data_7RK0 # _model_server_result.job_id 6rUeE2DP6JshbqnHZqoR1A _model_server_result.datetime_utc '2024-11-12 20:22:42' _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 7rk0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":302}' # _entry.id 7RK0 # _exptl.entry_id 7RK0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 598.352 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2-[(E)-[(4R)-5-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-4-oxidanyl-3-oxidanylidene-pentan-2-ylidene]amino]ethanoic acid' _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 96.979 _cell.angle_gamma 90 _cell.entry_id 7RK0 _cell.length_a 89.889 _cell.length_b 89.685 _cell.length_c 131.813 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7RK0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y (x,y,-x+z)' _symmetry.space_group_name_H-M 'I 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _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,J,K,L,M,N,O,P _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' 2_656 -x+1,y,-z+1 -1 0 0 0 1 0 0 0 -1 73.872989 0 130.836365 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 F N N ? 3 H N N ? 3 J N N ? 3 L N 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 160 A ASP 160 1_555 K FE FE . D FE 301 2_656 ? ? ? ? ? ? ? ? ? ? ? ? 2.591 ? metalc ? metalc2 A NE2 HIS 175 A HIS 175 1_555 E FE FE . A FE 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc3 E FE FE . A FE 301 1_555 F O8 48H . A 48H 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? metalc ? metalc4 E FE FE . A FE 301 1_555 F N1 48H . A 48H 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc5 E FE FE . A FE 301 1_555 F O10 48H . A 48H 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.527 ? metalc ? metalc6 E FE FE . A FE 301 1_555 B OD1 ASP 160 B ASP 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? metalc ? metalc7 B NE2 HIS 175 B HIS 175 1_555 G FE FE . B FE 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.442 ? metalc ? metalc8 G FE FE . B FE 301 1_555 H N1 48H . B 48H 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc9 G FE FE . B FE 301 1_555 H O9 48H . B 48H 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? metalc ? metalc10 G FE FE . B FE 301 1_555 H O8 48H . B 48H 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? metalc ? metalc11 C NE2 HIS 175 C HIS 175 1_555 I FE FE . C FE 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? metalc ? metalc12 I FE FE . C FE 301 1_555 J O8 48H . C 48H 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc13 I FE FE . C FE 301 1_555 J N1 48H . C 48H 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? metalc ? metalc14 I FE FE . C FE 301 1_555 J O9 48H . C 48H 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc15 I FE FE . C FE 301 1_555 D OD1 ASP 160 D ASP 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.741 ? metalc ? metalc16 D NE2 HIS 175 D HIS 175 1_555 K FE FE . D FE 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc17 K FE FE . D FE 301 1_555 L O8 48H . D 48H 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? metalc ? metalc18 K FE FE . D FE 301 1_555 L N1 48H . D 48H 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc19 K FE FE . D FE 301 1_555 L O9 48H . D 48H 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? # _chem_comp.formula 'C17 H24 N6 O14 P2' _chem_comp.formula_weight 598.352 _chem_comp.id 48H _chem_comp.mon_nstd_flag . _chem_comp.name '2-[(E)-[(4R)-5-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-4-oxidanyl-3-oxidanylidene-pentan-2-ylidene]amino]ethanoic 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 O13 C16 48H sing 1 n n O12 C15 48H sing 2 n n C16 C15 48H sing 3 n n C16 C17 48H sing 4 n n C15 C14 48H sing 5 n n C17 N2 48H sing 6 n n C17 O14 48H sing 7 n n N3 C1 48H doub 8 n y N3 C2 48H sing 9 n y C1 N4 48H sing 10 n y C14 O14 48H sing 11 n n C14 C13 48H sing 12 n n C2 N2 48H sing 13 n y C2 C3 48H doub 14 n y N2 C5 48H sing 15 n y O2 P1 48H doub 16 n n N4 C4 48H doub 17 n y O11 C13 48H sing 18 n n O11 P1 48H sing 19 n n O7 C7 48H sing 20 n n O1 P1 48H sing 21 n n P1 O3 48H sing 22 n n C5 N6 48H doub 23 n y C3 C4 48H sing 24 n y C3 N6 48H sing 25 n y C4 N5 48H sing 26 n n O8 C8 48H doub 27 n n C7 C8 48H sing 28 n n C7 C6 48H sing 29 n n C8 C9 48H sing 30 n n O3 P2 48H sing 31 n n O6 C6 48H sing 32 n n O6 P2 48H sing 33 n n O5 P2 48H doub 34 n n C9 N1 48H doub 35 n n C9 C10 48H sing 36 n n P2 O4 48H sing 37 n n O10 C12 48H doub 38 n n N1 C11 48H sing 39 n n C12 C11 48H sing 40 n n C12 O9 48H sing 41 n n C1 H1 48H sing 42 n n C5 H2 48H sing 43 n n O1 H3 48H sing 44 n n O4 H4 48H sing 45 n n C6 H5 48H sing 46 n n C6 H6 48H sing 47 n n C7 H7 48H sing 48 n n O7 H8 48H sing 49 n n C10 H9 48H sing 50 n n C10 H10 48H sing 51 n n C10 H11 48H sing 52 n n C11 H12 48H sing 53 n n C11 H13 48H sing 54 n n O9 H14 48H sing 55 n n C13 H15 48H sing 56 n n C13 H16 48H sing 57 n n C14 H17 48H sing 58 n n C15 H18 48H sing 59 n n O12 H19 48H sing 60 n n C16 H20 48H sing 61 n n O13 H21 48H sing 62 n n C17 H22 48H sing 63 n n N5 H23 48H sing 64 n n N5 H24 48H sing 65 n n # _atom_sites.entry_id 7RK0 _atom_sites.fract_transf_matrix[1][1] 0.011125 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001362 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01115 _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] 0.007643 _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 E 2 FE A 1 301 2 FE FE . F 3 48H A 1 302 302 48H 48H . G 2 FE B 1 301 5 FE FE . H 3 48H B 1 302 305 48H 48H . I 2 FE C 1 301 3 FE FE . J 3 48H C 1 302 303 48H 48H . K 2 FE D 1 301 4 FE FE . L 3 48H D 1 302 304 48H 48H . M 4 HOH A 1 401 29 HOH HOH . M 4 HOH A 2 402 77 HOH HOH . M 4 HOH A 3 403 4 HOH HOH . M 4 HOH A 4 404 60 HOH HOH . M 4 HOH A 5 405 46 HOH HOH . M 4 HOH A 6 406 26 HOH HOH . M 4 HOH A 7 407 23 HOH HOH . M 4 HOH A 8 408 9 HOH HOH . M 4 HOH A 9 409 28 HOH HOH . M 4 HOH A 10 410 67 HOH HOH . M 4 HOH A 11 411 63 HOH HOH . N 4 HOH B 1 401 72 HOH HOH . N 4 HOH B 2 402 78 HOH HOH . N 4 HOH B 3 403 79 HOH HOH . N 4 HOH B 4 404 75 HOH HOH . N 4 HOH B 5 405 68 HOH HOH . N 4 HOH B 6 406 74 HOH HOH . N 4 HOH B 7 407 70 HOH HOH . N 4 HOH B 8 408 71 HOH HOH . N 4 HOH B 9 409 69 HOH HOH . N 4 HOH B 10 410 76 HOH HOH . N 4 HOH B 11 411 80 HOH HOH . O 4 HOH C 1 401 88 HOH HOH . O 4 HOH C 2 402 90 HOH HOH . O 4 HOH C 3 403 81 HOH HOH . O 4 HOH C 4 404 84 HOH HOH . O 4 HOH C 5 405 87 HOH HOH . O 4 HOH