data_8I8D # _model_server_result.job_id 6RK36XFHklPbh1F67TqsaQ _model_server_result.datetime_utc '2025-07-03 15:03:17' _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 8i8d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":602}' # _entry.id 8I8D # _exptl.entry_id 8I8D _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 347.221 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ADENOSINE MONOPHOSPHATE' _entity.pdbx_number_of_molecules 6 _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 8I8D _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8I8D _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _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,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA _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 ? _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 N N N ? 4 P N N ? 4 R N N ? 4 T N N ? 4 V N N ? 4 X 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 covale ? covale1 M CBC OP3 . A OP3 601 1_555 Z S12 PN7 . a PN7 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.787 ? covale ? covale2 O CBC OP3 . B OP3 601 1_555 AA S12 PN7 . b PN7 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.795 ? covale ? covale3 Q CBC OP3 . C OP3 601 1_555 BA S12 PN7 . c PN7 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.809 ? covale ? covale4 S CBC OP3 . D OP3 601 1_555 CA S12 PN7 . d PN7 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.801 ? covale ? covale5 U CBC OP3 . E OP3 601 1_555 DA S12 PN7 . e PN7 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.806 ? covale ? covale6 W CBC OP3 . F OP3 601 1_555 Y S12 PN7 . f PN7 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.797 ? covale ? covale7 G CB SER 37 f SER 36 1_555 Y O4P PN7 . f PN7 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.383 ? covale ? covale8 H CB SER 37 a SER 36 1_555 Z O2P PN7 . a PN7 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.383 ? covale ? covale9 I CB SER 37 b SER 36 1_555 AA O4P PN7 . b PN7 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.383 ? covale ? covale10 J CB SER 37 c SER 36 1_555 BA O2P PN7 . c PN7 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.383 ? covale ? covale11 K CB SER 37 d SER 36 1_555 CA O4P PN7 . d PN7 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.384 ? covale ? covale12 L CB SER 37 e SER 36 1_555 DA O2P PN7 . e PN7 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.384 ? # _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 8I8D _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 M 3 OP3 A 1 601 601 OP3 MC7 . N 4 AMP A 1 602 701 AMP AMP . O 3 OP3 B 1 601 601 OP3 MC7 . P 4 AMP B 1 602 701 AMP AMP . Q 3 OP3 C 1 601 601 OP3 MC7 . R 4 AMP C 1 602 701 AMP AMP . S 3 OP3 D 1 601 601 OP3 MC7 . T 4 AMP D 1 602 701 AMP AMP . U 3 OP3 E 1 601 601 OP3 MC7 . V 4 AMP E 1 602 701 AMP AMP . W 3 OP3 F 1 601 601 OP3 MC7 . X 4 AMP F 1 602 701 AMP AMP . Y 5 PN7 f 1 101 101 PN7 PNS . Z 5 PN7 a 1 101 101 PN7 PNS . AA 5 PN7 b 1 101 101 PN7 PNS . BA 5 PN7 c 1 101 101 PN7 PNS . CA 5 PN7 d 1 101 101 PN7 PNS . DA 5 PN7 e 1 101 101 PN7 PNS . # 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 . . . N 4 185.709 126.965 156.07 1 78.52 ? P AMP 602 A 1 HETATM 2 O O1P AMP . . . N 4 185.608 128.297 155.468 1 66.47 -1 O1P AMP 602 A 1 HETATM 3 O O2P AMP . . . N 4 186.504 127.16 157.283 1 66.5 ? O2P AMP 602 A 1 HETATM 4 O O3P AMP . . . N 4 184.362 126.694 156.563 1 66.65 ? O3P AMP 602 A 1 HETATM 5 O O5' AMP . . . N 4 186.302 125.799 155.049 1 70.67 ? O5' AMP 602 A 1 HETATM 6 C C5' AMP . . . N 4 185.499 124.663 154.775 1 66.39 ? C5' AMP 602 A 1 HETATM 7 C C4' AMP . . . N 4 185.781 124.207 153.382 1 69.46 ? C4' AMP 602 A 1 HETATM 8 O O4' AMP . . . N 4 185.979 122.742 153.35 1 69.38 ? O4' AMP 602 A 1 HETATM 9 C C3' AMP . . . N 4 184.64 124.475 152.464 1 67.53 ? C3' AMP 602 A 1 HETATM 10 O O3' AMP . . . N 4 184.726 125.784 151.905 1 69.22 ? O3' AMP 602 A 1 HETATM 11 C C2' AMP . . . N 4 184.784 123.445 151.415 1 69.11 ? C2' AMP 602 A 1 HETATM 12 O O2' AMP . . . N 4 185.674 123.895 150.39 1 70.07 ? O2' AMP 602 A 1 HETATM 13 C C1' AMP . . . N 4 185.364 122.254 152.106 1 69.21 ? C1' AMP 602 A 1 HETATM 14 N N9 AMP . . . N 4 184.342 121.297 152.407 1 72.07 ? N9 AMP 602 A 1 HETATM 15 C C8 AMP . . . N 4 183.731 121.339 153.509 1 69.32 ? C8 AMP 602 A 1 HETATM 16 N N7 AMP . . . N 4 182.797 120.329 153.595 1 64.46 ? N7 AMP 602 A 1 HETATM 17 C C5 AMP . . . N 4 183.008 119.653 152.231 1 65.94 ? C5 AMP 602 A 1 HETATM 18 C C6 AMP . . . N 4 182.466 118.586 151.561 1 66.74 ? C6 AMP 602 A 1 HETATM 19 N N6 AMP . . . N 4 181.407 117.8 152.197 1 68.07 ? N6 AMP 602 A 1 HETATM 20 N N1 AMP . . . N 4 182.882 118.257 150.353 1 64.98 ? N1 AMP 602 A 1 HETATM 21 C C2 AMP . . . N 4 183.856 118.992 149.792 1 65.6 ? C2 AMP 602 A 1 HETATM 22 N N3 AMP . . . N 4 184.506 120.082 150.312 1 66.62 ? N3 AMP 602 A 1 HETATM 23 C C4 AMP . . . N 4 184.035 120.363 151.539 1 68.66 ? C4 AMP 602 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 62 _model_server_stats.query_time_ms 340 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 23 #