data_7K5J # _model_server_result.job_id LASc5bpv1mxVjD5qpcANpw _model_server_result.datetime_utc '2024-12-22 05:40:50' _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 7k5j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"DA","auth_seq_id":1101}' # _entry.id 7K5J # _exptl.entry_id 7K5J _exptl.method 'X-RAY DIFFRACTION' # _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 7 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 94.59 _cell.angle_gamma 90 _cell.entry_id 7K5J _cell.length_a 95.181 _cell.length_b 272.917 _cell.length_c 258.342 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7K5J _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 ? trimeric 3 author_defined_assembly 1 ? trimeric 3 author_defined_assembly 2 ? trimeric 3 author_defined_assembly 3 ? trimeric 3 author_defined_assembly 4 ? trimeric 3 author_defined_assembly 5 ? trimeric 3 author_defined_assembly 6 PISA trimeric 3 author_and_software_defined_assembly 7 PISA trimeric 3 author_and_software_defined_assembly 8 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,J,K,CA 1 1 F,G,O,AA 2 1 H,I,R,BA 3 1 L,M,P,DA 4 1 S,T,W,EA 5 1 U,V,X 6 1 B,C,N,Y 7 1 D,E,Q,Z 8 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 Y N N ? 4 Z N N ? 4 AA N N ? 4 BA N N ? 4 CA N N ? 4 DA N N ? 4 EA 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 disulf ? disulf1 B SG CYS 593 D CYS 600 1_555 C SG CYS 97 F CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 D SG CYS 593 A CYS 600 1_555 E SG CYS 97 B CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 H SG CYS 593 G CYS 600 1_555 I SG CYS 97 H CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 J SG CYS 593 I CYS 600 1_555 K SG CYS 97 J CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 L SG CYS 593 K CYS 600 1_555 M SG CYS 97 L CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A C GLY 83 N GLY 76 1_555 K NZ LYS 143 J LYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.275 sing covale ? covale2 C NZ LYS 143 F LYS 141 1_555 N C GLY 83 M GLY 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 sing covale ? covale3 E NZ LYS 143 B LYS 141 1_555 Q C GLY 83 Q GLY 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.308 sing covale ? covale4 M NZ LYS 143 L LYS 141 1_555 P C GLY 83 P GLY 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.677 sing covale ? covale5 S NE2 GLN 475 S GLN 482 1_555 EA O1P AMP . S AMP 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.3 ? # _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 7K5J _atom_sites.fract_transf_matrix[1][1] 0.010506 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000844 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.003664 _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] 0.003883 _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 Y 4 AMP D 1 1101 1103 AMP AMP . Z 4 AMP A 1 1101 1103 AMP AMP . AA 4 AMP C 1 1101 1103 AMP AMP . BA 4 AMP G 1 1101 1103 AMP AMP . CA 4 AMP I 1 1101 1103 AMP AMP . DA 4 AMP K 1 1101 1103 AMP AMP . EA 4 AMP S 1 1101 1103 AMP AMP . # 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 . . . DA 4 103.942 -1.168 368.09 1 112.83 ? P AMP 1101 K 1 HETATM 2 O O1P AMP . . . DA 4 104.215 -2.643 367.902 1 87.59 ? O1P AMP 1101 K 1 HETATM 3 O O2P AMP . . . DA 4 105.177 -0.311 368.232 1 141.81 ? O2P AMP 1101 K 1 HETATM 4 O O3P AMP . . . DA 4 102.863 -0.858 369.099 1 102.43 ? O3P AMP 1101 K 1 HETATM 5 O O5' AMP . . . DA 4 103.329 -0.704 366.694 1 81.72 ? O5' AMP 1101 K 1 HETATM 6 C C5' AMP . . . DA 4 104.153 -0.579 365.539 1 64.84 ? C5' AMP 1101 K 1 HETATM 7 C C4' AMP . . . DA 4 103.826 -1.621 364.495 1 65.66 ? C4' AMP 1101 K 1 HETATM 8 O O4' AMP . . . DA 4 103.51 -0.959 363.24 1 63.62 ? O4' AMP 1101 K 1 HETATM 9 C C3' AMP . . . DA 4 104.955 -2.61 364.185 1 76.68 ? C3' AMP 1101 K 1 HETATM 10 O O3' AMP . . . DA 4 104.405 -3.907 363.964 1 64.21 ? O3' AMP 1101 K 1 HETATM 11 C C2' AMP . . . DA 4 105.525 -2.077 362.874 1 74.11 ? C2' AMP 1101 K 1 HETATM 12 O O2' AMP . . . DA 4 106.159 -3.046 362.071 1 84.84 ? O2' AMP 1101 K 1 HETATM 13 C C1' AMP . . . DA 4 104.274 -1.535 362.202 1 62.07 ? C1' AMP 1101 K 1 HETATM 14 N N9 AMP . . . DA 4 104.534 -0.518 361.18 1 77.74 ? N9 AMP 1101 K 1 HETATM 15 C C8 AMP . . . DA 4 104.95 0.746 361.388 1 80.83 ? C8 AMP 1101 K 1 HETATM 16 N N7 AMP . . . DA 4 105.086 1.413 360.211 1 78.77 ? N7 AMP 1101 K 1 HETATM 17 C C5 AMP . . . DA 4 104.754 0.565 359.22 1 73.61 ? C5 AMP 1101 K 1 HETATM 18 C C6 AMP . . . DA 4 104.677 0.623 357.741 1 63.71 ? C6 AMP 1101 K 1 HETATM 19 N N6 AMP . . . DA 4 104.993 1.751 357.06 1 65.37 ? N6 AMP 1101 K 1 HETATM 20 N N1 AMP . . . DA 4 104.279 -0.493 357.093 1 69.17 ? N1 AMP 1101 K 1 HETATM 21 C C2 AMP . . . DA 4 103.961 -1.624 357.751 1 72.21 ? C2 AMP 1101 K 1 HETATM 22 N N3 AMP . . . DA 4 104.008 -1.749 359.089 1 72.56 ? N3 AMP 1101 K 1 HETATM 23 C C4 AMP . . . DA 4 104.393 -0.707 359.865 1 79.44 ? C4 AMP 1101 K 1 # _model_server_stats.io_time_ms 350 _model_server_stats.parse_time_ms 49 _model_server_stats.create_model_time_ms 121 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 23 #