data_8VDN # _model_server_result.job_id lu2fSnNvkENeDohrni0snQ _model_server_result.datetime_utc '2025-01-03 01:31:00' _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 8vdn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":101}' # _entry.id 8VDN # _exptl.entry_id 8VDN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 347.221 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ADENOSINE MONOPHOSPHATE' _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 8VDN _cell.length_a 64.977 _cell.length_b 115.631 _cell.length_c 126.175 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VDN _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 E _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 covale ? covale1 B P DG 1 C DG 1 1_555 E O3P AMP . C AMP 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.558 ? hydrog WATSON-CRICK hydrog1 C N1 DG 1 B DG 1 1_555 D N3 DC 18 D DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 C N2 DG 1 B DG 1 1_555 D O2 DC 18 D DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 C O6 DG 1 B DG 1 1_555 D N4 DC 18 D DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 C N3 DC 2 B DC 2 1_555 D N1 DG 17 D DG 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 C N4 DC 2 B DC 2 1_555 D O6 DG 17 D DG 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 C O2 DC 2 B DC 2 1_555 D N2 DG 17 D DG 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 C N3 DT 3 B DT 3 1_555 D N1 DA 16 D DA 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 C O4 DT 3 B DT 3 1_555 D N6 DA 16 D DA 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 C N1 DG 4 B DG 4 1_555 D N3 DC 15 D DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 C N2 DG 4 B DG 4 1_555 D O2 DC 15 D DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 C O6 DG 4 B DG 4 1_555 D N4 DC 15 D DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 C N1 DA 5 B DA 5 1_555 D N3 DT 14 D DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 C N6 DA 5 B DA 5 1_555 D O4 DT 14 D DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 C N3 DT 6 B DT 6 1_555 D N1 DA 13 D DA 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 C O4 DT 6 B DT 6 1_555 D N6 DA 13 D DA 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 C N1 DG 7 B DG 7 1_555 D N3 DC 12 D DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 C N2 DG 7 B DG 7 1_555 D O2 DC 12 D DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 C O6 DG 7 B DG 7 1_555 D N4 DC 12 D DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 C N3 DC 8 B DC 8 1_555 D N1 DG 11 D DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 C N4 DC 8 B DC 8 1_555 D O6 DG 11 D DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 C O2 DC 8 B DC 8 1_555 D N2 DG 11 D DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 C N1 DG 9 B DG 9 1_555 D N3 DC 10 D DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 C N2 DG 9 B DG 9 1_555 D O2 DC 10 D DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 C O6 DG 9 B DG 9 1_555 D N4 DC 10 D DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 C N3 DT 10 B DT 10 1_555 D N1 DA 9 D DA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 C O4 DT 10 B DT 10 1_555 D N6 DA 9 D DA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 