data_5O5C # _model_server_result.job_id QDl7b2ushWJGdcQifjeogw _model_server_result.datetime_utc '2024-12-12 11:09:47' _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 5o5c # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":601}' # _entry.id 5O5C # _exptl.entry_id 5O5C _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 6 _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 5O5C _cell.length_a 269.791 _cell.length_b 269.791 _cell.length_c 56.194 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5O5C _symmetry.cell_setting ? _symmetry.Int_Tables_number 145 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 software_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 PISA dimeric 2 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,G,H,M,N 1 1 C,D,I,J,O,P 2 1 E,K,Q 3 1 F,L,R 3 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' 1_556 x,y,z+1 1 0 0 0 1 0 0 0 1 0 0 56.194 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 G N N ? 2 H N N ? 2 I N N ? 2 J N N ? 2 K N N ? 2 L 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 330 A LYS 328 1_555 G C4A PLP . A PLP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.287 ? covale ? covale2 C NZ LYS 330 C LYS 328 1_555 I C4A PLP . C PLP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.268 ? covale ? covale3 E NZ LYS 330 E LYS 328 1_555 K C4A PLP . E PLP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.273 ? covale ? covale4 F NZ LYS 330 F LYS 328 1_555 L C4A PLP . F PLP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.25 ? # _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 5O5C _atom_sites.fract_transf_matrix[1][1] 0.003707 _atom_sites.fract_transf_matrix[1][2] 0.00214 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00428 _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] 0.017795 _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 G 2 PLP A 1 601 1 PLP PLP . H 2 PLP B 1 601 4 PLP PLP . I 2 PLP C 1 601 3 PLP PLP . J 2 PLP D 1 601 2 PLP PLP . K 2 PLP E 1 601 5 PLP PLP . L 2 PLP F 1 601 6 PLP PLP . M 3 HOH A 1 701 47 HOH HOH . M 3 HOH A 2 702 183 HOH HOH . M 3 HOH A 3 703 73 HOH HOH . M 3 HOH A 4 704 205 HOH HOH . M 3 HOH A 5 705 74 HOH HOH . M 3 HOH A 6 706 81 HOH HOH . M 3 HOH A 7 707 145 HOH HOH . M 3 HOH A 8 708 77 HOH HOH . M 3 HOH A 9 709 65 HOH HOH . M 3 HOH A 10 710 32 HOH HOH . M 3 HOH A 11 711 115 HOH HOH . M 3 HOH A 12 712 170 HOH HOH . M 3 HOH A 13 713 71 HOH HOH . M 3 HOH A 14 714 140 HOH HOH . M 3 HOH A 15 715 89 HOH HOH . M 3 HOH A 16 716 104 HOH HOH . M 3 HOH A 17 717 48 HOH HOH . M 3 HOH A 18 718 106 HOH HOH . M 3 HOH A 19 719 196 HOH HOH . M 3 HOH A 20 720 103 HOH HOH . M 3 HOH A 21 721 105 HOH HOH . M 3 HOH A 22 722 93 HOH HOH . M 3 HOH A 23 723 20 HOH HOH . M 3 HOH A 24 724 92 HOH HOH . M 3 HOH A 25 725 175 HOH HOH . M 3 HOH A 26 726 195 HOH HOH . M 3 HOH A 27 727 66 HOH HOH . M 3 HOH A 28 728 119 HOH HOH . M 3 HOH A 29 729 180 HOH HOH . M 3 HOH A 30 730 122 HOH HOH . N 3 HOH B 1 701 96 HOH HOH . N 3 HOH B 2 702 207 HOH HOH . N 3 HOH B 3 703 100 HOH HOH . N 3 HOH B 4 704 114 HOH HOH . N 3 HOH B 5 705 176 HOH HOH . N 3 HOH B 