH . G 5 HOH B 85 685 155 HOH HOH . G 5 HOH B 86 686 214 HOH HOH . G 5 HOH B 87 687 122 HOH HOH . G 5 HOH B 88 688 83 HOH HOH . G 5 HOH B 89 689 221 HOH HOH . G 5 HOH B 90 690 133 HOH HOH . G 5 HOH B 91 691 247 HOH HOH . G 5 HOH B 92 692 161 HOH HOH . G 5 HOH B 93 693 113 HOH HOH . G 5 HOH B 94 694 149 HOH HOH . G 5 HOH B 95 695 233 HOH HOH . G 5 HOH B 96 696 219 HOH HOH . G 5 HOH B 97 697 199 HOH HOH . G 5 HOH B 98 698 178 HOH HOH . G 5 HOH B 99 699 210 HOH HOH . G 5 HOH B 100 700 222 HOH HOH . G 5 HOH B 101 701 127 HOH HOH . G 5 HOH B 102 702 135 HOH HOH . G 5 HOH B 103 703 144 HOH HOH . G 5 HOH B 104 704 232 HOH HOH . G 5 HOH B 105 705 246 HOH HOH . G 5 HOH B 106 706 212 HOH HOH . G 5 HOH B 107 707 245 HOH HOH . G 5 HOH B 108 708 211 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 N N1 PLP . . . C 3 -12.56 -33.246 11.607 1 20.97 ? N1 PLP 501 A 1 HETATM 2 C C2 PLP . . . C 3 -12.238 -32.919 12.879 1 22.73 ? C2 PLP 501 A 1 HETATM 3 C C2A PLP . . . C 3 -12.955 -31.791 13.57 1 23.26 ? C2A PLP 501 A 1 HETATM 4 C C3 PLP . . . C 3 -11.179 -33.671 13.596 1 21.39 ? C3 PLP 501 A 1 HETATM 5 O O3 PLP . . . C 3 -10.836 -33.365 14.874 1 24.03 ? O3 PLP 501 A 1 HETATM 6 C C4 PLP . . . C 3 -10.509 -34.769 12.868 1 23.9 ? C4 PLP 501 A 1 HETATM 7 C C4A PLP . . . C 3 -9.443 -35.573 13.503 1 26.67 ? C4A PLP 501 A 1 HETATM 8 C C5 PLP . . . C 3 -10.953 -35.023 11.477 1 24.36 ? C5 PLP 501 A 1 HETATM 9 C C6 PLP . . . C 3 -11.963 -34.239 10.929 1 20.38 ? C6 PLP 501 A 1 HETATM 10 C C5A PLP . . . C 3 -10.327 -36.131 10.665 1 26.47 ? C5A PLP 501 A 1 HETATM 11 O O4P PLP . . . C 3 -9.044 -35.75 10.181 1 26.8 ? O4P PLP 501 A 1 HETATM 12 P P PLP . . . C 3 -8.266 -36.726 9.168 1 25.31 ? P PLP 501 A 1 HETATM 13 O O1P PLP . . . C 3 -9.252 -36.914 8.047 1 21.85 ? O1P PLP 501 A 1 HETATM 14 O O2P PLP . . . C 3 -8.003 -37.966 9.982 1 24.95 ? O2P PLP 501 A 1 HETATM 15 O O3P PLP . . . C 3 -7.027 -35.96 8.795 1 20.59 ? O3P PLP 501 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 216 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 15 #