data_2GZL # _model_server_result.job_id KA7NdLF_jhbzq8AXxwM18Q _model_server_result.datetime_utc '2024-11-24 20:24:23' _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 2gzl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":901}' # _entry.id 2GZL # _exptl.entry_id 2GZL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 679.53 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-O-{[({[2-({[5-(DIMETHYLAMINO)NAPHTHALEN-1-YL]SULFONYL}AMINO)ETHYL]OXY}PHOSPHINATO)OXY]PHOSPHINATO}CYT" _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 2GZL _cell.length_a 145.098 _cell.length_b 145.098 _cell.length_c 145.098 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2GZL _symmetry.cell_setting ? _symmetry.Int_Tables_number 199 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 21 3' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 1,2,3 # 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' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 3 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 10 A ASP 8 1_555 B ZN ZN . A ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc2 A NE2 HIS 12 A HIS 10 1_555 B ZN ZN . A ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc3 A ND1 HIS 44 A HIS 42 1_555 B ZN ZN . A ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc4 B ZN ZN . A ZN 900 1_555 C O1' 2AA . A 2AA 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? # _chem_comp.formula 'C23 H31 N5 O13 P2 S' _chem_comp.formula_weight 679.53 _chem_comp.id 2AA _chem_comp.mon_nstd_flag . _chem_comp.name "5'-O-{[({[2-({[5-(DIMETHYLAMINO)NAPHTHALEN-1-YL]SULFONYL}AMINO)ETHYL]OXY}PHOSPHINATO)OXY]PHOSPHINATO}CYT" _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 C13 N5 2AA sing 1 n n C13 H131 2AA sing 2 n n C13 H132 2AA sing 3 n n C13 H133 2AA sing 4 n n N5 C12 2AA sing 5 n n N5 C11 2AA sing 6 n n C12 H121 2AA sing 7 n n C12 H122 2AA sing 8 n n C12 H123 2AA sing 9 n n C11 C10 2AA doub 10 n y C11 C6' 2AA sing 11 n y C10 C9' 2AA sing 12 n y C10 H10 2AA sing 13 n n C9' C8' 2AA doub 14 n y C9' H9' 2AA sing 15 n n C8' C7' 2AA sing 16 n y C8' H8' 2AA sing 17 n n C7' C6' 2AA doub 18 n y C7' C2' 2AA sing 19 n y C6' C5' 2AA sing 20 n y C5' C4' 2AA doub 21 n y C5' H5' 2AA sing 22 n n C4' C3' 2AA sing 23 n y C4' H4' 2AA sing 24 n n C3' C2' 2AA doub 25 n y C3' H3' 2AA sing 26 n n C2' S1 2AA sing 27 n n S1 O3' 2AA doub 28 n n S1 O4' 2AA doub 29 n n S1 N4 2AA sing 30 n n N4 C1' 2AA sing 31 n n N4 HN4 2AA sing 32 n n C1' C9 2AA sing 33 n n C1' "H1'1" 2AA sing 34 n n C1' "H1'2" 2AA sing 35 n n C9 O2' 2AA sing 36 n n C9 H91 2AA sing 37 n n C9 H92 2AA sing 38 n n O2' P2 2AA sing 39 n n P2 O1' 2AA doub 40 n n P2 O9 2AA sing 41 n n P2 O8 2AA sing 42 n n O9 HO9 2AA sing 43 n n O8 P1 2AA sing 44 n n P1 O7 2AA doub 45 n n P1 O6 2AA sing 46 n n P1 O5 2AA sing 47 n n O6 HO6 2AA sing 48 n n O5 C14 2AA sing 49 n n C14 C8 2AA sing 