data_4EEC # _model_server_result.job_id '_FvQ8hp_7I-vLAkjccFVIg' _model_server_result.datetime_utc '2024-12-02 21:17:11' _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 4eec # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":301}' # _entry.id 4EEC # _exptl.entry_id 4EEC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-3'-5'-DIPHOSPHATE" _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 4EEC _cell.length_a 53.442 _cell.length_b 82.583 _cell.length_c 123.076 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4EEC _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 3 _struct_asym.id D _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 disulf ? disulf1 A SG CYS 36 A CYS 20 1_555 A SG CYS 212 A CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 sing disulf ? disulf2 B SG CYS 36 B CYS 20 1_555 B SG CYS 212 B CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 sing covale ? covale1 C C GHP 1 C GHP 401 1_555 C N 3MY 2 C 3MY 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.278 sing covale ? covale2 C C3 GHP 1 C GHP 401 1_555 C OD1 3FG 3 C 3FG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.345 sing covale ? covale3 C C 3MY 2 C 3MY 402 1_555 C N 3FG 3 C 3FG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.272 sing covale ? covale4 C OBD 3MY 2 C 3MY 402 1_555 C C3 GHP 4 C GHP 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.349 sing covale ? covale5 C C 3FG 3 C 3FG 403 1_555 C N GHP 4 C GHP 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.271 sing covale ? covale6 C C GHP 4 C GHP 404 1_555 C N 0UZ 5 C 0UZ 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.277 sing covale ? covale7 C C5 GHP 4 C GHP 404 1_555 C OCZ OMY 6 C OMY 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.358 sing covale ? covale8 C C 0UZ 5 C 0UZ 405 1_555 C N OMY 6 C OMY 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.291 sing covale ? covale9 C C5 0UZ 5 C 0UZ 405 1_555 C CG1 3FG 7 C 3FG 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.483 sing covale ? covale10 C C OMY 6 C OMY 406 1_555 C N 3FG 7 C 3FG 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.29 sing # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id A3P _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-3'-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 P1 O1P A3P doub 68 n n P1 O2P A3P sing 69 n n P1 O3P A3P sing 70 n n P1 O3' A3P sing 71 n n O2P HOP2 A3P sing 72 n n O3P HOP3 A3P sing 73 n n P2 O4P A3P doub 74 n n P2 O5P A3P sing 75 n n P2 O6P A3P sing 76 n n P2 O5' A3P sing 77 n n O5P HOP5 A3P sing 78 n n O6P HOP6 A3P sing 79 n n O5' C5' A3P sing 80 n n C5' C4' A3P sing 81 n n C5' "H5'1" A3P sing 82 n n C5' "H5'2" A3P sing 83 n n C4' O4' A3P sing 84 n n C4' C3' A3P sing 85 n n C4' H4' A3P sing 86 n n O4' C1' A3P sing 87 n n C3' O3' A3P sing 88 n n C3' C2' A3P sing 89 n n C3' H3' A3P sing 90 n n C2' O2' A3P sing 91 n n C2' C1' A3P sing 92 n n C2' H2' A3P sing 93 n n O2' HO2' A3P sing 94 n n C1' N9 A3P sing 95 n n C1' H1' A3P sing 96 n n N9 C8 A3P sing 97 n