C N1 DG 11 B DG 11 1_555 D N3 DC 8 D DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 C N2 DG 11 B DG 11 1_555 D O2 DC 8 D DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 C O6 DG 11 B DG 11 1_555 D N4 DC 8 D DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 B N1 DG 1 C DG 1 1_555 D N3 DC 7 D DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 B N2 DG 1 C DG 1 1_555 D O2 DC 7 D DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 B O6 DG 1 C DG 1 1_555 D N4 DC 7 D DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 B N3 DT 2 C DT 2 1_555 D N1 DA 6 D DA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 B O4 DT 2 C DT 2 1_555 D N6 DA 6 D DA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 B N3 DC 3 C DC 3 1_555 D N1 DG 5 D DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 B N4 DC 3 C DC 3 1_555 D O6 DG 5 D DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 B O2 DC 3 C DC 3 1_555 D N2 DG 5 D DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 B N1 DG 4 C DG 4 1_555 D N3 DC 4 D DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 B N2 DG 4 C DG 4 1_555 D O2 DC 4 D DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog40 B O6 DG 4 C DG 4 1_555 D N4 DC 4 D DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog41 B N1 DG 5 C DG 5 1_555 D N3 DC 3 D DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog42 B N2 DG 5 C DG 5 1_555 D O2 DC 3 D DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog43 B O6 DG 5 C DG 5 1_555 D N4 DC 3 D DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog44 B N1 DA 6 C DA 6 1_555 D N3 DT 2 D DT 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog45 B N6 DA 6 C DA 6 1_555 D O4 DT 2 D DT 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog46 B N3 DC 7 C DC 7 1_555 D N1 DG 1 D DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog47 B N4 DC 7 C DC 7 1_555 D O6 DG 1 D DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog48 B O2 DC 7 C DC 7 1_555 D N2 DG 1 D DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H14 N5 O7 P' _chem_comp.formula_weight 347.221 _chem_comp.id AMP _chem_comp.mon_nstd_flag . _chem_comp.name 'ADENOSINE MONOPHOSPHATE' _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 P O1P AMP doub 13 n n P O2P AMP sing 14 n n P O3P AMP sing 15 n n P O5' AMP sing 16 n n O2P HOP2 AMP sing 17 n n O3P HOP3 AMP sing 18 n n O5' C5' AMP sing 19 n n C5' C4' AMP sing 20 n n C5' "H5'1" AMP sing 21 n n C5' "H5'2" AMP sing 22 n n C4' O4' AMP sing 23 n n C4' C3' AMP sing 24 n n C4' H4' AMP sing 25 n n O4' C1' AMP sing 26 n n C3' O3' AMP sing 27 n n C3' C2' AMP sing 28 n n C3' H3' AMP sing 29 n n O3' HO3' AMP sing 30 n n C2' O2' AMP sing 31 n n C2' C1' AMP sing 32 n n C2' H2' AMP sing 33 n n O2' HO2' AMP sing 34 n n C1' N9 AMP sing 35 n n C1' H1' AMP sing 36 n n N9 C8 AMP sing 37 n y N9 C4 AMP sing 38 n y C8 N7 AMP doub 39 n y C8 H8 AMP sing 40 n n N7 C5 AMP sing 41 n y C5 C6 AMP sing 42 n y C5 C4 AMP doub 43 n y C6 N6 AMP sing 44 n n C6 N1 AMP doub 45 n y N6 HN61 AMP sing 46 n n N6 HN62 AMP sing 47 n n N1 C2 AMP sing 48 n y C2 N3 AMP doub 49 n y C2 H2 AMP sing 50 n n N3 C4 AMP sing 51 n y # _atom_sites.entry_id 8VDN _atom_sites.fract_transf_matrix[1][1] 0.01539 _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] 0.008648 _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] 0.007926 _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 5 AMP C 1 101 1003 AMP AMP . F 6 HOH A 1 1001 13 HOH HOH . F 6 HOH A 2 1002 15 HOH HOH . F 6 HOH A 3 1003 4 HOH HOH . F 6 HOH A 4 1004 5 HOH HOH . F 6 HOH A 5 1005 17 HOH HOH . F 6 HOH A 6 1006 22 HOH HOH . F 6 HOH A 7 1007 7 HOH HOH . F 6 HOH A 8 1008 1 HOH HOH . F 6 HOH A 9 1009 8 HOH HOH . F 6 HOH A 10 1010 26 HOH HOH . F 6 HOH A 11 1011 20 HOH HOH . F 6 HOH A 12 1012 9 HOH HOH . F 6 HOH A 13 1013 33 HOH HOH . F 6 HOH A 14 1014 28 HOH HOH . F 6 HOH A 15 1015 14 HOH HOH . G 6 HOH C 1 201 25 HOH HOH . G 6 HOH C 2 202 38 HOH HOH . G 6 HOH C 3 203 24 HOH HOH . G 6 HOH C 4 204 19 HOH HOH . G 6 HOH C 5 205 30 HOH HOH . G 6 HOH C 6 206 32 HOH HOH . G 6 HOH C 7 207 11 HOH HOH . G 6 HOH C 8 208 31 HOH HOH . G 6 HOH C 9 209 23 HOH HOH . H 6 HOH B 1 101 3 HOH HOH . H 6 HOH B 2 102 29 HOH HOH . H 6 HOH B 3 103 35 HOH HOH . H 6 HOH B 4 104 12 HOH HOH . H 6 HOH B 5 105 21 HOH HOH . I 6 HOH D 1 101 18 HOH HOH . I 6 HOH D 2 102 2 HOH HOH . I 6 HOH D 3 103 6 HOH HOH . I 6 HOH D 4 104 10 HOH HOH . I 6 HOH D 5 105 27 HOH HOH . I 6 HOH D 6 106 34 HOH HOH . I 6 HOH D 7 107 16 HOH HOH . I 6 HOH D 8 108 37 HOH HOH . I 6 HOH D 9 109 36 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 P AMP . . . E 5 -11.555 19.539 -23.252 1 82.97 ? P AMP 101 C 1 HETATM 2 O O1P AMP . . . E 5 -10.965 20.604 -24.146 1 83.84 ? O1P AMP 101 C 1 HETATM 3 O O2P AMP . . . E 5 -11 19.529 -21.848 1 65.93 ? O2P AMP 101 C 1 HETATM 4 O O3P AMP . . . E 5 -11.663 18.173 -23.886 1 103.37 ? O3P AMP 101 C 1 HETATM 5 O O5' AMP . . . E 5 -13.07 19.992 -23.058 1 84.77 ? O5' AMP 101 C 1 HETATM 6 C C5' AMP . . . E 5 -13.972 20.014 -24.153 1 68.9 ? C5' AMP 101 C 1 HETATM 7 C C4' AMP . . . E 5 -14.875 18.806 -24.147 1 64.09 ? C4' AMP 101 C 1 HETATM 8 O O4' AMP . . . E 5 -15.609 18.752 -22.907 1 75.73 ? O4' AMP 101 C 1 HETATM 9 C C3' AMP . . . E 5 -15.962 18.8 -25.207 1 71.61 ? C3' AMP 101 C 1 HETATM 10 O O3' AMP . . . E 5 -15.495 18.369 -26.473 1 73.2 ? O3' AMP 101 C 1 HETATM 11 C C2' AMP . . . E 5 -17.042 17.893 -24.61 1 71.83 ? C2' AMP 101 C 1 HETATM 12 O O2' AMP . . . E 5 -16.826 16.54 -24.985 1 65.43 ? O2' AMP 101 C 1 HETATM 13 C C1' AMP . . . E 5 -16.798 18.023 -23.099 1 62.28 ? C1' AMP 101 C 1 HETATM 14 N N9 AMP . . . E 5 -17.904 18.711 -22.402 1 72.91 ? N9 AMP 101 C 1 HETATM 15 C C8 AMP . . . E 5 -18.455 18.28 -21.252 1 78.42 ? C8 AMP 101 C 1 HETATM 16 N N7 AMP . . . E 5 -19.455 19.1 -20.844 1 70.44 ? N7 AMP 101 C 1 HETATM 17 C C5 AMP . . . E 5 -19.561 20.086 -21.752 1 78.34 ? C5 AMP 101 C 1 HETATM 18 C C6 AMP . . . E 5 -20.418 21.282 -21.923 1 75.82 ? C6 AMP 101 C 1 HETATM 19 N N6 AMP . . . E 5 -21.38 21.588 -21.019 1 65.58 ? N6 AMP 101 C 1 HETATM 20 N N1 AMP . . . E 5 -20.21 22.056 -23.01 1 71.64 ? N1 AMP 101 C 1 HETATM 21 C C2 AMP . . . E 5 -19.258 21.761 -23.913 1 79.17 ? C2 AMP 101 C 1 HETATM 22 N N3 AMP . . . E 5 -18.444 20.693 -23.82 1 76.83 ? N3 AMP 101 C 1 HETATM 23 C C4 AMP . . . E 5 -18.542 19.825 -22.783 1 69.99 ? C4 AMP 101 C 1 # _model_server_stats.io_time_ms 76 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 23 #