data_2GM3 # _model_server_result.job_id 0lzeTi1Wyo4hvlFE-y9dBQ _model_server_result.datetime_utc '2025-07-31 01:07:09' _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 2gm3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":176}' # _entry.id 2GM3 # _exptl.entry_id 2GM3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 347.221 _entity.id 2 _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 75.45 _cell.angle_beta 75.04 _cell.angle_gamma 66.11 _cell.entry_id 2GM3 _cell.length_a 63.351 _cell.length_b 65.662 _cell.length_c 73.014 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2GM3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 ? dimeric 2 author_defined_assembly 3 PISA dimeric 2 software_defined_assembly 4 PISA dimeric 2 software_defined_assembly 5 PISA dimeric 2 software_defined_assembly 6 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,G,H,M,N 1 1 C,D,I,J,O,P 2 1 E,F,K,L,Q 3 1 C,E,I,K,O 4 1 A,G,M 5 1 D,J,P 5 2 B,H,N 6 1 F,L,Q 6 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' 1_665 x+1,y+1,z 1 0 0 0 1 0 0 0 1 89.942929 60.036385 0 3 'crystal symmetry operation' 1_446 x-1,y-1,z+1 1 0 0 0 1 0 0 0 1 -71.094756 -48.32309 69.559969 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 G N N ? 2 H N N ? 2 I N N ? 2 J N N ? 2 K N N ? 2 L 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 A C VAL 8 A VAL 8 1_555 A N MSE 9 A MSE 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale2 A C MSE 9 A MSE 9 1_555 A N VAL 10 A VAL 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale3 A C ASP 76 A ASP 76 1_555 A N MSE 77 A MSE 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale4 A C MSE 77 A MSE 77 1_555 A N ARG 78 A ARG 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale5 A C VAL 158 A VAL 158 1_555 A N MSE 159 A MSE 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.316 ? covale ? covale6 A C MSE 159 A MSE 159 1_555 A N THR 160 A THR 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale7 B C VAL 8 B VAL 8 1_555 B N MSE 9 B MSE 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale8 B C MSE 9 B MSE 9 1_555 B N VAL 10 B VAL 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale9 B C ASP 76 B ASP 76 1_555 B N MSE 77 B MSE 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale10 B C VAL 158 B VAL 158 1_555 B N MSE 159 B MSE 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.315 ? covale ? covale11 B C MSE 159 B MSE 159 1_555 B N THR 160 B THR 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale12 C C VAL 8 C VAL 8 1_555 C N MSE 9 C MSE 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale13 C C MSE 9 C MSE 9 1_555 C N VAL 10 C VAL 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale14 C C ASP 76 C ASP 76 1_555 C N MSE 77 C MSE 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale15 C C MSE 77 C MSE 77 1_555 C N ARG 78 C ARG 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale16 C C VAL 158 C VAL 158 1_555 C N MSE 159 C MSE 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale17 C C MSE 159 C MSE 159 1_555 C N THR 160 C THR 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale18 D C VAL 8 D VAL 8 1_555 D N MSE 9 D MSE 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale19 D C MSE 9 D MSE 9 1_555 D N VAL 10 D VAL 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? covale ? covale20 D C ASP 76 D ASP 76 1_555 D N MSE 77 D MSE 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale21 D C MSE 77 D MSE 77 1_555 D N ARG 78 D ARG 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale22 D C VAL 158 D VAL 158 1_555 D N MSE 159 D MSE 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale23 D C MSE 159 D MSE 159 1_555 D N THR 160 D THR 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale24 E C VAL 8 E VAL 8 1_555 E N MSE 9 E MSE 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale25 E C MSE 9 E MSE 9 1_555 E N VAL 10 E VAL 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale26 