data_4F79 # _model_server_result.job_id CoC57Nap2hJSToV2viRuPQ _model_server_result.datetime_utc '2025-02-26 15:40:50' _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 4f79 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 4F79 # _exptl.entry_id 4F79 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 366.258 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description '2-(hydroxymethyl)phenyl 6-O-phosphono-beta-D-glucopyranoside' _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 4F79 _cell.length_a 82.278 _cell.length_b 82.278 _cell.length_c 221.211 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4F79 _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,C,D,E _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' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # _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 # _chem_comp.formula 'C13 H19 O10 P' _chem_comp.formula_weight 366.258 _chem_comp.id P53 _chem_comp.mon_nstd_flag n _chem_comp.name '2-(hydroxymethyl)phenyl 6-O-phosphono-beta-D-glucopyranoside' _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms 'Salicin-6-phosphate;2-(hydroxymethyl)phenyl 6-O-phosphono-beta-D-glucoside;2-(hydroxymethyl)phenyl 6-O-phosphono-D-glucoside;2-(hydroxymethyl)phenyl 6-O-phosphono-glucoside' # 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 O2P P53 sing 250 n n P O1P P53 sing 251 n n C1A C10 P53 sing 252 n y C1A H1A P53 sing 253 n n C2A C1A P53 doub 254 n y C2A C4A P53 sing 255 n y C2A H2A P53 sing 256 n n C4A C6A P53 doub 257 n y C4A H4A P53 sing 258 n n C6A C8 P53 sing 259 n y C6A H6 P53 sing 260 n n O6 P P53 sing 261 n n O6 C6 P53 sing 262 n n C8 O1 P53 sing 263 n n C10 C8 P53 doub 264 n y C10 C13 P53 sing 265 n n C13 H13 P53 sing 266 n n O15 C13 P53 sing 267 n n O1 C1 P53 sing 268 n n C1 O5 P53 sing 269 n n C1 H1 P53 sing 270 n n O1P HO1P P53 sing 271 n n C2 C1 P53 sing 272 n n C2 C3 P53 sing 273 n n C2 H2 P53 sing 274 n n C3 C4 P53 sing 275 n n C3 H3 P53 sing 276 n n C4 C5 P53 sing 277 n n C4 O4 P53 sing 278 n n C4 H4 P53 sing 279 n n C5 C6 P53 sing 280 n n C5 H5 P53 sing 281 n n O5 C5 P53 sing 282 n n O2P HO2P P53 sing 283 n n O2 C2 P53 sing 284 n n O2 HO2 P53 sing 285 n n O3 C3 P53 sing 286 n n O3 HO3 P53 sing 287 n n O4 HO4 P53 sing 288 n n C6 H61 P53 sing 289 n n C6 H62 P53 sing 290 n n O3P P P53 doub 291 n n C13 H18 P53 sing 292 n n O15 H191 P53 sing 293 n n # _atom_sites.entry_id 4F79 _atom_sites.fract_transf_matrix[1][1] 0.012154 _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] 0.012154 _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] 0.004521 _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 B 2 P53 A 1 501 1 P53 PSC . C 3 GOL A 1 502 1 GOL GOL . D 3 GOL A 1 503 2 GOL GOL . E 4 HOH A 1 601 1 HOH HOH . E 4 HOH A 2 602 2 HOH HOH . E 