data_8BIV # _model_server_result.job_id HQxOnD-bbI_Lck29ApwulQ _model_server_result.datetime_utc '2024-11-15 15:52:46' _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 8biv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":501}' # _entry.id 8BIV # _exptl.entry_id 8BIV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 247.142 _entity.id 2 _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 120 _cell.entry_id 8BIV _cell.length_a 157.738 _cell.length_b 157.738 _cell.length_c 93.331 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8BIV _symmetry.cell_setting ? _symmetry.Int_Tables_number 150 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 3 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 5_556 x-y,-y,-z+1 1 0 0 0 -1 0 0 0 -1 0 0 93.331 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 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 A NZ LYS 230 A LYS 230 1_555 C C4A PLP . A PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.272 ? covale ? covale2 B NZ LYS 230 E LYS 230 1_555 E C4A PLP . E PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.27 ? # _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 273 n y N1 C6 PLP sing 274 n y C2 C2A PLP sing 275 n n C2 C3 PLP sing 276 n y C2A H2A1 PLP sing 277 n n C2A H2A2 PLP sing 278 n n C2A H2A3 PLP sing 279 n n C3 O3 PLP sing 280 n n C3 C4 PLP doub 281 n y O3 HO3 PLP sing 282 n n C4 C4A PLP sing 283 n n C4 C5 PLP sing 284 n y C4A O4A PLP doub 285 n n C4A H4A PLP sing 286 n n C5 C6 PLP doub 287 n y C5 C5A PLP sing 288 n n C6 H6 PLP sing 289 n n C5A O4P PLP sing 290 n n C5A H5A1 PLP sing 291 n n C5A H5A2 PLP sing 292 n n O4P P PLP sing 293 n n P O1P PLP doub 294 n n P O2P PLP sing 295 n n P O3P PLP sing 296 n n O2P HOP2 PLP sing 297 n n O3P HOP3 PLP sing 298 n n # _atom_sites.entry_id 8BIV _atom_sites.fract_transf_matrix[1][1] 0.00634 _atom_sites.fract_transf_matrix[1][2] 0.00366 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00732 _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] 0.010715 _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 PLP A 1 501 519 PLP PLP . D 3 GOL A 1 502 601 GOL GOL . E 2 PLP E 1 501 519 PLP PLP . F 3 GOL E 1 502 601 GOL GOL . G 4 HOH A 1 601 266 HOH HOH . G 4 HOH A 2 602 278 HOH HOH . G 4 HOH A 3 603 148 HOH HOH . G 4 HOH A 4 604 515 HOH HOH . G 4 HOH A 5 605 20 HOH HOH . G 4 HOH A 6 606 268 HOH HOH . G 4 HOH A 7 607 118 HOH HOH . G 4 HOH A 8 608 52 HOH HOH . G 4 HOH A 9 609 235 HOH HOH . G 4 HOH A 10 610 509 HOH HOH . G 4 HOH A 11 611 196 HOH HOH . G 4 HOH A 12 612 88 HOH HOH . G 4 HOH A 13 613 4 HOH HOH . G 4 HOH A 14 614 512 HOH HOH . G 4 HOH A 15 615 48 HOH HOH . G 4 HOH A 16 616 23 HOH HOH . G 4 HOH A 17 617 187 HOH HOH . G 4 HOH A 18 618 124 HOH HOH . G 4 HOH A 19 619 82 HOH HOH . G 4 HOH A 20 620 128 HOH HOH . G 4 HOH A 