data_5XT5 # _model_server_result.job_id 5uL9b-1cVaN_UjAGQ0KSyA _model_server_result.datetime_utc '2024-11-27 15:24:58' _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 5xt5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":501}' # _entry.id 5XT5 # _exptl.entry_id 5XT5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 247.142 _entity.id 4 _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 5XT5 _cell.length_a 74.98 _cell.length_b 74.98 _cell.length_c 364.41 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5XT5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _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,I,J,K,L _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 ? 4 F N N ? 4 G 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 B NZ LYS 227 A LYS 224 1_555 F C4A PLP . A PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.253 ? covale ? covale2 C NZ LYS 227 B LYS 224 1_555 G C4A PLP . B PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.27 ? metalc ? metalc1 A OD2 ASP 43 D ASP 43 1_555 E ZN ZN . D ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc2 A SG CYS 66 D CYS 66 1_555 E ZN ZN . D ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc3 A SG CYS 128 D CYS 128 1_555 E ZN ZN . D ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc4 E ZN ZN . D ZN 201 1_555 C ND1 HIS 345 B HIS 342 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? metalc ? metalc5 B ND1 HIS 345 A HIS 342 1_555 H ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc6 D OD1 ASP 43 C ASP 43 1_555 H ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? metalc ? metalc7 D SG CYS 66 C CYS 66 1_555 H ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? metalc ? metalc8 D SG CYS 128 C CYS 128 1_555 H ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? # _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 260 n y N1 C6 PLP sing 261 n y C2 C2A PLP sing 262 n n C2 C3 PLP sing 263 n y C2A H2A1 PLP sing 264 n n C2A H2A2 PLP sing 265 n n C2A H2A3 PLP sing 266 n n C3 O3 PLP sing 267 n n C3 C4 PLP doub 268 n y O3 HO3 PLP sing 269 n n C4 C4A PLP sing 270 n n C4 C5 PLP sing 271 n y C4A O4A PLP doub 272 n n C4A H4A PLP sing 273 n n C5 C6 PLP doub 274 n y C5 C5A PLP sing 275 n n C6 H6 PLP sing 276 n n C5A O4P PLP sing 277 n n C5A H5A1 PLP sing 278 n n C5A H5A2 PLP sing 279 n n O4P P PLP sing 280 n n P O1P PLP doub 281 n n P O2P PLP sing 282 n n P O3P PLP sing 283 n n O2P HOP2 PLP sing 284 n n O3P HOP3 PLP sing 285 n n # _atom_sites.entry_id 