data_2YPI # _model_server_result.job_id -aXrSAFCjA3dWqqvTy67og _model_server_result.datetime_utc '2025-02-26 15:02:12' _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 2ypi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":249}' # _entry.id 2YPI # _exptl.entry_id 2YPI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 156.031 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description '2-PHOSPHOGLYCOLIC ACID' _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 99.7 _cell.angle_gamma 90 _cell.entry_id 2YPI _cell.length_a 74.35 _cell.length_b 83.97 _cell.length_c 38.67 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YPI _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _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,C,D,E,F _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 ? 2 C N N ? 2 D N N # _chem_comp.formula 'C2 H5 O6 P' _chem_comp.formula_weight 156.031 _chem_comp.id PGA _chem_comp.mon_nstd_flag . _chem_comp.name '2-PHOSPHOGLYCOLIC 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 P O1P PGA sing 218 n n P O2P PGA doub 219 n n P O3P PGA sing 220 n n P O4P PGA sing 221 n n O1P C2 PGA sing 222 n n O3P HOP3 PGA sing 223 n n O4P HOP4 PGA sing 224 n n C2 C1 PGA sing 225 n n C2 H21 PGA sing 226 n n C2 H22 PGA sing 227 n n C1 O1 PGA doub 228 n n C1 O2 PGA sing 229 n n O2 HO2 PGA sing 230 n n # _atom_sites.entry_id 2YPI _atom_sites.fract_transf_matrix[1][1] 0.01345 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002299 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011909 _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] 0.026235 _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 PGA A 1 249 249 PGA PGA . D 2 PGA B 1 249 249 PGA PGA . E 3 HOH A 1 602 602 HOH HOH . E 3 HOH A 2 603 603 HOH HOH . E 3 HOH A 3 607 607 HOH HOH . E 3 HOH A 4 608 608 HOH HOH . E 3 HOH A 5 609 609 HOH HOH . E 3 HOH A 6 612 612 HOH HOH . E 3 HOH A 7 621 621 HOH HOH . E 3 HOH A 8 631 631 HOH HOH . E 3 HOH A 9 632 632 HOH HOH . E 3 HOH A 10 633 633 HOH HOH . E 3 HOH A 11 640 640 HOH HOH . E 3 HOH A 12 651 651 HOH HOH . F 3 HOH B 1 601 601 HOH HOH . F 3 HOH B 2 604 604 HOH HOH . F 3 HOH B 3 605 605 HOH HOH . F 3 HOH B 4 606 606 HOH HOH . F 3 HOH B 5 619 619 HOH HOH . F 3 HOH B 6 620 620 HOH HOH . F 3 HOH B 7 622 622 HOH HOH . F 3 HOH B 8 623 623 HOH HOH . F 3 HOH B 9 625 625 HOH HOH . F 3 HOH B 10 630 630 HOH HOH . F 3 HOH B 11 641 641 HOH HOH . F 3 HOH B 12 643 643 HOH HOH . F 3 HOH B 13 650 650 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 P P PGA . . . D 2 53.911 41.565 56.07 1 6.6 ? P PGA 249 B 1 HETATM 2 O O1P PGA . . . D 2 55.366 42.069 55.384 1 6.6 ? O1P PGA 249 B 1 HETATM 3 O O2P PGA . . . D 2 53.284 40.474 55.384 1 6.6 ? O2P PGA 249 B 1 HETATM 4 O O3P PGA . . . D 2 53.322 43.077 56.032 1 6.6 ? O3P PGA 249 B 1 HETATM 5 O O4P PGA . . . D 2 54.332 41.397 57.519 1 6.6 ? O4P PGA 249 B 1 HETATM 6 C C2 PGA . . . D 2 55.378 41.733 54.012 1 6.6 ? C2 PGA 249 B 1 HETATM 7 C C1 PGA . . . D 2 56.433 41.985 53.059 1 6.6 ? C1 PGA 249 B 1 HETATM 8 O O1 PGA . . . D 2 57.515 42.573 53.25 1 6.6 ? O1 PGA 249 B 1 HETATM 9 O O2 PGA . . . D 2 56.357 41.565 51.763 1 6.6 ? O2 PGA 249 B 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 214 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 9 #