data_1TB5 # _model_server_result.job_id E2tbO2AtnbLU1N-3MfBSeQ _model_server_result.datetime_utc '2024-11-24 16:31:40' _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 1tb5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":102}' # _entry.id 1TB5 # _exptl.entry_id 1TB5 _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 2 _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 1TB5 _cell.length_a 89.547 _cell.length_b 94.241 _cell.length_c 107.243 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1TB5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,I 1 1 B,F,G,H,J 2 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 E N N ? 4 H 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 metalc ? metalc1 E O2P AMP . A AMP 102 1_555 C ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc2 E O1P AMP . A AMP 102 1_555 D MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc3 A NE2 HIS 91 A HIS 238 1_555 C ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc4 A NE2 HIS 127 A HIS 274 1_555 C ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? metalc ? metalc5 A OD2 ASP 128 A ASP 275 1_555 C ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc6 A OD1 ASP 128 A ASP 275 1_555 D MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? metalc ? metalc7 A OD2 ASP 245 A ASP 392 1_555 C ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc8 C ZN ZN . A ZN 1001 1_555 I O HOH . A HOH 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.772 ? metalc ? metalc9 D MG MG . A MG 1002 1_555 I O HOH . A HOH 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.974 ? metalc ? metalc10 D MG MG . A MG 1002 1_555 I O HOH . A HOH 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.955 ? metalc ? metalc11 D MG MG . A MG 1002 1_555 I O HOH . A HOH 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc12 D MG MG . A MG 1002 1_555 I O HOH . A HOH 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc13 H O2P AMP . B AMP 101 1_555 F ZN ZN . B ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.468 ? metalc ? metalc14 H O1P AMP . B AMP 101 1_555 G MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc15 B NE2 HIS 91 B HIS 238 1_555 F ZN ZN . B ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc16 B NE2 HIS 127 B HIS 274 1_555 F ZN ZN . B ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? metalc ? metalc17 B OD2 ASP 128 B ASP 275 1_555 F ZN ZN . B ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? metalc ? metalc18 B OD1 ASP 128 B ASP 275 1_555 G MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc19 B OD2 ASP 245 B ASP 392 1_555 F ZN ZN . B ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc20 F ZN ZN . B ZN 1001 1_555 J O HOH . B HOH 2007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.92 ? metalc ? metalc21 G MG MG . B MG 1002 1_555 J O HOH . B HOH 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc22 G MG MG . B MG 1002 1_555 J O HOH . B HOH 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? metalc ? metalc23 G MG MG . B MG 1002 1_555 J O HOH . B HOH 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? metalc ? metalc24 G MG MG . B MG 1002 1_555 J O HOH . B HOH 2007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? # _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 1TB5 _atom_sites.fract_transf_matrix[1][1] 0.011167 _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] 0.010611 _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] 0.009325 _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 C 2 ZN A 1 1001 1001 ZN ZN . D 3 MG A 1 1002 1002 MG MG . E 4 AMP A 1 102 102 AMP AMP . F 2 ZN B 1 1001 1001 ZN ZN . G 3 MG B 1 1002 1002 MG MG . H 4 AMP B 1 101 101 AMP AMP . I 5 HOH A 1 4 4 HOH HOH . I 5 HOH A 2 5 5 HOH HOH . I 5 HOH A 3 7 7 HOH HOH . I 5 HOH A 4 8 