50 n n C14 H141 2AA sing 51 n n C14 H142 2AA sing 52 n n C8 O2 2AA sing 53 n n C8 C7 2AA sing 54 n n C8 H8 2AA sing 55 n n O2 C5 2AA sing 56 n n C7 O4 2AA sing 57 n n C7 C6 2AA sing 58 n n C7 H7 2AA sing 59 n n O4 HO4 2AA sing 60 n n C6 O3 2AA sing 61 n n C6 C5 2AA sing 62 n n C6 H6 2AA sing 63 n n O3 HO3 2AA sing 64 n n C5 N3 2AA sing 65 n n C5 H5 2AA sing 66 n n N3 C4 2AA sing 67 n y N3 C1 2AA sing 68 n y C4 C3 2AA doub 69 n y C4 H4 2AA sing 70 n n C3 C2 2AA sing 71 n y C3 H3 2AA sing 72 n n C2 N2 2AA sing 73 n n C2 N1 2AA doub 74 n y N2 HN21 2AA sing 75 n n N2 HN22 2AA sing 76 n n N1 C1 2AA sing 77 n y C1 O1 2AA doub 78 n n # _atom_sites.entry_id 2GZL _atom_sites.fract_transf_matrix[1][1] 0.006892 _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] 0.006892 _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] 0.006892 _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 ZN A 1 900 900 ZN ZN . C 3 2AA A 1 901 901 2AA 2AA . D 4 GPP A 1 903 903 GPP GPP . E 5 HOH A 1 904 1 HOH HOH . E 5 HOH A 2 905 2 HOH HOH . E 5 HOH A 3 906 4 HOH HOH . E 5 HOH A 4 907 5 HOH HOH . E 5 HOH A 5 908 6 HOH HOH . E 5 HOH A 6 909 7 HOH HOH . E 5 HOH A 7 910 8 HOH HOH . E 5 HOH A 8 911 9 HOH HOH . E 5 HOH A 9 912 10 HOH HOH . E 5 HOH A 10 913 11 HOH HOH . E 5 HOH A 11 914 12 HOH HOH . E 5 HOH A 12 915 13 HOH HOH . E 5 HOH A 13 916 14 HOH HOH . E 5 HOH A 14 917 15 HOH HOH . E 5 HOH A 15 918 16 HOH HOH . E 5 HOH A 16 919 17 HOH HOH . E 5 HOH A 17 920 18 HOH HOH . E 5 HOH A 18 921 19 HOH HOH . E 5 HOH A 19 922 20 HOH HOH . E 5 HOH A 20 923 21 HOH HOH . E 5 HOH A 21 924 22 HOH HOH . E 5 HOH A 22 925 23 HOH HOH . E 5 HOH A 23 926 24 HOH HOH . E 5 HOH A 24 927 25 HOH HOH . E 5 HOH A 25 928 26 HOH HOH . E 5 HOH A 26 929 27 HOH HOH . E 5 HOH A 27 930 28 HOH HOH . E 5 HOH A 28 931 29 HOH HOH . E 5 HOH A 29 932 30 HOH HOH . E 5 HOH A 30 933 31 HOH HOH . E 5 HOH A 31 934 32 HOH HOH . E 5 HOH A 32 935 33 HOH HOH . E 5 HOH A 33 936 34 HOH HOH . E 5 HOH A 34 937 35 HOH HOH . E 5 HOH A 35 938 36 HOH HOH . E 5 HOH A 36 939 37 HOH HOH . E 5 HOH A 37 940 38 HOH HOH . E 5 HOH A 38 941 39 HOH HOH . E 5 HOH A 39 942 40 HOH HOH . E 5 HOH A 40 943 41 HOH HOH . E 5 HOH A 41 944 43 HOH HOH . E 5 HOH A 42 945 44 HOH HOH . E 5 HOH A 43 946 45 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 C13 2AA . . . C 3 2.043 21.152 38.901 1 123.83 ? C13 2AA 901 A 1 HETATM 2 N N5 2AA . . . C 3 3.25 20.992 38.381 1 123.82 ? N5 2AA 901 A 1 HETATM 3 C C12 2AA . . . C 3 4.31 21.339 39.095 1 124.02 ? C12 2AA 901 A 1 HETATM 4 C C11 2AA . . . C 3 3.387 20.491 37.142 1 123.81 ? C11 2AA 901 A 1 HETATM 5 C C10 2AA . . . C 3 3.106 21.323 36.056 1 123.76 ? C10 2AA 901 A 1 HETATM 6 C C9' 2AA . . . C 3 3.231 20.852 34.752 1 123.81 ? C9' 2AA 901 A 1 HETATM 7 C C8' 2AA . . . C 3 3.635 19.539 34.525 1 123.74 ? C8' 2AA 901 A 1 HETATM 8 C C7' 2AA . . . C 3 3.921 18.677 35.589 