21 621 37 HOH HOH . G 4 HOH A 22 622 40 HOH HOH . G 4 HOH A 23 623 16 HOH HOH . G 4 HOH A 24 624 14 HOH HOH . G 4 HOH A 25 625 113 HOH HOH . G 4 HOH A 26 626 323 HOH HOH . G 4 HOH A 27 627 59 HOH HOH . G 4 HOH A 28 628 9 HOH HOH . G 4 HOH A 29 629 71 HOH HOH . G 4 HOH A 30 630 314 HOH HOH . G 4 HOH A 31 631 296 HOH HOH . G 4 HOH A 32 632 87 HOH HOH . G 4 HOH A 33 633 344 HOH HOH . G 4 HOH A 34 634 53 HOH HOH . G 4 HOH A 35 635 15 HOH HOH . G 4 HOH A 36 636 269 HOH HOH . G 4 HOH A 37 637 346 HOH HOH . G 4 HOH A 38 638 27 HOH HOH . G 4 HOH A 39 639 24 HOH HOH . G 4 HOH A 40 640 513 HOH HOH . G 4 HOH A 41 641 172 HOH HOH . G 4 HOH A 42 642 60 HOH HOH . G 4 HOH A 43 643 51 HOH HOH . G 4 HOH A 44 644 139 HOH HOH . G 4 HOH A 45 645 161 HOH HOH . G 4 HOH A 46 646 245 HOH HOH . G 4 HOH A 47 647 290 HOH HOH . G 4 HOH A 48 648 313 HOH HOH . G 4 HOH A 49 649 348 HOH HOH . G 4 HOH A 50 650 21 HOH HOH . G 4 HOH A 51 651 282 HOH HOH . G 4 HOH A 52 652 237 HOH HOH . G 4 HOH A 53 653 185 HOH HOH . G 4 HOH A 54 654 117 HOH HOH . G 4 HOH A 55 655 65 HOH HOH . G 4 HOH A 56 656 135 HOH HOH . G 4 HOH A 57 657 212 HOH HOH . G 4 HOH A 58 658 122 HOH HOH . G 4 HOH A 59 659 203 HOH HOH . G 4 HOH A 60 660 126 HOH HOH . G 4 HOH A 61 661 110 HOH HOH . G 4 HOH A 62 662 138 HOH HOH . G 4 HOH A 63 663 304 HOH HOH . G 4 HOH A 64 664 2 HOH HOH . G 4 HOH A 65 665 67 HOH HOH . G 4 HOH A 66 666 438 HOH HOH . G 4 HOH A 67 667 100 HOH HOH . G 4 HOH A 68 668 80 HOH HOH . G 4 HOH A 69 669 165 HOH HOH . G 4 HOH A 70 670 5 HOH HOH . G 4 HOH A 71 671 233 HOH HOH . G 4 HOH A 72 672 328 HOH HOH . G 4 HOH A 73 673 163 HOH HOH . G 4 HOH A 74 674 402 HOH HOH . G 4 HOH A 75 675 91 HOH HOH . G 4 HOH A 76 676 3 HOH HOH . G 4 HOH A 77 677 104 HOH HOH . G 4 HOH A 78 678 34 HOH HOH . G 4 HOH A 79 679 191 HOH HOH . G 4 HOH A 80 680 29 HOH HOH . G 4 HOH A 81 681 171 HOH HOH . G 4 HOH A 82 682 246 HOH HOH . G 4 HOH A 83 683 137 HOH HOH . G 4 HOH A 84 684 66 HOH HOH . G 4 HOH A 85 685 140 HOH HOH . G 4 HOH A 86 686 280 HOH HOH . G 4 HOH A 87 687 106 HOH HOH . G 4 HOH A 88 688 299 HOH HOH . G 4 HOH A 89 689 358 HOH HOH . G 4 HOH A 90 690 310 HOH HOH . G 4 HOH A 91 691 177 HOH HOH . G 4 HOH A 92 692 63 HOH HOH . G 4 HOH A 93 693 54 HOH HOH . G 4 HOH A 94 694 195 HOH HOH . G 4 HOH A 95 695 42 HOH HOH . G 4 HOH A 96 696 99 HOH HOH . G 4 HOH A 97 697 294 HOH HOH . G 4 HOH A 98 698 238 HOH HOH . G 4 HOH A 99 699 174 HOH HOH . G 4 HOH A 100 700 208 HOH HOH . G 4 HOH A 101 701 149 HOH HOH . G 4 HOH A 102 702 410 HOH HOH . G 4 HOH A 103 703 284 HOH HOH . G 4 HOH A 104 704 74 HOH HOH . G 4 HOH A 105 705 330 HOH HOH . G 4 HOH A 106 706 223 HOH HOH . G 4 HOH A 107 707 83 HOH HOH . G 4 HOH A 108 708 273 HOH HOH . G 4 HOH A 109 709 263 HOH HOH . G 4 HOH A 110 710 134 HOH HOH . G 4 HOH A 111 711 309 HOH HOH . G 4 HOH A 112 712 