8 HOH HOH . I 5 HOH A 5 10 10 HOH HOH . I 5 HOH A 6 12 12 HOH HOH . I 5 HOH A 7 21 21 HOH HOH . I 5 HOH A 8 22 22 HOH HOH . I 5 HOH A 9 24 24 HOH HOH . I 5 HOH A 10 27 27 HOH HOH . I 5 HOH A 11 28 28 HOH HOH . I 5 HOH A 12 29 29 HOH HOH . I 5 HOH A 13 30 30 HOH HOH . I 5 HOH A 14 33 33 HOH HOH . I 5 HOH A 15 34 34 HOH HOH . I 5 HOH A 16 36 36 HOH HOH . I 5 HOH A 17 37 37 HOH HOH . I 5 HOH A 18 38 38 HOH HOH . I 5 HOH A 19 39 39 HOH HOH . I 5 HOH A 20 40 40 HOH HOH . I 5 HOH A 21 41 41 HOH HOH . I 5 HOH A 22 43 43 HOH HOH . I 5 HOH A 23 45 45 HOH HOH . I 5 HOH A 24 46 46 HOH HOH . I 5 HOH A 25 47 47 HOH HOH . I 5 HOH A 26 49 49 HOH HOH . I 5 HOH A 27 50 50 HOH HOH . I 5 HOH A 28 56 56 HOH HOH . I 5 HOH A 29 57 57 HOH HOH . I 5 HOH A 30 58 58 HOH HOH . I 5 HOH A 31 59 59 HOH HOH . I 5 HOH A 32 60 60 HOH HOH . I 5 HOH A 33 61 61 HOH HOH . I 5 HOH A 34 1003 1003 HOH HOH . I 5 HOH A 35 1004 1004 HOH HOH . I 5 HOH A 36 1005 1005 HOH HOH . I 5 HOH A 37 1007 1007 HOH HOH . J 5 HOH B 1 1 1 HOH HOH . J 5 HOH B 2 2 2 HOH HOH . J 5 HOH B 3 3 3 HOH HOH . J 5 HOH B 4 6 6 HOH HOH . J 5 HOH B 5 9 9 HOH HOH . J 5 HOH B 6 11 11 HOH HOH . J 5 HOH B 7 13 13 HOH HOH . J 5 HOH B 8 14 14 HOH HOH . J 5 HOH B 9 15 15 HOH HOH . J 5 HOH B 10 16 16 HOH HOH . J 5 HOH B 11 17 17 HOH HOH . J 5 HOH B 12 18 18 HOH HOH . J 5 HOH B 13 19 19 HOH HOH . J 5 HOH B 14 20 20 HOH HOH . J 5 HOH B 15 23 23 HOH HOH . J 5 HOH B 16 25 25 HOH HOH . J 5 HOH B 17 26 26 HOH HOH . J 5 HOH B 18 31 31 HOH HOH . J 5 HOH B 19 32 32 HOH HOH . J 5 HOH B 20 35 35 HOH HOH . J 5 HOH B 21 42 42 HOH HOH . J 5 HOH B 22 44 44 HOH HOH . J 5 HOH B 23 48 48 HOH HOH . J 5 HOH B 24 51 51 HOH HOH . J 5 HOH B 25 52 52 HOH HOH . J 5 HOH B 26 53 53 HOH HOH . J 5 HOH B 27 54 54 HOH HOH . J 5 HOH B 28 55 55 HOH HOH . J 5 HOH B 29 2003 2003 HOH HOH . J 5 HOH B 30 2004 2004 HOH HOH . J 5 HOH B 31 2005 2005 HOH HOH . J 5 HOH B 32 2007 2007 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 4 39.101 4.328 58.949 0.8 40.65 ? P AMP 102 A 1 HETATM 2 O O1P AMP . . . E 4 37.799 5.04 58.569 0.8 30.25 ? O1P AMP 102 A 1 HETATM 3 O O2P AMP . . . E 4 40.351 4.641 58.075 0.8 18.29 ? O2P AMP 102 A 1 HETATM 4 O O3P AMP . . . E 4 39.491 4.738 60.383 0.8 33.56 ? O3P AMP 102 A 1 HETATM 5 O O5' AMP . . . E 4 38.8 2.728 59.012 0.8 40.72 ? O5' AMP 102 A 1 HETATM 6 C C5' AMP . . . E 4 39.753 1.834 59.497 0.8 49.03 ? C5' AMP 102 A 1 HETATM 7 C C4' AMP . . . E 4 39.468 1.51 60.962 0.8 54.77 ? C4' AMP 102 A 1 HETATM 8 O O4' AMP . . . E 4 40.388 0.524 61.39 0.8 57.13 ? O4' AMP 102 A 1 HETATM 9 C C3' AMP . . . E 4 39.644 2.667 61.938 0.8 56.87 ? C3' AMP 102 A 1 HETATM 10 O O3' AMP . . . E 4 38.494 3.463 62.064 0.8 53.91 ? O3' AMP 102 A 1 HETATM 11 C C2' AMP . . . E 4 40.009 1.96 63.216 0.8 59.25 ? C2' AMP 102 A 1 HETATM 12 O O2' AMP . . . E 4 38.885 1.515 63.955 0.8 60.42 ? O2' AMP 102 A 1 HETATM 13 C C1' AMP . . . E 4 40.785 0.762 62.72 0.8 60.03 ? C1' AMP 102 A 1 HETATM 14 N N9 AMP . . . E 4 42.235 1.012 62.802 0.8 62.19 ? N9 AMP 102 A 1 HETATM 15 C C8 AMP . . . E 4 43.112 1.329 61.792 0.8 62.41 ? C8 AMP 102 A 1 HETATM 16 N N7 AMP . . . E 4 44.347 1.455 62.335 0.8 62.74 ? N7 AMP 102 A 1 HETATM 17 C C5 AMP . . . E 4 44.262 1.21 63.666 0.8 64.18 ? C5 AMP 102 A 1 HETATM 18 C C6 AMP . . . E 4 45.199 1.185 64.695 0.8 64.52 ? C6 AMP 102 A 1 HETATM 19 N N6 AMP . . . E 4 46.488 1.444 64.434 0.8 66.19 ? N6 AMP 102 A 1 HETATM 20 N N1 AMP . . . E 4 44.781 0.899 65.984 0.8 63.04 ? N1 AMP 102 A 1 HETATM 21 C C2 AMP . . . E 4 43.464 0.621 66.263 0.8 63.01 ? C2 AMP 102 A 1 HETATM 22 N N3 AMP . . . E 4 42.545 0.636 65.24 0.8 63.21 ? N3 AMP 102 A 1 HETATM 23 C C4 AMP . . . E 4 42.936 0.928 63.972 0.8 63.26 ? C4 AMP 102 A 1 # _model_server_stats.io_time_ms 44 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 23 #