4 HOH A 3 603 3 HOH HOH . E 4 HOH A 4 604 4 HOH HOH . E 4 HOH A 5 605 5 HOH HOH . E 4 HOH A 6 606 6 HOH HOH . E 4 HOH A 7 607 7 HOH HOH . E 4 HOH A 8 608 8 HOH HOH . E 4 HOH A 9 609 9 HOH HOH . E 4 HOH A 10 610 10 HOH HOH . E 4 HOH A 11 611 11 HOH HOH . E 4 HOH A 12 612 12 HOH HOH . E 4 HOH A 13 613 13 HOH HOH . E 4 HOH A 14 614 14 HOH HOH . E 4 HOH A 15 615 15 HOH HOH . E 4 HOH A 16 616 16 HOH HOH . E 4 HOH A 17 617 17 HOH HOH . E 4 HOH A 18 618 18 HOH HOH . E 4 HOH A 19 619 19 HOH HOH . E 4 HOH A 20 620 20 HOH HOH . E 4 HOH A 21 621 21 HOH HOH . E 4 HOH A 22 622 22 HOH HOH . E 4 HOH A 23 623 23 HOH HOH . E 4 HOH A 24 624 24 HOH HOH . E 4 HOH A 25 625 25 HOH HOH . E 4 HOH A 26 626 26 HOH HOH . E 4 HOH A 27 627 27 HOH HOH . E 4 HOH A 28 628 28 HOH HOH . E 4 HOH A 29 629 29 HOH HOH . E 4 HOH A 30 630 30 HOH HOH . E 4 HOH A 31 631 31 HOH HOH . E 4 HOH A 32 632 32 HOH HOH . E 4 HOH A 33 633 33 HOH HOH . E 4 HOH A 34 634 34 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 P53 . . . B 2 37.465 2.929 10.981 1 64.2 ? P P53 501 A 1 HETATM 2 C C1A P53 . . . B 2 34.777 4.915 6.843 1 87.12 ? C1A P53 501 A 1 HETATM 3 C C2A P53 . . . B 2 35.913 4.127 6.746 1 85.65 ? C2A P53 501 A 1 HETATM 4 C C4A P53 . . . B 2 35.913 2.823 7.233 1 84.59 ? C4A P53 501 A 1 HETATM 5 C C6A P53 . . . B 2 34.756 2.308 7.833 1 86.22 ? C6A P53 501 A 1 HETATM 6 O O6 P53 . . . B 2 35.951 3.013 10.59 1 60.18 ? O6 P53 501 A 1 HETATM 7 C C8 P53 . . . B 2 33.617 3.098 7.951 1 89.86 ? C8 P53 501 A 1 HETATM 8 C C10 P53 . . . B 2 33.621 4.408 7.435 1 94.87 ? C10 P53 501 A 1 HETATM 9 C C13 P53 . . . B 2 32.402 5.272 7.539 1 96.31 ? C13 P53 501 A 1 HETATM 10 O O15 P53 . . . B 2 31.626 5.517 6.442 1 93.02 ? O15 P53 501 A 1 HETATM 11 O O1 P53 . . . B 2 32.405 2.592 8.52 1 87.36 ? O1 P53 501 A 1 HETATM 12 C C1 P53 . . . B 2 32.402 1.9 9.685 1 75.5 ? C1 P53 501 A 1 HETATM 13 O O1P P53 . . . B 2 37.729 4.128 11.88 1 50.64 ? O1P P53 501 A 1 HETATM 14 C C2 P53 . . . B 2 32.768 0.421 9.463 1 69.76 ? C2 P53 501 A 1 HETATM 15 C C3 P53 . . . B 2 33.312 -0.188 10.639 1 67.51 ? C3 P53 501 A 1 HETATM 16 C C4 P53 . . . B 2 34.444 0.58 11.029 1 65.14 ? C4 P53 501 A 1 HETATM 17 C C5 P53 . . . B 2 33.982 1.93 11.55 1 66.4 ? C5 P53 501 A 1 HETATM 18 O O5 P53 . . . B 2 33.049 2.629 10.693 1 67.31 ? O5 P53 501 A 1 HETATM 19 O O2P P53 . . . B 2 37.624 1.647 11.764 1 63.55 ? O2P P53 501 A 1 HETATM 20 O O2 P53 . . . B 2 31.611 -0.288 9.089 1 60.39 ? O2 P53 501 A 1 HETATM 21 O O3 P53 . . . B 2 33.595 -1.619 10.362 1 54.14 ? O3 P53 501 A 1 HETATM 22 O O4 P53 . . . B 2 35.258 -0.104 12.023 1 60.8 ? O4 P53 501 A 1 HETATM 23 C C6 P53 . . . B 2 35.105 2.854 11.698 1 64.85 ? C6 P53 501 A 1 HETATM 24 O O3P P53 . . . B 2 38.393 2.928 9.758 1 48.43 ? O3P P53 501 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 24 #