C 6 406 86 HOH HOH . O 4 HOH C 7 407 73 HOH HOH . O 4 HOH C 8 408 89 HOH HOH . O 4 HOH C 9 409 82 HOH HOH . P 4 HOH D 1 401 85 HOH HOH . P 4 HOH D 2 402 18 HOH HOH . P 4 HOH D 3 403 83 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 C1 48H . . . F 3 22.614 81.032 65.756 1 37.6 ? C1 48H 302 A 1 HETATM 2 C C2 48H . . . F 3 21.569 82.942 66.595 1 31.82 ? C2 48H 302 A 1 HETATM 3 C C3 48H . . . F 3 21.484 83.447 65.368 1 33.72 ? C3 48H 302 A 1 HETATM 4 C C4 48H . . . F 3 21.964 82.722 64.281 1 33.39 ? C4 48H 302 A 1 HETATM 5 C C5 48H . . . F 3 20.596 84.883 66.72 1 31.5 ? C5 48H 302 A 1 HETATM 6 O O1 48H . . . F 3 16.802 86.888 71.819 1 42.41 ? O1 48H 302 A 1 HETATM 7 P P1 48H . . . F 3 16.516 85.512 72.413 1 37.3 ? P1 48H 302 A 1 HETATM 8 O O2 48H . . . F 3 16.43 85.529 73.968 1 38.62 ? O2 48H 302 A 1 HETATM 9 O O3 48H . . . F 3 15.1 85.023 71.667 1 40.71 ? O3 48H 302 A 1 HETATM 10 P P2 48H . . . F 3 13.787 84.467 72.389 1 34.09 ? P2 48H 302 A 1 HETATM 11 O O4 48H . . . F 3 12.713 84.457 71.269 1 43.17 ? O4 48H 302 A 1 HETATM 12 O O5 48H . . . F 3 14.017 83.073 72.913 1 34.01 ? O5 48H 302 A 1 HETATM 13 O O6 48H . . . F 3 13.282 85.465 73.669 1 37.21 ? O6 48H 302 A 1 HETATM 14 C C6 48H . . . F 3 13.149 86.839 73.437 1 39.51 ? C6 48H 302 A 1 HETATM 15 C C7 48H . . . F 3 13.417 87.606 74.748 1 50.4 ? C7 48H 302 A 1 HETATM 16 O O7 48H . . . F 3 14.743 87.439 75.137 1 49.97 ? O7 48H 302 A 1 HETATM 17 C C8 48H . . . F 3 13.127 89.073 74.435 1 54.07 ? C8 48H 302 A 1 HETATM 18 O O8 48H . . . F 3 13.99 89.755 74.001 1 53.62 ? O8 48H 302 A 1 HETATM 19 C C9 48H . . . F 3 11.742 89.693 74.644 1 56.14 ? C9 48H 302 A 1 HETATM 20 C C10 48H . . . F 3 10.694 89.008 75.553 1 50.71 ? C10 48H 302 A 1 HETATM 21 N N1 48H . . . F 3 11.501 90.81 74.03 1 58.6 ? N1 48H 302 A 1 HETATM 22 C C11 48H . . . F 3 10.256 91.534 74.128 1 56.06 ? C11 48H 302 A 1 HETATM 23 C C12 48H . . . F 3 10.475 93.006 73.783 1 59.59 ? C12 48H 302 A 1 HETATM 24 O O9 48H . . . F 3 9.483 93.823 73.82 1 54.31 ? O9 48H 302 A 1 HETATM 25 O O10 48H . . . F 3 11.647 93.441 73.446 1 63.37 ? O10 48H 302 A 1 HETATM 26 O O11 48H . . . F 3 17.583 84.374 71.945 1 34.28 ? O11 48H 302 A 1 HETATM 27 C C13 48H . . . F 3 17.903 84.437 70.553 1 35.24 ? C13 48H 302 A 1 HETATM 28 C C14 48H . . . F 3 19.106 83.555 70.383 1 38.06 ? C14 48H 302 A 1 HETATM 29 C C15 48H . . . F 3 20.321 84.406 70.89 1 42.82 ? C15 48H 302 A 1 HETATM 30 O O12 48H . . . F 3 20.876 83.767 71.907 1 37.96 ? O12 48H 302 A 1 HETATM 31 C C16 48H . . . F 3 21.262 84.543 69.643 1 39.17 ? C16 48H 302 A 1 HETATM 32 O O13 48H . . . F 3 22.649 84.348 70.159 1 40.63 ? O13 48H 302 A 1 HETATM 33 C C17 48H . . . F 3 20.927 83.574 68.854 1 35.52 ? C17 48H 302 A 1 HETATM 34 O O14 48H . . . F 3 19.317 83.351 69.128 1 39.14 ? O14 48H 302 A 1 HETATM 35 N N2 48H . . . F 3 21.026 83.829 67.439 1 34.16 ? N2 48H 302 A 1 HETATM 36 N N3 48H . . . F 3 22.132 81.721 66.804 1 31.65 ? N3 48H 302 A 1 HETATM 37 N N4 48H . . . F 3 22.523 81.556 64.468 1 36.09 ? N4 48H 302 A 1 HETATM 38 N N5 48H . . . F 3 22.081 82.879 62.875 1 32.82 ? N5 48H 302 A 1 HETATM 39 N N6 48H . . . F 3 20.886 84.66 65.454 1 31.02 ? N6 48H 302 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 39 #