data_5JUC # _model_server_result.job_id 5oDmLwUlETqUZDVskDmbsg _model_server_result.datetime_utc '2025-01-09 15:27:03' _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 5juc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":405}' # _entry.id 5JUC # _exptl.entry_id 5JUC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 348.198 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2R)-2-(alpha-D-glucopyranosyloxy)-3-(phosphonooxy)propanoic acid' _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 5JUC _cell.length_a 99.434 _cell.length_b 99.434 _cell.length_c 126.785 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JUC _symmetry.cell_setting ? _symmetry.Int_Tables_number 80 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 41' # _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,G _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' 6_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 99.434 0 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id F _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 metalc ? metalc1 A OD1 ASP 140 A ASP 136 1_555 E MN MN . A MN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc2 A ND1 HIS 262 A HIS 258 1_555 E MN MN . A MN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc3 E MN MN . A MN 404 1_555 G O HOH . A HOH 515 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? # _chem_comp.formula 'C9 H17 O12 P' _chem_comp.formula_weight 348.198 _chem_comp.id XDX _chem_comp.mon_nstd_flag n _chem_comp.name '(2R)-2-(alpha-D-glucopyranosyloxy)-3-(phosphonooxy)propanoic acid' _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms '(2R)-2-(alpha-D-glucosyloxy)-3-(phosphonooxy)propanoic acid;(2R)-2-(D-glucosyloxy)-3-(phosphonooxy)propanoic acid;(2R)-2-(glucosyloxy)-3-(phosphonooxy)propanoic acid' # 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 O6 C6 XDX sing 425 n n C6 C5 XDX sing 426 n n O5 C5 XDX sing 427 n n O5 C1 XDX sing 428 n n C5 C4 XDX sing 429 n n C4 O4 XDX sing 430 n n C4 C3 XDX sing 431 n n C1 C2 XDX sing 432 n n C1 O1 XDX sing 433 n n C2 C3 XDX sing 434 n n C2 O2 XDX sing 435 n n OAU CAS XDX doub 436 n n C3 O3 XDX sing 437 n n CAS CAR XDX sing 438 n n CAS OAV XDX sing 439 n n O1 CAR XDX sing 440 n n CAR CAQ XDX sing 441 n n CAQ OAM XDX sing 442 n n OAM PAL XDX sing 443 n n OAP PAL XDX doub 444 n n PAL OAO XDX sing 445 n n PAL OAN XDX sing 446 n n OAN H1A XDX sing 447 n n OAO H2A XDX sing 448 n n CAQ H3A XDX sing 449 n n CAQ H4A XDX sing 450 n n CAR H5A XDX sing 451 n n OAV H6 XDX sing 452 n n C1 H1 XDX sing 453 n n C5 H5 XDX sing 454 n n C6 H61 XDX sing 455 n n C6 H62 XDX sing 456 n n O6 HO6 XDX sing 457 n n C4 H4 XDX sing 458 n n O4 HO4 XDX sing 459 n n C3 H3 XDX sing 460 n n O3 HO3 XDX sing 461 n n C2 H2 XDX sing 462 n n O2 HO2 XDX sing 463 n n # _atom_sites.entry_id 5JUC _atom_sites.fract_transf_matrix[1][1] 0.010057 _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] 0.010057 _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] 