E C ASP 76 E ASP 76 1_555 E N MSE 77 E MSE 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale27 E C MSE 77 E MSE 77 1_555 E N ARG 78 E ARG 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale28 E C VAL 158 E VAL 158 1_555 E N MSE 159 E MSE 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale29 E C MSE 159 E MSE 159 1_555 E N THR 160 E THR 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale30 F C VAL 8 F VAL 8 1_555 F N MSE 9 F MSE 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale31 F C MSE 9 F MSE 9 1_555 F N VAL 10 F VAL 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale32 F C ASP 76 F ASP 76 1_555 F N MSE 77 F MSE 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale33 F C MSE 77 F MSE 77 1_555 F N ARG 78 F ARG 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.345 ? covale ? covale34 F C VAL 158 F VAL 158 1_555 F N MSE 159 F MSE 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale35 F C MSE 159 F MSE 159 1_555 F N THR 160 F THR 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? # _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 2GM3 _atom_sites.fract_transf_matrix[1][1] 0.015785 _atom_sites.fract_transf_matrix[1][2] -0.006992 _atom_sites.fract_transf_matrix[1][3] -0.0031 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016657 _atom_sites.fract_transf_matrix[2][3] -0.002805 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.014376 _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 G 2 AMP A 1 176 101 AMP AMP . H 2 AMP B 1 176 102 AMP AMP . I 2 AMP C 1 176 103 AMP AMP . J 2 AMP D 1 176 104 AMP AMP . K 2 AMP E 1 176 105 AMP AMP . L 2 AMP F 1 176 106 AMP AMP . M 3 HOH A 1 177 1 HOH HOH . M 3 HOH A 2 178 2 HOH HOH . M 3 HOH A 3 179 3 HOH HOH . N 3 HOH B 1 177 6 HOH HOH . N 3 HOH B 2 178 7 HOH HOH . O 3 HOH C 1 177 8 HOH HOH . O 3 HOH C 2 178 9 HOH HOH . O 3 HOH C 3 179 10 HOH HOH . P 3 HOH D 1 177 11 HOH HOH . P 3 HOH D 2 178 12 HOH HOH . P 3 HOH D 3 179 13 HOH HOH . Q 3 HOH F 1 177 4 HOH HOH . Q 3 HOH F 2 178 5 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 . . . K 2 24.339 15.488 15.152 1 48.95 ? P AMP 176 E 1 HETATM 2 O O1P AMP . . . K 2 24.668 16.838 15.251 1 50.48 ? O1P AMP 176 E 1 HETATM 3 O O2P AMP . . . K 2 22.966 15.165 15.373 1 51.55 ? O2P AMP 176 E 1 HETATM 4 O O3P AMP . . . K 2 24.787 14.798 13.953 1 48.91 ? O3P AMP 176 E 1 HETATM 5 O O5' AMP . . . K 2 25.097 14.693 16.335 1 50.2 ? O5' AMP 176 E 1 HETATM 6 C C5' AMP . . . K 2 24.976 13.279 16.61 1 49.66 ? C5' AMP 176 E 1 HETATM 7 C C4' AMP . . . K 2 25.532 13.032 17.985 1 48.28 ? C4' AMP 176 E 1 HETATM 8 O O4' AMP . . . K 2 24.629 13.691 18.936 1 49.54 ? O4' AMP 176 E 1 HETATM 9 C C3' AMP . . . K 2 25.587 11.573 18.376 1 49.17 ? C3' AMP 176 E 1 HETATM 10 O O3' AMP . . . K 2 26.863 11.053 17.969 1 48.99 ? O3' AMP 176 E 1 HETATM 11 C C2' AMP . . . K 2 25.466 11.656 19.905 1 48.98 ? C2' AMP 176 E 1 HETATM 12 O O2' AMP . . . K 2 26.746 11.925 20.552 1 47.04 ? O2' AMP 176 E 1 HETATM 13 C C1' AMP . . . K 2 24.532 12.86 20.116 1 49.24 ? C1' AMP 176 E 1 HETATM 14 N N9 AMP . . . K 2 23.128 12.42 20.254 1 50.36 ? N9 AMP 176 E 1 HETATM 15 C C8 AMP . . . K 2 22.188 12.427 19.301 1 49.33 ? C8 AMP 176 E 1 HETATM 16 N N7 AMP . . . K 2 21.055 11.955 19.793 1 48.18 ? N7 AMP 176 E 1 HETATM 17 C C5 AMP . . . K 2 21.259 11.652 21.068 1 50.04 ? C5 AMP 176 E 1 HETATM 18 C C6 AMP . . . K 2 20.462 11.129 22.076 1 49.9 ? C6 AMP 176 E 1 HETATM 19 N N6 AMP . . . K 2 19.188 10.828 21.837 1 50.23 ? N6 AMP 176 E 1 HETATM 20 N N1 AMP . . . K 2 20.997 10.942 23.294 1 49.9 ? N1 AMP 176 E 1 HETATM 21 C C2 AMP . . . K 2 22.264 11.239 23.555 1 49.44 ? C2 AMP 176 E 1 HETATM 22 N N3 AMP . . . K 2 23.053 11.726 22.615 1 50.39 ? N3 AMP 176 E 1 HETATM 23 C C4 AMP . . . K 2 22.578 11.951 21.373 1 50.79 ? C4 AMP 176 E 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 359 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 23 #