421 HOH HOH . G 4 HOH A 113 713 224 HOH HOH . G 4 HOH A 114 714 197 HOH HOH . G 4 HOH A 115 715 10 HOH HOH . G 4 HOH A 116 716 35 HOH HOH . G 4 HOH A 117 717 114 HOH HOH . G 4 HOH A 118 718 46 HOH HOH . G 4 HOH A 119 719 271 HOH HOH . G 4 HOH A 120 720 181 HOH HOH . G 4 HOH A 121 721 500 HOH HOH . G 4 HOH A 122 722 250 HOH HOH . G 4 HOH A 123 723 352 HOH HOH . G 4 HOH A 124 724 396 HOH HOH . G 4 HOH A 125 725 190 HOH HOH . H 4 HOH E 1 601 267 HOH HOH . H 4 HOH E 2 602 93 HOH HOH . H 4 HOH E 3 603 287 HOH HOH . H 4 HOH E 4 604 70 HOH HOH . H 4 HOH E 5 605 41 HOH HOH . H 4 HOH E 6 606 130 HOH HOH . H 4 HOH E 7 607 143 HOH HOH . H 4 HOH E 8 608 45 HOH HOH . H 4 HOH E 9 609 136 HOH HOH . H 4 HOH E 10 610 249 HOH HOH . H 4 HOH E 11 611 121 HOH HOH . H 4 HOH E 12 612 105 HOH HOH . H 4 HOH E 13 613 125 HOH HOH . H 4 HOH E 14 614 226 HOH HOH . H 4 HOH E 15 615 75 HOH HOH . H 4 HOH E 16 616 510 HOH HOH . H 4 HOH E 17 617 270 HOH HOH . H 4 HOH E 18 618 298 HOH HOH . H 4 HOH E 19 619 72 HOH HOH . H 4 HOH E 20 620 109 HOH HOH . H 4 HOH E 21 621 295 HOH HOH . H 4 HOH E 22 622 145 HOH HOH . H 4 HOH E 23 623 157 HOH HOH . H 4 HOH E 24 624 26 HOH HOH . H 4 HOH E 25 625 419 HOH HOH . H 4 HOH E 26 626 50 HOH HOH . H 4 HOH E 27 627 192 HOH HOH . H 4 HOH E 28 628 514 HOH HOH . H 4 HOH E 29 629 325 HOH HOH . H 4 HOH E 30 630 49 HOH HOH . H 4 HOH E 31 631 36 HOH HOH . H 4 HOH E 32 632 43 HOH HOH . H 4 HOH E 33 633 316 HOH HOH . H 4 HOH E 34 634 17 HOH HOH . H 4 HOH E 35 635 12 HOH HOH . H 4 HOH E 36 636 8 HOH HOH . H 4 HOH E 37 637 30 HOH HOH . H 4 HOH E 38 638 7 HOH HOH . H 4 HOH E 39 639 81 HOH HOH . H 4 HOH E 40 640 516 HOH HOH . H 4 HOH E 41 641 68 HOH HOH . H 4 HOH E 42 642 84 HOH HOH . H 4 HOH E 43 643 28 HOH HOH . H 4 HOH E 44 644 25 HOH HOH . H 4 HOH E 45 645 57 HOH HOH . H 4 HOH E 46 646 47 HOH HOH . H 4 HOH E 47 647 116 HOH HOH . H 4 HOH E 48 648 357 HOH HOH . H 4 HOH E 49 649 92 HOH HOH . H 4 HOH E 50 650 77 HOH HOH . H 4 HOH E 51 651 200 HOH HOH . H 4 HOH E 52 652 32 HOH HOH . H 4 HOH E 53 653 175 HOH HOH . H 4 HOH E 54 654 215 HOH HOH . H 4 HOH E 55 655 326 HOH HOH . H 4 HOH E 56 656 517 HOH HOH . H 4 HOH E 57 657 101 HOH HOH . H 4 HOH E 58 658 293 HOH HOH . H 4 HOH E 59 659 61 HOH HOH . H 4 HOH E 60 660 169 HOH HOH . H 4 HOH E 61 661 19 HOH HOH . H 4 HOH E 62 662 210 HOH HOH . H 4 HOH E 63 663 144 HOH HOH . H 4 HOH E 64 664 242 HOH HOH . H 4 HOH E 65 665 511 HOH HOH . H 4 HOH E 66 666 79 HOH HOH . H 4 HOH E 67 667 286 HOH HOH . H 4 HOH E 68 668 38 HOH HOH . H 4 HOH E 69 669 55 HOH HOH . H 4 HOH E 70 670 147 HOH HOH . H 4 HOH E 71 671 213 HOH HOH . H 4 HOH E 72 672 232 HOH HOH . H 4 HOH E 73 673 58 HOH HOH . H 4 HOH E 74 674 291 HOH HOH . H 4 HOH E 75 675 6 HOH HOH . H 4 HOH E 76 676 133 HOH HOH . H 4 HOH E 77 677 167 HOH HOH . H 4 HOH E 78 678 1 HOH HOH . H 4 HOH