1 123.66 ? C7' 2AA 901 A 1 HETATM 9 C C6' 2AA . . . C 3 3.793 19.161 36.908 1 123.76 ? C6' 2AA 901 A 1 HETATM 10 C C5' 2AA . . . C 3 4.076 18.305 37.98 1 123.72 ? C5' 2AA 901 A 1 HETATM 11 C C4' 2AA . . . C 3 4.479 16.991 37.753 1 123.6 ? C4' 2AA 901 A 1 HETATM 12 C C3' 2AA . . . C 3 4.607 16.517 36.449 1 123.45 ? C3' 2AA 901 A 1 HETATM 13 C C2' 2AA . . . C 3 4.331 17.345 35.356 1 123 ? C2' 2AA 901 A 1 HETATM 14 S S1 2AA . . . C 3 4.509 16.682 33.812 1 122.28 ? S1 2AA 901 A 1 HETATM 15 O O3' 2AA . . . C 3 3.925 15.293 33.797 1 122.05 ? O3' 2AA 901 A 1 HETATM 16 O O4' 2AA . . . C 3 3.801 17.515 32.784 1 121.8 ? O4' 2AA 901 A 1 HETATM 17 N N4 2AA . . . C 3 6.117 16.578 33.434 1 118.19 ? N4 2AA 901 A 1 HETATM 18 C C1' 2AA . . . C 3 6.382 16.848 32.01 1 112.68 ? C1' 2AA 901 A 1 HETATM 19 C C9 2AA . . . C 3 5.99 15.631 31.172 1 107.98 ? C9 2AA 901 A 1 HETATM 20 O O2' 2AA . . . C 3 7.155 14.874 30.837 1 102.58 ? O2' 2AA 901 A 1 HETATM 21 P P2 2AA . . . C 3 7.65 14.793 29.297 1 99.03 ? P2 2AA 901 A 1 HETATM 22 O O1' 2AA . . . C 3 6.75 15.635 28.465 1 98.31 ? O1' 2AA 901 A 1 HETATM 23 O O9 2AA . . . C 3 9.118 15.023 29.231 1 99.79 ? O9 2AA 901 A 1 HETATM 24 O O8 2AA . . . C 3 7.372 13.206 28.957 1 92.56 ? O8 2AA 901 A 1 HETATM 25 P P1 2AA . . . C 3 8.508 12.042 28.841 1 85.51 ? P1 2AA 901 A 1 HETATM 26 O O7 2AA . . . C 3 7.8 10.744 28.852 1 86.74 ? O7 2AA 901 A 1 HETATM 27 O O6 2AA . . . C 3 9.452 12.328 27.747 1 85.78 ? O6 2AA 901 A 1 HETATM 28 O O5 2AA . . . C 3 9.316 12.181 30.221 1 81.46 ? O5 2AA 901 A 1 HETATM 29 C C14 2AA . . . C 3 8.929 11.429 31.392 1 73.96 ? C14 2AA 901 A 1 HETATM 30 C C8 2AA . . . C 3 10.137 11.005 32.233 1 68.7 ? C8 2AA 901 A 1 HETATM 31 O O2 2AA . . . C 3 10.452 9.641 31.915 1 65.14 ? O2 2AA 901 A 1 HETATM 32 C C7 2AA . . . C 3 11.367 11.81 31.823 1 66.78 ? C7 2AA 901 A 1 HETATM 33 O O4 2AA . . . C 3 11.45 12.979 32.634 1 67.92 ? O4 2AA 901 A 1 HETATM 34 C C6 2AA . . . C 3 12.508 10.868 32.144 1 64.38 ? C6 2AA 901 A 1 HETATM 35 O O3 2AA . . . C 3 12.912 11.064 33.493 1 64.63 ? O3 2AA 901 A 1 HETATM 36 C C5 2AA . . . C 3 11.88 9.476 32.022 1 61.29 ? C5 2AA 901 A 1 HETATM 37 N N3 2AA . . . C 3 12.291 8.707 30.818 1 58.64 ? N3 2AA 901 A 1 HETATM 38 C C4 2AA . . . C 3 11.923 9.082 29.507 1 56.68 ? C4 2AA 901 A 1 HETATM 39 C C3 2AA . . . C 3 12.347 8.288 28.443 1 55.3 ? C3 2AA 901 A 1 HETATM 40 C C2 2AA . . . C 3 13.107 7.148 28.698 1 55.61 ? C2 2AA 901 A 1 HETATM 41 N N2 2AA . . . C 3 13.523 6.373 27.7 1 56.35 ? N2 2AA 901 A 1 HETATM 42 N N1 2AA . . . C 3 13.436 6.809 29.95 1 55.5 ? N1 2AA 901 A 1 HETATM 43 C C1 2AA . . . C 3 13.057 7.551 30.998 1 56.87 ? C1 2AA 901 A 1 HETATM 44 O O1 2AA . . . C 3 13.388 7.208 32.125 1 56.61 ? O1 2AA 901 A 1 # _model_server_stats.io_time_ms 69 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 41 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 44 #