data_3G8M # _model_server_result.job_id 90CJpcb7wjp_nvpDzWPcTQ _model_server_result.datetime_utc '2024-10-11 11:18:43' _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 3g8m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":418}' # _entry.id 3G8M # _exptl.entry_id 3G8M _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 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 3G8M _cell.length_a 112.59 _cell.length_b 112.59 _cell.length_c 68.929 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3G8M _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _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 _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' 8_555 -y,-x,-z+1/2 0 -1 0 -1 0 0 0 0 -1 0 0 34.4645 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 covale ? covale1 A NZ LYS 229 A LYS 229 1_555 B C4A PLP . A PLP 418 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.528 ? covale ? covale2 A NZ LYS 229 A LYS 229 1_555 B C4A PLP . A PLP 418 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.524 ? # _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 258 n y N1 C6 PLP sing 259 n y C2 C2A PLP sing 260 n n C2 C3 PLP sing 261 n y C2A H2A1 PLP sing 262 n n C2A H2A2 PLP sing 263 n n C2A H2A3 PLP sing 264 n n C3 O3 PLP sing 265 n n C3 C4 PLP doub 266 n y O3 HO3 PLP sing 267 n n C4 C4A PLP sing 268 n n C4 C5 PLP sing 269 n y C4A O4A PLP doub 270 n n C4A H4A PLP sing 271 n n C5 C6 PLP doub 272 n y C5 C5A PLP sing 273 n n C6 H6 PLP sing 274 n n C5A O4P PLP sing 275 n n C5A H5A1 PLP sing 276 n n C5A H5A2 PLP sing 277 n n O4P P PLP sing 278 n n P O1P PLP doub 279 n n P O2P PLP sing 280 n n P O3P PLP sing 281 n n O2P HOP2 PLP sing 282 n n O3P HOP3 PLP sing 283 n n # _atom_sites.entry_id 3G8M _atom_sites.fract_transf_matrix[1][1] 0.008882 _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] 0.008882 _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] 0.014508 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id PLP _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 418 _pdbx_nonpoly_scheme.auth_seq_num 1 _pdbx_nonpoly_scheme.pdb_mon_id PLP _pdbx_nonpoly_scheme.auth_mon_id PLP _pdbx_nonpoly_scheme.pdb_ins_code . # 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 . A . B 2 -34.866 24.719 7.504 0.5 42.94 ? N1 PLP 418 A 1 HETATM 2 N N1 PLP . B . B 2 -35.003 23.462 7.573 0.5 43.16 ? N1 PLP 418 A 1 HETATM 3 C C2 PLP . A . B 2 -35.109 24.1 6.289 0.5 42.98 ? C2 PLP 418 A 1 HETATM 4 C C2 PLP . B . B 2 -35.248 23.481 6.211 0.5 43.17 ? C2 PLP 418 A 1 HETATM 5 C C2A PLP . A . B 2 -36.524 23.794 5.887 0.5 42.98 ? C2A PLP 418 A 1 HETATM 6 C C2A PLP . B . B 2 -36.654 23.683 5.719 0.5 43.16 ? C2A PLP 418 A 1 HETATM 7 C C3 PLP . A . B 2 -34.041 23.769 5.449 0.5 42.86 ? C3 PLP 418 A 1 HETATM 8 C C3 PLP . B . B 2 -34.192 23.315 5.31 0.5 43.03 ? C3 PLP 418 A 1 HETATM 9 O O3 PLP . A . B 2 -34.275 23.156 4.241 0.5 42.96 ? O3 PLP 418 A 1 HETATM 10 O O3 PLP . B . B 2 -34.426 23.333 3.957 0.5 43.14 ? O3 PLP 418 A 1 HETATM 11 C C4 PLP . A . B 2 -32.731 24.065 5.836 0.5 42.72 ? C4 PLP 418 A 1 HETATM 12 C C4 PLP . B . B 2 -32.892 23.128 5.79 0.5 42.89 ? C4 PLP 418 A 1 HETATM 13 C C4A PLP . A . B 2 -31.655 24.063 4.785 0.5 41.91 ? C4A PLP 418 A 1 HETATM 14 C C4A PLP . B . B 2 -31.784 22.83 4.818 0.5 42.02 ? C4A PLP 418 A 1 HETATM 15 C C5 PLP . A . B 2 -32.499 24.687 7.068 0.5 42.88 ? C5 PLP 418 A 1 HETATM 16 C C5 PLP . B . B 2 -32.654 23.111 7.17 0.5 43.06 ? C5 PLP 418 A 1 HETATM 17 C C6 PLP . A . B 2 -33.572 25.013 7.896 0.5 42.9 ? C6 PLP 418 A 1 HETATM 18 C C6 PLP . B . B 2 -33.72 23.278 8.055 0.5 43.12 ? C6 PLP 418 A 1 HETATM 19 C C5A PLP . A . B 2 -31.089 25.018 7.517 0.5 43.07 ? C5A PLP 418 A 1 HETATM 20 C C5A PLP . B . B 2 -31.255 22.912 7.719 0.5 43.25 ? C5A PLP 418 A 1 HETATM 21 O O4P PLP . A . B 2 -30.715 24.244 8.64 0.5 43.41 ? O4P PLP 418 A 1 HETATM 22 O O4P PLP . B . B 2 -30.999 23.831 8.763 0.5 43.61 ? O4P PLP 418 A 1 HETATM 23 P P PLP . A . B 2 -30.717 22.63 8.63 0.5 43.52 ? P PLP 418 A 1 HETATM 24 P P PLP . B . B 2 -30.618 25.376 8.49 0.5 43.72 ? P PLP 418 A 1 HETATM 25 O O1P PLP . A . B 2 -30.507 22.126 7.22 0.5 43.47 ? O1P PLP 418 A 1 HETATM 26 O O1P PLP . B . B 2 -30.875 25.727 7.043 0.5 43.76 ? O1P PLP 418 A 1 HETATM 27 O O2P PLP . A . B 2 -32.046 22.139 9.147 0.5 43.55 ? O2P PLP 418 A 1 HETATM 28 O O2P PLP . B . B 2 -29.157 25.597 8.808 0.5 43.69 ? O2P PLP 418 A 1 HETATM 29 O O3P PLP . A . B 2 -29.611 22.115 9.521 0.5 43.45 ? O3P PLP 418 A 1 HETATM 30 O O3P PLP . B . B 2 -31.463 26.263 9.375 0.5 43.65 ? O3P PLP 418 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 30 #