data_4Y7U # _model_server_result.job_id sNMCoToqBY_099V_FhJtAg _model_server_result.datetime_utc '2024-12-26 15:27:55' _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":"G","auth_seq_id":306}' # _entry.id 4Y7U # _exptl.entry_id 4Y7U _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 483.156 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine" _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 5 _struct_asym.id G _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 'C9 H16 N3 O14 P3' _chem_comp.formula_weight 483.156 _chem_comp.id 2KH _chem_comp.mon_nstd_flag . _chem_comp.name "5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine" _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 O2' C2' 2KH sing 1 n n O3' C3' 2KH sing 2 n n C2' C3' 2KH sing 3 n n C2' C1' 2KH sing 4 n n O2 C2 2KH doub 5 n n C3' C4' 2KH sing 6 n n C1' N1 2KH sing 7 n n C1' O4' 2KH sing 8 n n C2 N1 2KH sing 9 n n C2 N3 2KH sing 10 n n C4' O4' 2KH sing 11 n n C4' C5' 2KH sing 12 n n N1 C6 2KH sing 13 n n N3 C4 2KH sing 14 n n C5' O5' 2KH sing 15 n n C6 C5 2KH doub 16 n n C4 C5 2KH sing 17 n n C4 O4 2KH doub 18 n n O2B PB 2KH doub 19 n n O5' PA 2KH sing 20 n n N3A PB 2KH sing 21 n n N3A PA 2KH sing 22 n n PB O1B 2KH sing 23 n n PB O3B 2KH sing 24 n n PA O1A 2KH doub 25 n n PA O2A 2KH sing 26 n n O3B PG 2KH sing 27 n n PG O2G 2KH doub 28 n n PG O1G 2KH sing 29 n n PG O3G 2KH sing 30 n n O2A H1 2KH sing 31 n n N3A H2 2KH sing 32 n n O1B H3 2KH sing 33 n n O1G H4 2KH sing 34 n n O3G H5 2KH sing 35 n n C5' H6 2KH sing 36 n n C5' H7 2KH sing 37 n n C4' H8 2KH sing 38 n n C1' H9 2KH sing 39 n n C2' H10 2KH sing 40 n n O2' H11 2KH sing 41 n n C3' H12 2KH sing 42 n n O3' H13 2KH sing 43 n n C6 H14 2KH sing 44 n n N3 H15 2KH sing 45 n n C5 H16 2KH sing 46 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 P PA 2KH . . . G 5 -11.548 -39.845 11.219 0.72 196.44 ? PA 2KH 306 A 1 HETATM 2 O O1A 2KH . . . G 5 -12.229 -41.153 10.998 0.72 195.76 ? O1A 2KH 306 A 1 HETATM 3 O O2A 2KH . . . G 5 -11.821 -39.53 12.717 0.72 143.65 ? O2A 2KH 306 A 1 HETATM 4 N N3A 2KH . . . G 5 -9.898 -40.088 11.043 0.72 159.16 ? N3A 2KH 306 A 1 HETATM 5 O O5' 2KH . . . G 5 -12.144 -38.616 10.365 0.72 95.55 ? O5' 2KH 306 A 1 HETATM 6 P PB 2KH . . . G 5 -9.407 -41.342 10.048 0.72 131.87 ? PB 2KH 306 A 1 HETATM 7 O O1B 2KH . . . G 5 -7.896 -41.628 10.196 0.72 89.76 ? O1B 2KH 306 A 1 HETATM 8 O O2B 2KH . . . G 5 -9.657 -40.956 8.624 0.72 133.11 ? O2B 2KH 306 A 1 HETATM 9 O O3B 2KH . . . G 5 -10.029 -42.683 10.333 0.72 124.14 ? O3B 2KH 306 A 1 HETATM 10 P PG 2KH . . . G 5 -9.568 -43.661 9.28 0.72 101.07 ? PG 2KH 306 A 1 HETATM 11 O O1G 2KH . . . G 5 -8.099 -43.594 9.07 0.72 97.36 ? O1G 2KH 306 A 1 HETATM 12 O O2G 2KH . . . G 5 -10.222 -43.356 7.967 0.72 97.42 ? O2G 2KH 306 A 1 HETATM 13 O O3G 2KH . . . G 5 -10.024 -44.995 9.736 0.72 94.07 ? O3G 2KH 306 A 1 HETATM 14 C C5' 2KH . . . G 5 -11.644 -38.082 9.143 0.72 93.63 ? C5' 2KH 306 A 1 HETATM 15 C C4' 2KH . . . G 5 -11.813 -36.678 8.691 0.72 92.05 ? C4' 2KH 306 A 1 HETATM 16 O O4' 2KH . . . G 5 -12.124 -35.779 9.756 0.72 90.37 ? O4' 2KH 306 A 1 HETATM 17 C C1' 2KH . . . G 5 -11.152 -34.757 9.656 0.72 90.25 ? C1' 2KH 306 A 1 HETATM 18 C C2' 2KH . . . G 5 -10.702 -34.777 8.256 0.72 89.76 ? C2' 2KH 306 A 1 HETATM 19 O O2' 2KH . . . G 5 -11.685 -34.316 7.401 0.72 86.34 ? O2' 2KH 306 A 1 HETATM 20 C C3' 2KH . . . G 5 -10.577 -36.162 8.036 0.72 91.95 ? C3' 2KH 306 A 1 HETATM 21 O O3' 2KH . . . G 5 -10.474 -36.317 6.662 0.72 92.58 ? O3' 2KH 306 A 1 HETATM 22 N N1 2KH . . . G 5 -10.081 -34.815 10.62 0.72 89.63 ? N1 2KH 306 A 1 HETATM 23 C C6 2KH . . . G 5 -9.76 -36.026 11.324 0.72 89.8 ? C6 2KH 306 A 1 HETATM 24 C C2 2KH . . . G 5 -9.399 -33.548 10.833 0.72 86.32 ? C2 2KH 306 A 1 HETATM 25 O O2 2KH . . . G 5 -9.678 -32.533 10.222 0.72 79.69 ? O2 2KH 306 A 1 HETATM 26 N N3 2KH . . . G 5 -8.328 -33.583 11.83 0.72 88.85 ? N3 2KH 306 A 1 HETATM 27 C C4 2KH . . . G 5 -7.954 -34.75 12.569 0.72 89.16 ? C4 2KH 306 A 1 HETATM 28 O O4 2KH . . . G 5 -7.057 -34.721 13.394 0.72 89.75 ? O4 2KH 306 A 1 HETATM 29 C C5 2KH . . . G 5 -8.678 -36.002 12.321 0.72 89.66 ? C5 2KH 306 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 29 #