y N9 C4 A3P sing 98 n y C8 N7 A3P doub 99 n y C8 H8 A3P sing 100 n n N7 C5 A3P sing 101 n y C5 C6 A3P sing 102 n y C5 C4 A3P doub 103 n y C6 N6 A3P sing 104 n n C6 N1 A3P doub 105 n y N6 HN61 A3P sing 106 n n N6 HN62 A3P sing 107 n n N1 C2 A3P sing 108 n y C2 N3 A3P doub 109 n y C2 H2 A3P sing 110 n n N3 C4 A3P sing 111 n y # _atom_sites.entry_id 4EEC _atom_sites.fract_transf_matrix[1][1] 0.018712 _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] 0.012109 _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] 0.008125 _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 D 3 A3P A 1 301 100 A3P 0UZ . E 4 HOH A 1 401 1 HOH HOH . E 4 HOH A 2 402 7 HOH HOH . E 4 HOH A 3 403 10 HOH HOH . F 4 HOH B 1 301 2 HOH HOH . F 4 HOH B 2 302 3 HOH HOH . F 4 HOH B 3 303 4 HOH HOH . F 4 HOH B 4 304 5 HOH HOH . F 4 HOH B 5 305 6 HOH HOH . F 4 HOH B 6 306 8 HOH HOH . F 4 HOH B 7 307 9 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 P1 A3P . . . D 3 -32.928 0.112 -1.515 1 60.9 ? P1 A3P 301 A 1 HETATM 2 O O1P A3P . . . D 3 -32.567 0.971 -2.721 1 58.74 ? O1P A3P 301 A 1 HETATM 3 O O2P A3P . . . D 3 -33.836 -1.041 -1.926 1 60.18 ? O2P A3P 301 A 1 HETATM 4 O O3P A3P . . . D 3 -33.351 0.858 -0.247 1 59.07 ? O3P A3P 301 A 1 HETATM 5 P P2 A3P . . . D 3 -26.843 -0.504 2.943 1 61.59 ? P2 A3P 301 A 1 HETATM 6 O O4P A3P . . . D 3 -25.377 -0.388 2.609 1 57.5 ? O4P A3P 301 A 1 HETATM 7 O O5P A3P . . . D 3 -27.164 -1.892 3.467 1 62.98 ? O5P A3P 301 A 1 HETATM 8 O O6P A3P . . . D 3 -27.445 0.681 3.73 1 62.21 ? O6P A3P 301 A 1 HETATM 9 O O5' A3P . . . D 3 -27.694 -0.432 1.563 1 60.14 ? O5' A3P 301 A 1 HETATM 10 C C5' A3P . . . D 3 -29.109 -0.472 1.636 1 57.46 ? C5' A3P 301 A 1 HETATM 11 C C4' A3P . . . D 3 -29.649 -0.859 0.288 1 58.1 ? C4' A3P 301 A 1 HETATM 12 O O4' A3P . . . D 3 -29.334 -2.235 0.029 1 59.74 ? O4' A3P 301 A 1 HETATM 13 C C3' A3P . . . D 3 -31.164 -0.78 0.284 1 58.44 ? C3' A3P 301 A 1 HETATM 14 O O3' A3P . . . D 3 -31.539 -0.556 -1.069 1 59.37 ? O3' A3P 301 A 1 HETATM 15 C C2' A3P . . . D 3 -31.538 -2.197 0.626 1 58.35 ? C2' A3P 301 A 1 HETATM 16 O O2' A3P . . . D 3 -32.89 -2.542 0.343 1 58.12 ? O2' A3P 301 A 1 HETATM 17 C C1' A3P . . . D 3 -30.561 -2.939 -0.264 1 58.48 ? C1' A3P 301 A 1 HETATM 18 N N9 A3P . . . D 3 -30.576 -4.401 0.059 1 58.16 ? N9 A3P 301 A 1 HETATM 19 C C8 A3P . . . D 3 -30.559 -4.926 1.312 1 57.04 ? C8 A3P 301 A 1 HETATM 20 N N7 A3P . . . D 3 -30.604 -6.285 1.255 1 57.35 ? N7 A3P 301 A 1 HETATM 21 C C5 A3P . . . D 3 -30.645 -6.664 -0.042 1 55.6 ? C5 A3P 301 A 1 HETATM 22 C C6 A3P . . . D 3 -30.683 -7.957 -0.767 1 54.29 ? C6 A3P 301 A 1 HETATM 23 N N6 A3P . . . D 3 -30.686 -9.129 -0.066 1 54.08 ? N6 A3P 301 A 1 HETATM 24 N N1 A3P . . . D 3 -30.706 -7.913 -2.13 1 53.41 ? N1 A3P 301 A 1 HETATM 25 C C2 A3P . . . D 3 -30.703 -6.743 -2.815 1 52.74 ? C2 A3P 301 A 1 HETATM 26 N N3 A3P . . . D 3 -30.659 -5.53 -2.22 1 53.74 ? N3 A3P 301 A 1 HETATM 27 C C4 A3P . . . D 3 -30.631 -5.42 -0.849 1 56.63 ? C4 A3P 301 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 27 #