E 79 679 202 HOH HOH . H 4 HOH E 80 680 156 HOH HOH . H 4 HOH E 81 681 85 HOH HOH . H 4 HOH E 82 682 18 HOH HOH . H 4 HOH E 83 683 127 HOH HOH . H 4 HOH E 84 684 115 HOH HOH . H 4 HOH E 85 685 33 HOH HOH . H 4 HOH E 86 686 364 HOH HOH . H 4 HOH E 87 687 329 HOH HOH . H 4 HOH E 88 688 86 HOH HOH . H 4 HOH E 89 689 311 HOH HOH . H 4 HOH E 90 690 183 HOH HOH . H 4 HOH E 91 691 216 HOH HOH . H 4 HOH E 92 692 234 HOH HOH . H 4 HOH E 93 693 166 HOH HOH . H 4 HOH E 94 694 64 HOH HOH . H 4 HOH E 95 695 347 HOH HOH . H 4 HOH E 96 696 73 HOH HOH . H 4 HOH E 97 697 184 HOH HOH . H 4 HOH E 98 698 519 HOH HOH . H 4 HOH E 99 699 518 HOH HOH . H 4 HOH E 100 700 274 HOH HOH . H 4 HOH E 101 701 307 HOH HOH . H 4 HOH E 102 702 62 HOH HOH . H 4 HOH E 103 703 155 HOH HOH . H 4 HOH E 104 704 89 HOH HOH . H 4 HOH E 105 705 90 HOH HOH . H 4 HOH E 106 706 129 HOH HOH . H 4 HOH E 107 707 170 HOH HOH . H 4 HOH E 108 708 182 HOH HOH . H 4 HOH E 109 709 102 HOH HOH . H 4 HOH E 110 710 103 HOH HOH . H 4 HOH E 111 711 142 HOH HOH . H 4 HOH E 112 712 94 HOH HOH . H 4 HOH E 113 713 179 HOH HOH . H 4 HOH E 114 714 214 HOH HOH . H 4 HOH E 115 715 176 HOH HOH . H 4 HOH E 116 716 11 HOH HOH . H 4 HOH E 117 717 119 HOH HOH . H 4 HOH E 118 718 76 HOH HOH . H 4 HOH E 119 719 324 HOH HOH . H 4 HOH E 120 720 283 HOH HOH . H 4 HOH E 121 721 351 HOH HOH . H 4 HOH E 122 722 230 HOH HOH . H 4 HOH E 123 723 507 HOH HOH . H 4 HOH E 124 724 457 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 . . . E 2 -70.029 13.195 24.261 1 20.09 ? N1 PLP 501 E 1 HETATM 2 C C2 PLP . . . E 2 -69.379 14.094 24.996 1 20.33 ? C2 PLP 501 E 1 HETATM 3 C C2A PLP . . . E 2 -69.458 15.534 24.603 1 20.24 ? C2A PLP 501 E 1 HETATM 4 C C3 PLP . . . E 2 -68.636 13.689 26.117 1 20.4 ? C3 PLP 501 E 1 HETATM 5 O O3 PLP . . . E 2 -67.994 14.633 26.844 1 21.15 ? O3 PLP 501 E 1 HETATM 6 C C4 PLP . . . E 2 -68.585 12.324 26.462 1 20.05 ? C4 PLP 501 E 1 HETATM 7 C C4A PLP . . . E 2 -67.814 11.91 27.636 1 20.28 ? C4A PLP 501 E 1 HETATM 8 C C5 PLP . . . E 2 -69.282 11.405 25.662 1 19.61 ? C5 PLP 501 E 1 HETATM 9 C C6 PLP . . . E 2 -69.979 11.886 24.587 1 19.79 ? C6 PLP 501 E 1 HETATM 10 C C5A PLP . . . E 2 -69.272 9.929 25.946 1 18.88 ? C5A PLP 501 E 1 HETATM 11 O O4P PLP . . . E 2 -69.903 9.637 27.231 1 18.19 ? O4P PLP 501 E 1 HETATM 12 P P PLP . . . E 2 -69.392 8.417 28.15 1 17.5 ? P PLP 501 E 1 HETATM 13 O O1P PLP . . . E 2 -69.567 7.167 27.303 1 17.07 ? O1P PLP 501 E 1 HETATM 14 O O2P PLP . . . E 2 -67.94 8.715 28.458 1 17.42 -1 O2P PLP 501 E 1 HETATM 15 O O3P PLP . . . E 2 -70.279 8.441 29.379 1 17.41 ? O3P PLP 501 E 1 # _model_server_stats.io_time_ms 101 _model_server_stats.parse_time_ms 114 _model_server_stats.create_model_time_ms 65 _model_server_stats.query_time_ms 363 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 15 #