data_4Y7U # _model_server_result.job_id XMNvsbOOHKnw-lRoTVizAA _model_server_result.datetime_utc '2024-12-26 15:24:21' _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 4y7u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":307}' # _entry.id 4Y7U # _exptl.entry_id 4Y7U _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 373.25 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-1-O-phosphono-alpha-D-glucopyranose _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 120 _cell.entry_id 4Y7U _cell.length_a 72.75 _cell.length_b 72.75 _cell.length_c 163.13 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4Y7U _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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,H,I _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 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id H _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 OD2 ASP 107 A ASP 107 1_555 E MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.834 ? metalc ? metalc2 A OD1 ASP 205 A ASP 205 1_555 E MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.685 ? metalc ? metalc3 F MG MG . A MG 305 1_555 G O1B 2KH . A 2KH 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? # _chem_comp.formula 'C11 H20 N O11 P' _chem_comp.formula_weight 373.25 _chem_comp.id 491 _chem_comp.mon_nstd_flag n _chem_comp.name 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-1-O-phosphono-alpha-D-glucopyranose _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms 2-(acetylamino)-3-O-[(1R)-1-carboxyethyl]-2-deoxy-1-O-phosphono-alpha-D-glucopyranose;N-acetyl-3-O-[(1R)-1-carboxyethyl]-1-O-phosphono-alpha-D-glucosamine;2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-1-O-phosphono-alpha-D-glucose;2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-1-O-phosphono-D-glucose;2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-1-O-phosphono-glucose # 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 O20 P17 491 doub 47 n n O6 C6 491 sing 48 n n O5 C1 491 sing 49 n n O5 C5 491 sing 50 n n O7 C7 491 doub 51 n n O19 P17 491 sing 52 n n P17 O18 491 sing 53 n n P17 O1 491 sing 54 n n C6 C5 491 sing 55 n n C1 O1 491 sing 56 n n C1 C2 491 sing 57 n n C5 C4 491 sing 58 n n C7 C8 491 sing 59 n n C7 N2 491 sing 60 n n C2 N2 491 sing 61 n n C2 C3 491 sing 62 n n C4 C3 491 sing 63 n n C4 O4 491 sing 64 n n C3 O3 491 sing 65 n n O3 C02 491 sing 66 n n C02 C03 491 sing 67 n n C02 C01 491 sing 68 n n C03 O05 491 doub 69 n n C03 O04 491 sing 70 n n C01 H1A 491 sing 71 n n C01 H2A 491 sing 72 n n C01 H3A 491 sing 73 n n C02 H4A 491 sing 74 n n O04 H5A 491 sing 75 n n C3 H3 491 sing 76 n n C2 H2 491 sing 77 n n C1 H1 491 sing 78 n n C5 H5 491 sing 79 n n C4 H4 491 sing 80 n n O4 HO4 491 sing 81 n n C6 H61 491 sing 82 n n C6 H62 491 sing 83 n n O6 HO6 491 sing 84 n n O18 H15 491 sing 85 n n O19 H16 491 sing 86 n n N2 HN2 491 sing 87 n n C8 H81 491 sing 88 n n C8 H82 491 sing 89 n n C8 H83 491 sing 90 n n # _atom_sites.entry_id 4Y7U _atom_sites.fract_transf_matrix[1][1] 0.013746 _atom_sites.fract_transf_matrix[1][2] 0.007936 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015872 _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] 0.00613 _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 GOL A 1 301 1 GOL GOL . C 2 GOL A 1 302 2 GOL GOL . D 3 SO4 A 1 303 1 SO4 SO4 . E 4 MG A 1 304 1 MG MG . F 4 MG A 1 305 3 MG MG . G 5 2KH A 1 306 1 2KH LIG . H 6 491 A 1 307 1 491 M1P . I 7 HOH A 1 401 20 HOH HOH . I 7 HOH A 2 402 34 HOH HOH . I 7 HOH A 3 403 40 HOH HOH . I 7 HOH A 4 404 15 HOH HOH . I 7 HOH A 5 405 37 HOH HOH . I 7 HOH A 6 406 30 HOH HOH . I 7 HOH A 7 407 47 HOH HOH . I 7 HOH A 8 408 45 HOH HOH . I 7 HOH A 9 409 18 HOH HOH . I 7 HOH A 10 410 13 HOH HOH . I 7 HOH A 11 411 41 HOH HOH . I 7 HOH A 12 412 52 HOH HOH . I 7 HOH A 13 413 11 HOH HOH . I 7 HOH A 14 414 24 HOH HOH . I 7 HOH A 15 415 12 HOH HOH . I 7 HOH A 16 416 36 HOH HOH . I 7 HOH A 17 417 43 HOH HOH . I 7 HOH A 18 418 1 HOH HOH . I 7 HOH A 19 419 2 HOH HOH . I 7 HOH A 20 420 3 HOH HOH . I 7 HOH A 21 421 4 HOH HOH . I 7 HOH A 22 422 5 HOH HOH . I 7 HOH A 23 423 6 HOH HOH . I 7 HOH A 24 424 7 HOH HOH . I 7 HOH A 25 425 8 HOH HOH . I 7 HOH A 26 426 9 HOH HOH . I 7 HOH A 27 427 10 HOH HOH . I 7 HOH A 28 428 14 HOH HOH . I 7 HOH A 29 429 16 HOH HOH . I 7 HOH A 30 430 17 HOH HOH . I 7 HOH A 31 431 19 HOH HOH . I 7 HOH A 32 432 21 HOH HOH . I 7 HOH A 33 433 22 HOH HOH . I 7 HOH A 34 434 23 HOH HOH . I 7 HOH A 35 435 25 HOH HOH . I 7 HOH A 36 436 26 HOH HOH . I 7 HOH A 37 437 27 HOH HOH . I 7 HOH A 38 438 28 HOH HOH . I 7 HOH A 39 439 29 HOH HOH . I 7 HOH A 40 440 31 HOH HOH . I 7 HOH A 41 441 32 HOH HOH . I 7 HOH A 42 442 33 HOH HOH . I 7 HOH A 43 443 35 HOH HOH . I 7 HOH A 44 444 38 HOH HOH . I 7 HOH A 45 445 39 HOH HOH . I 7 HOH A 46 446 42 HOH HOH . I 7 HOH A 47 447 44 HOH HOH . I 7 HOH A 48 448 46 HOH HOH . I 7 HOH A 49 449 48 HOH HOH . I 7 HOH A 50 450 49 HOH HOH . I 7 HOH A 51 451 50 HOH HOH . I 7 HOH A 52 452 51 HOH HOH . I 7 HOH A 53 453 53 HOH HOH . I 7 HOH A 54 454 54 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 C C01 491 . . . H 6 -20.573 -36.854 17.515 0.73 63.25 ? C01 491 307 A 1 HETATM 2 C C02 491 . . . H 6 -19.471 -37.173 16.527 0.73 66.8 ? C02 491 307 A 1 HETATM 3 C C03 491 . . . H 6 -18.254 -36.435 16.906 0.73 68.52 ? C03 491 307 A 1 HETATM 4 O O04 491 . . . H 6 -17.204 -37.061 17.163 0.73 68.76 ? O04 491 307 A 1 HETATM 5 O O05 491 . . . H 6 -18.271 -35.179 16.974 0.73 71.11 -1 O05 491 307 A 1 HETATM 6 O O3 491 . . . H 6 -19.875 -36.793 15.203 0.73 66.49 ? O3 491 307 A 1 HETATM 7 C C3 491 . . . H 6 -19.272 -37.612 14.13 0.73 64.48 ? C3 491 307 A 1 HETATM 8 C C2 491 . . . H 6 -18.834 -36.754 13.031 0.73 64.01 ? C2 491 307 A 1 HETATM 9 C C1 491 . . . H 6 -18.088 -37.564 12.004 0.73 67.37 ? C1 491 307 A 1 HETATM 10 O O5 491 . . . H 6 -18.955 -38.672 11.486 0.73 63.44 ? O5 491 307 A 1 HETATM 11 C C5 491 . . . H 6 -19.596 -39.464 12.529 0.73 63.17 ? C5 491 307 A 1 HETATM 12 C C4 491 . . . H 6 -20.24 -38.629 13.612 0.73 63.46 ? C4 491 307 A 1 HETATM 13 O O4 491 . . . H 6 -20.671 -39.472 14.664 0.73 60.94 ? O4 491 307 A 1 HETATM 14 C C6 491 . . . H 6 -20.632 -40.325 11.872 0.73 64.13 ? C6 491 307 A 1 HETATM 15 O O6 491 . . . H 6 -19.963 -41.156 10.952 0.73 61.99 ? O6 491 307 A 1 HETATM 16 O O1 491 . . . H 6 -16.967 -38.075 12.562 0.73 71.82 ? O1 491 307 A 1 HETATM 17 P P17 491 . . . H 6 -16.028 -39.035 11.765 0.73 88.86 ? P17 491 307 A 1 HETATM 18 O O18 491 . . . H 6 -14.699 -39.112 12.486 0.73 90.96 -1 O18 491 307 A 1 HETATM 19 O O19 491 . . . H 6 -16.633 -40.416 11.704 0.73 87.21 ? O19 491 307 A 1 HETATM 20 O O20 491 . . . H 6 -15.798 -38.526 10.365 0.73 90.34 -1 O20 491 307 A 1 HETATM 21 N N2 491 . . . H 6 -18.001 -35.652 13.576 0.73 62.59 ? N2 491 307 A 1 HETATM 22 C C7 491 . . . H 6 -17.535 -34.565 12.727 0.73 60.93 ? C7 491 307 A 1 HETATM 23 O O7 491 . . . H 6 -17.811 -34.546 11.543 0.73 62.35 ? O7 491 307 A 1 HETATM 24 C C8 491 . . . H 6 -16.673 -33.423 13.343 0.73 40.11 ? C8 491 307 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 24 #