5XT5 _atom_sites.fract_transf_matrix[1][1] 0.013337 _atom_sites.fract_transf_matrix[1][2] 0.0077 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.0154 _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] 0.002744 _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 E 3 ZN D 1 201 150 ZN ZN . F 4 PLP A 1 501 501 PLP PLP . G 4 PLP B 1 501 501 PLP PLP . H 3 ZN C 1 201 150 ZN ZN . I 5 HOH D 1 301 180 HOH HOH . I 5 HOH D 2 302 179 HOH HOH . I 5 HOH D 3 303 178 HOH HOH . J 5 HOH A 1 601 177 HOH HOH . J 5 HOH A 2 602 157 HOH HOH . J 5 HOH A 3 603 76 HOH HOH . J 5 HOH A 4 604 82 HOH HOH . J 5 HOH A 5 605 55 HOH HOH . J 5 HOH A 6 606 60 HOH HOH . J 5 HOH A 7 607 28 HOH HOH . J 5 HOH A 8 608 62 HOH HOH . J 5 HOH A 9 609 141 HOH HOH . J 5 HOH A 10 610 125 HOH HOH . J 5 HOH A 11 611 151 HOH HOH . J 5 HOH A 12 612 4 HOH HOH . J 5 HOH A 13 613 150 HOH HOH . J 5 HOH A 14 614 1 HOH HOH . J 5 HOH A 15 615 58 HOH HOH . J 5 HOH A 16 616 5 HOH HOH . J 5 HOH A 17 617 9 HOH HOH . J 5 HOH A 18 618 21 HOH HOH . J 5 HOH A 19 619 159 HOH HOH . J 5 HOH A 20 620 72 HOH HOH . J 5 HOH A 21 621 45 HOH HOH . J 5 HOH A 22 622 68 HOH HOH . J 5 HOH A 23 623 181 HOH HOH . J 5 HOH A 24 624 59 HOH HOH . J 5 HOH A 25 625 81 HOH HOH . J 5 HOH A 26 626 64 HOH HOH . J 5 HOH A 27 627 52 HOH HOH . J 5 HOH A 28 628 19 HOH HOH . J 5 HOH A 29 629 152 HOH HOH . J 5 HOH A 30 630 69 HOH HOH . J 5 HOH A 31 631 12 HOH HOH . J 5 HOH A 32 632 57 HOH HOH . J 5 HOH A 33 633 147 HOH HOH . J 5 HOH A 34 634 34 HOH HOH . J 5 HOH A 35 635 160 HOH HOH . J 5 HOH A 36 636 23 HOH HOH . J 5 HOH A 37 637 65 HOH HOH . J 5 HOH A 38 638 16 HOH HOH . J 5 HOH A 39 639 38 HOH HOH . J 5 HOH A 40 640 26 HOH HOH . J 5 HOH A 41 641 33 HOH HOH . J 5 HOH A 42 642 139 HOH HOH . J 5 HOH A 43 643 149 HOH HOH . J 5 HOH A 44 644 73 HOH HOH . J 5 HOH A 45 645 84 HOH HOH . J 5 HOH A 46 646 162 HOH HOH . J 5 HOH A 47 647 135 HOH HOH . J 5 HOH A 48 648 156 HOH HOH . J 5 HOH A 49 649 47 HOH HOH . J 5 HOH A 50 650 8 HOH HOH . J 5 HOH A 51 651 182 HOH HOH . J 5 HOH A 52 652 14 HOH HOH . J 5 HOH A 53 653 74 HOH HOH . J 5 HOH A 54 654 63 HOH HOH . J 5 HOH A 55 655 66 HOH HOH . J 5 HOH A 56 656 85 HOH HOH . J 5 HOH A 57 657 41 HOH HOH . J 5 HOH A 58 658 70 HOH HOH . J 5 HOH A 59 659 148 HOH HOH . J 5 HOH A 60 660 108 HOH HOH . J 5 HOH A 61 661 71 HOH HOH . J 5 HOH A 62 662 142 HOH HOH . J 5 HOH A 63 663 124 HOH HOH . J 5 HOH A 64 664 130 HOH HOH . J 5 HOH A 65 665 27 HOH HOH . J 5 HOH A 66 666 80 HOH HOH . J 5 HOH