6 706 2 HOH HOH . N 3 HOH B 7 707 213 HOH HOH . N 3 HOH B 8 708 25 HOH HOH . N 3 HOH B 9 709 194 HOH HOH . N 3 HOH B 10 710 54 HOH HOH . N 3 HOH B 11 711 188 HOH HOH . N 3 HOH B 12 712 161 HOH HOH . N 3 HOH B 13 713 37 HOH HOH . N 3 HOH B 14 714 72 HOH HOH . N 3 HOH B 15 715 40 HOH HOH . N 3 HOH B 16 716 165 HOH HOH . N 3 HOH B 17 717 69 HOH HOH . N 3 HOH B 18 718 206 HOH HOH . N 3 HOH B 19 719 9 HOH HOH . N 3 HOH B 20 720 146 HOH HOH . N 3 HOH B 21 721 22 HOH HOH . N 3 HOH B 22 722 214 HOH HOH . N 3 HOH B 23 723 58 HOH HOH . N 3 HOH B 24 724 116 HOH HOH . N 3 HOH B 25 725 178 HOH HOH . N 3 HOH B 26 726 201 HOH HOH . N 3 HOH B 27 727 141 HOH HOH . N 3 HOH B 28 728 117 HOH HOH . N 3 HOH B 29 729 87 HOH HOH . N 3 HOH B 30 730 111 HOH HOH . N 3 HOH B 31 731 123 HOH HOH . O 3 HOH C 1 701 160 HOH HOH . O 3 HOH C 2 702 44 HOH HOH . O 3 HOH C 3 703 167 HOH HOH . O 3 HOH C 4 704 23 HOH HOH . O 3 HOH C 5 705 95 HOH HOH . O 3 HOH C 6 706 42 HOH HOH . O 3 HOH C 7 707 131 HOH HOH . O 3 HOH C 8 708 11 HOH HOH . O 3 HOH C 9 709 112 HOH HOH . O 3 HOH C 10 710 154 HOH HOH . O 3 HOH C 11 711 192 HOH HOH . O 3 HOH C 12 712 51 HOH HOH . O 3 HOH C 13 713 134 HOH HOH . O 3 HOH C 14 714 34 HOH HOH . O 3 HOH C 15 715 63 HOH HOH . O 3 HOH C 16 716 174 HOH HOH . O 3 HOH C 17 717 193 HOH HOH . O 3 HOH C 18 718 113 HOH HOH . O 3 HOH C 19 719 1 HOH HOH . O 3 HOH C 20 720 85 HOH HOH . O 3 HOH C 21 721 64 HOH HOH . O 3 HOH C 22 722 185 HOH HOH . O 3 HOH C 23 723 136 HOH HOH . O 3 HOH C 24 724 60 HOH HOH . O 3 HOH C 25 725 49 HOH HOH . O 3 HOH C 26 726 211 HOH HOH . O 3 HOH C 27 727 16 HOH HOH . O 3 HOH C 28 728 62 HOH HOH . O 3 HOH C 29 729 6 HOH HOH . O 3 HOH C 30 730 138 HOH HOH . O 3 HOH C 31 731 24 HOH HOH . O 3 HOH C 32 732 152 HOH HOH . O 3 HOH C 33 733 59 HOH HOH . O 3 HOH C 34 734 33 HOH HOH . O 3 HOH C 35 735 126 HOH HOH . O 3 HOH C 36 736 164 HOH HOH . O 3 HOH C 37 737 179 HOH HOH . O 3 HOH C 38 738 91 HOH HOH . O 3 HOH C 39 739 28 HOH HOH . O 3 HOH C 40 740 57 HOH HOH . O 3 HOH C 41 741 79 HOH HOH . O 3 HOH C 42 742 132 HOH HOH . O 3 HOH C 43 743 215 HOH HOH . P 3 HOH D 1 701 4 HOH HOH . P 3 HOH D 2 702 163 HOH HOH . P 3 HOH D 3 703 148 HOH HOH . P 3 HOH D 4 704 118 HOH HOH . P 3 HOH D 5 705 153 HOH HOH . P 3 HOH D 6 706 159 HOH HOH . P 3 HOH D 7 707 10 HOH HOH . P 3 HOH D 8 708 191 HOH HOH . P 3 HOH D 9 709 50 HOH HOH . P 3 HOH D 10 710 149 HOH HOH . P 3 HOH D 11 711 162 HOH HOH . P 3 HOH D 12 712 137 HOH HOH . P 3 HOH D 13 713 18 HOH HOH . P 3 HOH D 14 714 210 HOH HOH . P 3 HOH D 15 715 7 HOH HOH . P 3 HOH D 16 716 151 HOH HOH . P 3 HOH D 17 717 124 HOH HOH . P 3 HOH D 18 718 97 HOH HOH . P 3 HOH D 19 719 94 HOH HOH . P 3 HOH D 20 720 13 HOH HOH . P 3 HOH D 21 721 29 HOH HOH . P 3 HOH D 22 722 198 HOH HOH . P 3 HOH D 23 723 133 HOH HOH . P 3 HOH D 24 724 68 HOH HOH . P 3 HOH D 25 725 76 HOH HOH . P 3 HOH D 26 726 187 HOH HOH . P 3 HOH D 27 727 86 HOH HOH . P 3 HOH D 28 728 109 HOH HOH . P 3 HOH D 29 729 200 HOH HOH . P 3 HOH D 30 730 45 HOH HOH . P 3 HOH D 31 731 202 HOH HOH . P 3 HOH D 32 732 78 HOH HOH . P 3 HOH D 33 733 56 HOH HOH . P 3 HOH D 34 734 102 HOH HOH . P 3 HOH D 35 735 177 HOH HOH . P 3 HOH D 36 736 75 HOH HOH . P 3 HOH D 37 737 31 HOH HOH . P 3 HOH D 38 738 99 HOH HOH . P 3 HOH D 39 739 43 HOH HOH . P 3 HOH D 40 740 46 HOH HOH . P 3 HOH D 41 741 125 HOH HOH . P 3 HOH D 42 742 12 HOH HOH . Q 3 HOH E 1 701 108 HOH HOH . Q 3 HOH E 2 702 181 HOH HOH . Q 3 HOH E 3 703 84 HOH HOH . Q 3 HOH E 4 704 150 HOH HOH . Q 3 HOH E 5 705 208 HOH HOH . Q 3 HOH E 6 706 107 HOH HOH . Q 3 HOH E 7 707 184 HOH HOH . Q 3 HOH E 8 708 173 HOH HOH . Q 3 HOH E 9 709 36 HOH HOH . Q 3 HOH E 10 710 139 HOH HOH . Q 3 HOH E 11 711 172 HOH HOH . Q 3 HOH E 12 712 82 HOH HOH . Q 3 HOH E 13 713 14 HOH HOH . Q 3 HOH E 14 714 8 HOH HOH . Q 3 HOH E 15 715 39 HOH HOH . Q 3 HOH E 16 716 197 HOH HOH . Q 3 HOH E 17 717 38 HOH HOH . Q 3 HOH E 18 718 83 HOH HOH . Q 3 HOH E 19 719 52 HOH HOH . Q 3 HOH E 20 720 26 HOH HOH . Q 3 HOH E 21 721 80 HOH HOH . Q 3 HOH E 22 722 35 HOH HOH . Q 3 HOH E 23 723 209 HOH HOH . R 3 HOH F 1 701 190 HOH HOH . R 3 HOH F 2 702 101 HOH HOH . R 3 HOH F 3 703 15 HOH HOH . R 3 HOH F 4 704 53 HOH HOH . R 3 HOH F 5 705 143 HOH HOH . R 3 HOH F 6 706 88 HOH HOH . R 3 HOH F 7 707 61 HOH HOH . R 3 HOH F 8 708 55 HOH HOH . R 3 HOH F 9 709 3 HOH HOH . R 3 HOH F 10 710 171 HOH HOH . R 3 HOH F 11 711 17 HOH HOH . R 3 HOH F 12 712 70 HOH HOH . R 3 HOH F 13 713 182 HOH HOH . R 3 HOH F 14 714 156 HOH HOH . R 3 HOH F 15 715 129 HOH HOH . R 3 HOH F 16 716 98 HOH HOH . R 3 HOH F 17 717 5 HOH HOH . R 3 HOH F 18 718 19 HOH HOH . R 3 HOH F 19 719 203 HOH HOH . R 3 HOH F 20 720 199 HOH HOH . R 3 HOH F 21 721 21 HOH HOH . R 3 HOH F 22 722 128 HOH HOH . R 3 HOH F 23 723 67 HOH HOH . R 3 HOH F 24 724 147 HOH HOH . R 3 HOH F 25 725 212 HOH HOH . R 3 HOH F 26 726 204 HOH HOH . R 3 HOH F 27 727 110 HOH HOH . R 3 HOH F 28 728 41 HOH HOH . R 3 HOH F 29 729 27 HOH HOH . R 3 HOH F 30 730 127 HOH HOH . R 3 HOH F 31 731 30 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 . . . J 2 122.221 157.533 23.152 1 41.23 ? N1 PLP 601 D 1 HETATM 2 C C2 PLP . . . J 2 121.014 158.124 23.087 1 42.48 ? C2 PLP 601 D 1 HETATM 3 C C2A PLP . . . J 2 119.892 157.747 24.02 1 43.03 ? C2A PLP 601 D 1 HETATM 4 C C3 PLP . . . J 2 120.827 159.19 22.094 1 46.19 ? C3 PLP 601 D 1 HETATM 5 O O3 PLP . . . J 2 119.625 159.816 22.016 1 47.77 ? O3 PLP 601 D 1 HETATM 6 C C4 PLP . . . J 2 121.986 159.524 21.217 1 46.19 ? C4 PLP 601 D 1 HETATM 7 C C4A PLP . . . J 2 121.902 160.539 20.14 1 48.96 ? C4A PLP 601 D 1 HETATM 8 C C5 PLP . . . J 2 123.241 158.802 21.394 1 42.23 ? C5 PLP 601 D 1 HETATM 9 C C6 PLP . . . J 2 123.285 157.824 22.38 1 44.93 ? C6 PLP 601 D 1 HETATM 10 C C5A PLP . . . J 2 124.429 159.162 20.532 1 42.87 ? C5A PLP 601 D 1 HETATM 11 O O4P PLP . . . J 2 124.85 160.48 20.936 1 41.86 ? O4P PLP 601 D 1 HETATM 12 P P PLP . . . J 2 125.781 161.467 20.052 1 42.23 ? P PLP 601 D 1 HETATM 13 O O1P PLP . . . J 2 124.912 162.025 18.928 1 42.33 ? O1P PLP 601 D 1 HETATM 14 O O2P PLP . . . J 2 126.886 160.584 19.56 1 44.01 ? O2P PLP 601 D 1 HETATM 15 O O3P PLP . . . J 2 126.239 162.537 21.031 1 39.77 ? O3P PLP 601 D 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 15 #