0.007887 _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 UDP A 1 401 1 UDP UDP . C 3 EDO A 1 402 1 EDO EDO . D 3 EDO A 1 403 2 EDO EDO . E 4 MN A 1 404 1 MN MN . F 5 XDX A 1 405 1 XDX XDX . G 6 HOH A 1 501 31 HOH HOH . G 6 HOH A 2 502 15 HOH HOH . G 6 HOH A 3 503 32 HOH HOH . G 6 HOH A 4 504 2 HOH HOH . G 6 HOH A 5 505 22 HOH HOH . G 6 HOH A 6 506 9 HOH HOH . G 6 HOH A 7 507 7 HOH HOH . G 6 HOH A 8 508 4 HOH HOH . G 6 HOH A 9 509 1 HOH HOH . G 6 HOH A 10 510 26 HOH HOH . G 6 HOH A 11 511 34 HOH HOH . G 6 HOH A 12 512 10 HOH HOH . G 6 HOH A 13 513 12 HOH HOH . G 6 HOH A 14 514 17 HOH HOH . G 6 HOH A 15 515 29 HOH HOH . G 6 HOH A 16 516 20 HOH HOH . G 6 HOH A 17 517 13 HOH HOH . G 6 HOH A 18 518 28 HOH HOH . G 6 HOH A 19 519 5 HOH HOH . G 6 HOH A 20 520 21 HOH HOH . G 6 HOH A 21 521 23 HOH HOH . G 6 HOH A 22 522 33 HOH HOH . G 6 HOH A 23 523 3 HOH HOH . G 6 HOH A 24 524 8 HOH HOH . G 6 HOH A 25 525 27 HOH HOH . G 6 HOH A 26 526 19 HOH HOH . G 6 HOH A 27 527 16 HOH HOH . G 6 HOH A 28 528 25 HOH HOH . G 6 HOH A 29 529 18 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 O OAN XDX . . . F 5 42.419 -2.112 32.863 0.71 93.68 ? OAN XDX 405 A 1 HETATM 2 P PAL XDX . . . F 5 42.85 -2.427 31.447 0.71 95.98 ? PAL XDX 405 A 1 HETATM 3 O OAO XDX . . . F 5 43.942 -3.475 31.388 0.71 79.81 ? OAO XDX 405 A 1 HETATM 4 O OAP XDX . . . F 5 43.186 -1.188 30.645 0.71 78.12 ? OAP XDX 405 A 1 HETATM 5 O OAM XDX . . . F 5 41.585 -3.112 30.699 0.71 82.3 ? OAM XDX 405 A 1 HETATM 6 C CAQ XDX . . . F 5 40.798 -2.323 29.792 0.71 85.36 ? CAQ XDX 405 A 1 HETATM 7 C CAR XDX . . . F 5 40.928 -2.905 28.403 0.71 87.83 ? CAR XDX 405 A 1 HETATM 8 C CAS XDX . . . F 5 41.997 -2.199 27.503 0.71 72.89 ? CAS XDX 405 A 1 HETATM 9 O OAV XDX . . . F 5 43.166 -2.628 27.642 0.71 69.8 ? OAV XDX 405 A 1 HETATM 10 O OAU XDX . . . F 5 41.643 -1.274 26.738 0.71 56.81 ? OAU XDX 405 A 1 HETATM 11 O O1 XDX . . . F 5 39.578 -3 27.93 0.71 92.3 ? O1 XDX 405 A 1 HETATM 12 C C1 XDX . . . F 5 39.422 -3.036 26.534 0.71 114.65 ? C1 XDX 405 A 1 HETATM 13 O O5 XDX . . . F 5 38.56 -4.102 26.215 0.71 114.65 ? O5 XDX 405 A 1 HETATM 14 C C5 XDX . . . F 5 37.338 -4.058 26.963 0.71 114.65 ? C5 XDX 405 A 1 HETATM 15 C C6 XDX . . . F 5 36.606 -5.335 26.639 0.71 114.65 ? C6 XDX 405 A 1 HETATM 16 O O6 XDX . . . F 5 36.552 -5.56 25.235 0.71 114.65 ? O6 XDX 405 A 1 HETATM 17 C C4 XDX . . . F 5 36.55 -2.806 26.589 0.71 114.65 ? C4 XDX 405 A 1 HETATM 18 O O4 XDX . . . F 5 35.403 -2.72 27.428 0.71 114.65 ? O4 XDX 405 A 1 HETATM 19 C C3 XDX . . . F 5 37.408 -1.547 26.725 0.71 114.65 ? C3 XDX 405 A 1 HETATM 20 O O3 XDX . . . F 5 36.764 -0.433 26.121 0.71 114.65 ? O3 XDX 405 A 1 HETATM 21 C C2 XDX . . . F 5 38.791 -1.72 26.104 0.71 114.65 ? C2 XDX 405 A 1 HETATM 22 O O2 XDX . . . F 5 39.629 -0.635 26.487 0.71 114.65 ? O2 XDX 405 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 256 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 22 #