A 67 667 94 HOH HOH . J 5 HOH A 68 668 25 HOH HOH . J 5 HOH A 69 669 61 HOH HOH . J 5 HOH A 70 670 140 HOH HOH . J 5 HOH A 71 671 92 HOH HOH . J 5 HOH A 72 672 121 HOH HOH . J 5 HOH A 73 673 50 HOH HOH . J 5 HOH A 74 674 30 HOH HOH . J 5 HOH A 75 675 143 HOH HOH . J 5 HOH A 76 676 137 HOH HOH . J 5 HOH A 77 677 87 HOH HOH . J 5 HOH A 78 678 161 HOH HOH . J 5 HOH A 79 679 154 HOH HOH . J 5 HOH A 80 680 67 HOH HOH . J 5 HOH A 81 681 49 HOH HOH . J 5 HOH A 82 682 93 HOH HOH . J 5 HOH A 83 683 77 HOH HOH . J 5 HOH A 84 684 15 HOH HOH . J 5 HOH A 85 685 51 HOH HOH . J 5 HOH A 86 686 79 HOH HOH . J 5 HOH A 87 687 83 HOH HOH . J 5 HOH A 88 688 183 HOH HOH . J 5 HOH A 89 689 120 HOH HOH . J 5 HOH A 90 690 22 HOH HOH . J 5 HOH A 91 691 56 HOH HOH . J 5 HOH A 92 692 155 HOH HOH . J 5 HOH A 93 693 48 HOH HOH . J 5 HOH A 94 694 86 HOH HOH . J 5 HOH A 95 695 138 HOH HOH . J 5 HOH A 96 696 122 HOH HOH . J 5 HOH A 97 697 153 HOH HOH . K 5 HOH B 1 601 136 HOH HOH . K 5 HOH B 2 602 116 HOH HOH . K 5 HOH B 3 603 98 HOH HOH . K 5 HOH B 4 604 78 HOH HOH . K 5 HOH B 5 605 145 HOH HOH . K 5 HOH B 6 606 37 HOH HOH . K 5 HOH B 7 607 164 HOH HOH . K 5 HOH B 8 608 106 HOH HOH . K 5 HOH B 9 609 44 HOH HOH . K 5 HOH B 10 610 173 HOH HOH . K 5 HOH B 11 611 110 HOH HOH . K 5 HOH B 12 612 184 HOH HOH . K 5 HOH B 13 613 2 HOH HOH . K 5 HOH B 14 614 35 HOH HOH . K 5 HOH B 15 615 20 HOH HOH . K 5 HOH B 16 616 115 HOH HOH . K 5 HOH B 17 617 75 HOH HOH . K 5 HOH B 18 618 175 HOH HOH . K 5 HOH B 19 619 123 HOH HOH . K 5 HOH B 20 620 127 HOH HOH . K 5 HOH B 21 621 97 HOH HOH . K 5 HOH B 22 622 104 HOH HOH . K 5 HOH B 23 623 167 HOH HOH . K 5 HOH B 24 624 90 HOH HOH . K 5 HOH B 25 625 3 HOH HOH . K 5 HOH B 26 626 103 HOH HOH . K 5 HOH B 27 627 111 HOH HOH . K 5 HOH B 28 628 113 HOH HOH . K 5 HOH B 29 629 95 HOH HOH . K 5 HOH B 30 630 36 HOH HOH . K 5 HOH B 31 631 46 HOH HOH . K 5 HOH B 32 632 91 HOH HOH . K 5 HOH B 33 633 40 HOH HOH . K 5 HOH B 34 634 176 HOH HOH . K 5 HOH B 35 635 186 HOH HOH . K 5 HOH B 36 636 13 HOH HOH . K 5 HOH B 37 637 43 HOH HOH . K 5 HOH B 38 638 187 HOH HOH . K 5 HOH B 39 639 31 HOH HOH . K 5 HOH B 40 640 29 HOH HOH . K 5 HOH B 41 641 146 HOH HOH . K 5 HOH B 42 642 128 HOH HOH . K 5 HOH B 43 643 7 HOH HOH . K 5 HOH B 44 644 132 HOH HOH . K 5 HOH B 45 645 165 HOH HOH . K 5 HOH B 46 646 18 HOH HOH . K 5 HOH B 47 647 10 HOH HOH . K 5 HOH B 48 648 42 HOH HOH . K 5 HOH B 49 649 39 HOH HOH . K 5 HOH B 50 650 114 HOH HOH . K 5 HOH B 51 651 129 HOH HOH . K 5 HOH B 