data_6BKF # _model_server_result.job_id zzjonR5B9rqUJPgwt8Axow _model_server_result.datetime_utc '2024-11-29 08:56:09' _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 6bkf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":701}' # _entry.id 6BKF # _exptl.entry_id 6BKF _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 6BKF _cell.length_a 119.22 _cell.length_b 119.22 _cell.length_c 137.414 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6BKF _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 43 21 2' # _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 _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 A NZ LYS 274 A LYS 273 1_555 E P AMP . A AMP 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.676 ? hydrog WATSON-CRICK hydrog1 B N1 DG 1 P DG 1 1_555 C N3 DC 18 T DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N2 DG 1 P DG 1 1_555 C O2 DC 18 T DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O6 DG 1 P DG 1 1_555 C N4 DC 18 T DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N3 DC 2 P DC 2 1_555 C N1 DG 17 T DG 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N4 DC 2 P DC 2 1_555 C O6 DG 17 T DG 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B O2 DC 2 P DC 2 1_555 C N2 DG 17 T DG 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N3 DT 3 P DT 3 1_555 C N1 DA 16 T DA 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B O4 DT 3 P DT 3 1_555 C N6 DA 16 T DA 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N1 DG 4 P DG 4 1_555 C N3 DC 15 T DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N2 DG 4 P DG 4 1_555 C O2 DC 15 T DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B O6 DG 4 P DG 4 1_555 C N4 DC 15 T DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N1 DA 5 P DA 5 1_555 C N3 DT 14 T DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N6 DA 5 P DA 5 1_555 C O4 DT 14 T DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N3 DT 6 P DT 6 1_555 C N1 DA 13 T DA 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B O4 DT 6 P DT 6 1_555 C N6 DA 13 T DA 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N1 DG 7 P DG 7 1_555 C N3 DC 12 T DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N2 DG 7 P DG 7 1_555 C O2 DC 12 T DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O6 DG 7 P DG 7 1_555 C N4 DC 12 T DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N3 DC 8 P DC 8 1_555 C N1 DG 11 T DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N4 DC 8 P DC 8 1_555 C O6 DG 11 T DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B O2 DC 8 P DC 8 1_555 C N2 DG 11 T DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N1 DG 9 P DG 9 1_555 C N3 DC 10 T DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B N2 DG 9 P DG 9 1_555 C O2 DC 10 T DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B O6 DG 9 P DG 9 1_555 C N4 DC 10 T DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B N3 DT 10 P DT 10 1_555 C N1 DA 9 T DA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 B O4 DT 10 P DT 10 1_555 C N6 DA 9 T DA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 B N3 DC 11 P DC 11 1_555 C N1 DG 8 T DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 B N4 DC 11 P DC 11 1_555 C O6 DG 8 T DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 B O2 DC 11 P DC 11 1_555 C N2 DG 8 T DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 C N1 DG 1 T DG 1 1_555 D N3 DC 7 D DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 C N2 DG 1 T DG 1 1_555 D O2 DC 7 D DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 C O6 DG 1 T DG 1 1_555 D N4 DC 7 D DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 C N3 DT 2 T DT 2 1_555 D N1 DA 6 D DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 C O4 DT 2 T DT 2 1_555 D N6 DA 6 D DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 C N3 DC 3 T DC 3 1_555 D N1 DG 5 D DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 C N4 DC 3 T DC 3 1_555 D O6 DG 5 D DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 C O2 DC 3 T DC 3 1_555 D N2 DG 5 D DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 C N3 DC 4 T DC 4 1_555 D N1 DG 4 D DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 C N4 DC 4 T DC 4 1_555 D O6 DG 4 D DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog40 C O2 DC 4 T DC 4 1_555 D N2 DG 4 D DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog41 C N1 DG 5 T DG 5 1_555 D N3 DC 3 D DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog42 C N2 DG 5 T DG 5 1_555 D O2 DC 3 D DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog43 C O6 DG 5 T DG 5 1_555 D N4 DC 3 D DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog44 C N1 DA 6 T DA 6 1_555 D N3 DT 2 D DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog45 C N6 DA 6 T DA 6 1_555 D O4 DT 2 D DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog46 C N3 DC 7 T DC 7 1_555 D N1 DG 1 D DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog47 C N4 DC 7 T DC 7 1_555 D O6 DG 1 D DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog48 C O2 DC 7 T DC 7 1_555 D N2 DG 1 D DG 2 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 6BKF _atom_sites.fract_transf_matrix[1][1] 0.008388 _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] 0.008388 _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] 0.007277 _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 A 1 701 1 AMP AMP . F 6 HOH A 1 801 5 HOH HOH . F 6 HOH A 2 802 4 HOH HOH . F 6 HOH A 3 803 6 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 24.097 -17.568 6.457 1 40.68 ? P AMP 701 A 1 HETATM 2 O O1P AMP . . . E 5 25.463 -18.1 6.824 1 46.18 ? O1P AMP 701 A 1 HETATM 3 O O2P AMP . . . E 5 22.98 -17.73 7.466 1 43.46 ? O2P AMP 701 A 1 HETATM 4 O O5' AMP . . . E 5 23.67 -18.367 5.154 1 40.69 ? O5' AMP 701 A 1 HETATM 5 C C5' AMP . . . E 5 24.659 -18.999 4.369 1 45.01 ? C5' AMP 701 A 1 HETATM 6 C C4' AMP . . . E 5 24.063 -20.01 3.433 1 41.73 ? C4' AMP 701 A 1 HETATM 7 O O4' AMP . . . E 5 22.982 -19.394 2.696 1 27.41 ? O4' AMP 701 A 1 HETATM 8 C C3' AMP . . . E 5 25.014 -20.515 2.358 1 48.59 ? C3' AMP 701 A 1 HETATM 9 O O3' AMP . . . E 5 25.866 -21.561 2.806 1 54.98 ? O3' AMP 701 A 1 HETATM 10 C C2' AMP . . . E 5 24.079 -20.921 1.23 1 37.38 ? C2' AMP 701 A 1 HETATM 11 O O2' AMP . . . E 5 23.577 -22.238 1.427 1 34.72 ? O2' AMP 701 A 1 HETATM 12 C C1' AMP . . . E 5 22.936 -19.912 1.389 1 32.72 ? C1' AMP 701 A 1 HETATM 13 N N9 AMP . . . E 5 23.046 -18.778 0.455 1 43.01 ? N9 AMP 701 A 1 HETATM 14 C C8 AMP . . . E 5 22.443 -17.56 0.644 1 49.5 ? C8 AMP 701 A 1 HETATM 15 N N7 AMP . . . E 5 22.651 -16.695 -0.32 1 52.04 ? N7 AMP 701 A 1 HETATM 16 C C5 AMP . . . E 5 23.443 -17.392 -1.22 1 54.19 ? C5 AMP 701 A 1 HETATM 17 C C6 AMP . . . E 5 23.998 -17.02 -2.456 1 54.87 ? C6 AMP 701 A 1 HETATM 18 N N6 AMP . . . E 5 23.828 -15.815 -2.996 1 57.58 ? N6 AMP 701 A 1 HETATM 19 N N1 AMP . . . E 5 24.741 -17.925 -3.131 1 51.42 ? N1 AMP 701 A 1 HETATM 20 C C2 AMP . . . E 5 24.911 -19.128 -2.58 1 47.85 ? C2 AMP 701 A 1 HETATM 21 N N3 AMP . . . E 5 24.44 -19.598 -1.43 1 49.11 ? N3 AMP 701 A 1 HETATM 22 C C4 AMP . . . E 5 23.696 -18.682 -0.772 1 52.04 ? C4 AMP 701 A 1 # _model_server_stats.io_time_ms 82 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 22 #