data_6XYL # _model_server_result.job_id omWDg47qVrsykj40YVp60A _model_server_result.datetime_utc '2024-12-07 02:20:49' _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 6xyl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":601}' # _entry.id 6XYL # _exptl.entry_id 6XYL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 318.22 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC ACID' _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 6XYL _cell.length_a 82.441 _cell.length_b 82.441 _cell.length_c 421.254 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6XYL _symmetry.cell_setting ? _symmetry.Int_Tables_number 144 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31' # 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 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_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,F,G,L 1 1 B,D,H,J 2 1 C,E,I,K 3 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 ? 2 G N N ? 2 H N N ? 2 I N N ? 2 J N N ? 2 K N N ? 2 L N N # _chem_comp.formula 'C11 H15 N2 O7 P' _chem_comp.formula_weight 318.22 _chem_comp.id P1T _chem_comp.mon_nstd_flag . _chem_comp.name '2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC ACID' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 OP1 P P1T sing 235 n n OP1 HOP1 P1T sing 236 n n P OP2 P1T doub 237 n n P OP4 P1T sing 238 n n P OP3 P1T sing 239 n n OP3 HOP3 P1T sing 240 n n OP4 C5A P1T sing 241 n n C5A C5 P1T sing 242 n n C5A H5A1 P1T sing 243 n n C5A H5A2 P1T sing 244 n n C5 C4 P1T sing 245 n y C5 C6 P1T doub 246 n y C6 N1 P1T sing 247 n y C6 H6 P1T sing 248 n n N1 C2 P1T doub 249 n y C2 C3 P1T sing 250 n y C2 C2A P1T sing 251 n n C2A H2A1 P1T sing 252 n n C2A H2A2 P1T sing 253 n n C2A H2A3 P1T sing 254 n n C3 O3A P1T sing 255 n n C3 C4 P1T doub 256 n y O3A HO3A P1T sing 257 n n C4 C4A P1T sing 258 n n C4A N P1T sing 259 n n C4A H4A1 P1T sing 260 n n C4A H4A2 P1T sing 261 n n N CA P1T sing 262 n n N HN P1T sing 263 n n CA C P1T sing 264 n n CA CB P1T doub 265 n n CB HB1 P1T sing 266 n n CB HB2 P1T sing 267 n n C OXT P1T doub 268 n n C O P1T sing 269 n n O HO P1T sing 270 n n # _atom_sites.entry_id 6XYL _atom_sites.fract_transf_matrix[1][1] 0.01213 _atom_sites.fract_transf_matrix[1][2] 0.007003 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014006 _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] 0.002374 _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 P1T A 1 601 601 P1T P1T . H 2 P1T B 1 601 601 P1T P1T . I 2 P1T C 1 601 601 P1T P1T . J 2 P1T D 1 601 601 P1T P1T . K 2 P1T E 1 601 601 P1T P1T . L 2 P1T F 1 601 601 P1T P1T . # 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 O OP1 P1T . . . H 2 -25.955 14.016 64.124 1 74.59 ? OP1 P1T 601 B 1 HETATM 2 P P P1T . . . H 2 -25.526 13.569 62.747 1 73.7 ? P P1T 601 B 1 HETATM 3 O OP2 P1T . . . H 2 -24.311 12.68 62.862 1 72.86 ? OP2 P1T 601 B 1 HETATM 4 O OP3 P1T . . . H 2 -25.188 14.778 61.908 1 72.56 ? OP3 P1T 601 B 1 HETATM 5 O OP4 P1T . . . H 2 -26.753 12.731 62.035 1 74.91 ? OP4 P1T 601 B 1 HETATM 6 C C5A P1T . . . H 2 -26.936 11.39 62.387 1 75.8 ? C5A P1T 601 B 1 HETATM 7 C C5 P1T . . . H 2 -27.191 10.563 61.13 1 76.06 ? C5 P1T 601 B 1 HETATM 8 C C6 P1T . . . H 2 -28.483 10.194 60.794 1 77.59 ? C6 P1T 601 B 1 HETATM 9 N N1 P1T . . . H 2 -28.711 9.461 59.682 1 77.85 ? N1 P1T 601 B 1 HETATM 10 C C2 P1T . . . H 2 -27.678 9.086 58.894 1 76.61 ? C2 P1T 601 B 1 HETATM 11 C C2A P1T . . . H 2 -27.937 8.259 57.638 1 76.93 ? C2A P1T 601 B 1 HETATM 12 C C3 P1T . . . H 2 -26.383 9.454 59.227 1 75.11 ? C3 P1T 601 B 1 HETATM 13 O O3A P1T . . . H 2 -25.314 9.066 58.412 1 73.9 ? O3A P1T 601 B 1 HETATM 14 C C4 P1T . . . H 2 -26.154 10.188 60.342 1 74.85 ? C4 P1T 601 B 1 HETATM 15 C C4A P1T . . . H 2 -24.726 10.593 60.71 1 73.24 ? C4A P1T 601 B 1 HETATM 16 N N P1T . . . H 2 -23.788 9.901 59.844 1 72.5 ? N P1T 601 B 1 HETATM 17 C CA P1T . . . H 2 -22.38 9.841 60.197 1 71.07 ? CA P1T 601 B 1 HETATM 18 C CB P1T . . . H 2 -22.021 9.758 61.46 1 71.07 ? CB P1T 601 B 1 HETATM 19 C C P1T . . . H 2 -21.315 9.875 59.101 1 70.39 ? C P1T 601 B 1 HETATM 20 O O P1T . . . H 2 -20.095 9.823 59.408 1 69.93 ? O P1T 601 B 1 HETATM 21 O OXT P1T . . . H 2 -21.657 9.954 57.892 1 70.31 ? OXT P1T 601 B 1 # _model_server_stats.io_time_ms 36 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 53 _model_server_stats.query_time_ms 237 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 21 #