52 652 101 HOH HOH . K 5 HOH B 53 653 185 HOH HOH . K 5 HOH B 54 654 11 HOH HOH . K 5 HOH B 55 655 105 HOH HOH . K 5 HOH B 56 656 99 HOH HOH . K 5 HOH B 57 657 168 HOH HOH . K 5 HOH B 58 658 6 HOH HOH . K 5 HOH B 59 659 54 HOH HOH . K 5 HOH B 60 660 144 HOH HOH . K 5 HOH B 61 661 174 HOH HOH . K 5 HOH B 62 662 119 HOH HOH . K 5 HOH B 63 663 107 HOH HOH . K 5 HOH B 64 664 118 HOH HOH . K 5 HOH B 65 665 126 HOH HOH . K 5 HOH B 66 666 53 HOH HOH . K 5 HOH B 67 667 109 HOH HOH . K 5 HOH B 68 668 188 HOH HOH . K 5 HOH B 69 669 112 HOH HOH . K 5 HOH B 70 670 169 HOH HOH . K 5 HOH B 71 671 163 HOH HOH . K 5 HOH B 72 672 166 HOH HOH . K 5 HOH B 73 673 96 HOH HOH . K 5 HOH B 74 674 170 HOH HOH . K 5 HOH B 75 675 32 HOH HOH . K 5 HOH B 76 676 189 HOH HOH . K 5 HOH B 77 677 24 HOH HOH . K 5 HOH B 78 678 102 HOH HOH . K 5 HOH B 79 679 89 HOH HOH . K 5 HOH B 80 680 100 HOH HOH . K 5 HOH B 81 681 17 HOH HOH . K 5 HOH B 82 682 88 HOH HOH . L 5 HOH C 1 301 131 HOH HOH . L 5 HOH C 2 302 171 HOH HOH . L 5 HOH C 3 303 134 HOH HOH . L 5 HOH C 4 304 117 HOH HOH . L 5 HOH C 5 305 133 HOH HOH . L 5 HOH C 6 306 172 HOH HOH . L 5 HOH C 7 307 158 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 . . . F 4 9.226 7.84 -13.151 1 38.32 ? N1 PLP 501 A 1 HETATM 2 C C2 PLP . . . F 4 10.322 7.094 -13.043 1 42.6 ? C2 PLP 501 A 1 HETATM 3 C C2A PLP . . . F 4 11.43 7.225 -14.067 1 35.98 ? C2A PLP 501 A 1 HETATM 4 C C3 PLP . . . F 4 10.402 6.148 -11.902 1 40.74 ? C3 PLP 501 A 1 HETATM 5 O O3 PLP . . . F 4 11.483 5.358 -11.694 1 42.49 ? O3 PLP 501 A 1 HETATM 6 C C4 PLP . . . F 4 9.29 6.096 -10.955 1 40.69 ? C4 PLP 501 A 1 HETATM 7 C C4A PLP . . . F 4 9.369 5.202 -9.8 1 40.9 ? C4A PLP 501 A 1 HETATM 8 C C5 PLP . . . F 4 8.16 6.968 -11.206 1 43.34 ? C5 PLP 501 A 1 HETATM 9 C C6 PLP . . . F 4 8.203 7.8 -12.329 1 41.34 ? C6 PLP 501 A 1 HETATM 10 C C5A PLP . . . F 4 6.958 7.008 -10.316 1 39.65 ? C5A PLP 501 A 1 HETATM 11 O O4P PLP . . . F 4 7.307 7.441 -9.01 1 47.81 ? O4P PLP 501 A 1 HETATM 12 P P PLP . . . F 4 6.363 7.11 -7.717 1 38.31 ? P PLP 501 A 1 HETATM 13 O O1P PLP . . . F 4 5.232 8.051 -7.9 1 34.72 ? O1P PLP 501 A 1 HETATM 14 O O2P PLP . . . F 4 5.993 5.684 -7.847 1 41.13 ? O2P PLP 501 A 1 HETATM 15 O O3P PLP . . . F 4 7.312 7.387 -6.626 1 41.46 ? O3P PLP 501 A 1 # _model_server_stats.io_time_ms 48 _model_server_stats.parse_time_ms 62 _model_server_stats.create_model_time_ms 42 _model_server_stats.query_time_ms 1152 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 15 #