data_3GQI # _model_server_result.job_id 7kMg_Yqcpkx9yy0_YNe2xA _model_server_result.datetime_utc '2024-10-11 01:27:29' _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 3gqi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":775}' # _entry.id 3GQI # _exptl.entry_id 3GQI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _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 96.5 _cell.angle_gamma 90 _cell.entry_id 3GQI _cell.length_a 133.935 _cell.length_b 64.596 _cell.length_c 94.209 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3GQI _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 4 _struct_asym.id D _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 C ASP 204 A ASP 652 1_555 A N PTR 205 A PTR 653 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale2 A C PTR 205 A PTR 653 1_555 A N PTR 206 A PTR 654 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? covale ? covale3 A C PTR 206 A PTR 654 1_555 A N LYS 207 A LYS 655 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale4 A C GLU 317 A GLU 765 1_555 A N PTR 318 A PTR 766 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale5 A C PTR 318 A PTR 766 1_555 A N LEU 319 A LEU 767 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id ACP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE" # 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 PG O1G ACP doub 1 n n PG O2G ACP sing 2 n n PG O3G ACP sing 3 n n PG C3B ACP sing 4 n n O2G HOG2 ACP sing 5 n n O3G HOG3 ACP sing 6 n n PB O1B ACP doub 7 n n PB O2B ACP sing 8 n n PB C3B ACP sing 9 n n PB O3A ACP sing 10 n n O2B HOB2 ACP sing 11 n n C3B H3B1 ACP sing 12 n n C3B H3B2 ACP sing 13 n n PA O1A ACP doub 14 n n PA O2A ACP sing 15 n n PA O3A ACP sing 16 n n PA O5' ACP sing 17 n n O2A HOA2 ACP sing 18 n n O5' C5' ACP sing 19 n n C5' C4' ACP sing 20 n n C5' "H5'1" ACP sing 21 n n C5' "H5'2" ACP sing 22 n n C4' O4' ACP sing 23 n n C4' C3' ACP sing 24 n n C4' H4' ACP sing 25 n n O4' C1' ACP sing 26 n n C3' O3' ACP sing 27 n n C3' C2' ACP sing 28 n n C3' H3' ACP sing 29 n n O3' HO3' ACP sing 30 n n C2' O2' ACP sing 31 n n C2' C1' ACP sing 32 n n C2' H2' ACP sing 33 n n O2' HO2' ACP sing 34 n n C1' N9 ACP sing 35 n n C1' H1' ACP sing 36 n n N9 C8 ACP sing 37 n y N9 C4 ACP sing 38 n y C8 N7 ACP doub 39 n y C8 H8 ACP sing 40 n n N7 C5 ACP sing 41 n y C5 C6 ACP sing 42 n y C5 C4 ACP doub 43 n y C6 N6 ACP sing 44 n n C6 N1 ACP doub 45 n y N6 HN61 ACP sing 46 n n N6 HN62 ACP sing 47 n n N1 C2 ACP sing 48 n y C2 N3 ACP doub 49 n y C2 H2 ACP sing 50 n n N3 C4 ACP sing 51 n y # _atom_sites.entry_id 3GQI _atom_sites.fract_transf_matrix[1][1] 0.007466 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000851 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015481 _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] 0.010683 _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 3 DVT A 1 1 1 DVT DVT . D 4 ACP A 1 775 1 ACP ACP . E 5 MG A 1 776 1 MG MG . F 6 HOH A 1 4 4 HOH HOH . F 6 HOH A 2 5 5 HOH HOH . F 6 HOH A 3 6 6 HOH HOH . F 6 HOH A 4 7 7 HOH HOH . F 6 HOH A 5 8 8 HOH HOH . F 6 HOH A 6 9 9 HOH HOH . F 6 HOH A 7 10 10 HOH HOH . F 6 HOH A 8 12 12 HOH HOH . F 6 HOH A 9 13 13 HOH HOH . F 6 HOH A 10 14 14 HOH HOH . F 6 HOH A 11 16 16 HOH HOH . F 6 HOH A 12 17 17 HOH HOH . F 6 HOH A 13 19 19 HOH HOH . F 6 HOH A 14 22 22 HOH HOH . F 6 HOH A 15 23 23 HOH HOH . F 6 HOH A 16 24 24 HOH HOH . F 6 HOH A 17 28 28 HOH HOH . F 6 HOH A 18 31 31 HOH HOH . F 6 HOH A 19 32 32 HOH HOH . F 6 HOH A 20 33 33 HOH HOH . F 6 HOH A 21 35 35 HOH HOH . F 6 HOH A 22 36 36 HOH HOH . F 6 HOH A 23 37 37 HOH HOH . F 6 HOH A 24 39 39 HOH HOH . F 6 HOH A 25 40 40 HOH HOH . F 6 HOH A 26 41 41 HOH HOH . F 6 HOH A 27 42 42 HOH HOH . F 6 HOH A 28 44 44 HOH HOH . F 6 HOH A 29 45 45 HOH HOH . F 6 HOH A 30 46 46 HOH HOH . F 6 HOH A 31 47 47 HOH HOH . F 6 HOH A 32 48 48 HOH HOH . F 6 HOH A 33 49 49 HOH HOH . F 6 HOH A 34 50 50 HOH HOH . F 6 HOH A 35 51 51 HOH HOH . F 6 HOH A 36 52 52 HOH HOH . F 6 HOH A 37 53 53 HOH HOH . F 6 HOH A 38 54 54 HOH HOH . F 6 HOH A 39 55 55 HOH HOH . F 6 HOH A 40 59 59 HOH HOH . F 6 HOH A 41 60 60 HOH HOH . F 6 HOH A 42 61 61 HOH HOH . F 6 HOH A 43 63 63 HOH HOH . F 6 HOH A 44 65 65 HOH HOH . F 6 HOH A 45 66 66 HOH HOH . F 6 HOH A 46 67 67 HOH HOH . F 6 HOH A 47 69 69 HOH HOH . F 6 HOH A 48 70 70 HOH HOH . F 6 HOH A 49 71 71 HOH HOH . F 6 HOH A 50 73 73 HOH HOH . F 6 HOH A 51 74 74 HOH HOH . F 6 HOH A 52 76 76 HOH HOH . F 6 HOH A 53 77 77 HOH HOH . F 6 HOH A 54 78 78 HOH HOH . F 6 HOH A 55 777 1 HOH HOH . G 6 HOH B 1 2 2 HOH HOH . G 6 HOH B 2 11 11 HOH HOH . G 6 HOH B 3 15 15 HOH HOH . G 6 HOH B 4 18 18 HOH HOH . G 6 HOH B 5 20 20 HOH HOH . G 6 HOH B 6 21 21 HOH HOH . G 6 HOH B 7 25 25 HOH HOH . G 6 HOH B 8 26 26 HOH HOH . G 6 HOH B 9 27 27 HOH HOH . G 6 HOH B 10 29 29 HOH HOH . G 6 HOH B 11 30 30 HOH HOH . G 6 HOH B 12 34 34 HOH HOH . G 6 HOH B 13 38 38 HOH HOH . G 6 HOH B 14 43 43 HOH HOH . G 6 HOH B 15 56 56 HOH HOH . G 6 HOH B 16 57 57 HOH HOH . G 6 HOH B 17 58 58 HOH HOH . G 6 HOH B 18 62 62 HOH HOH . G 6 HOH B 19 64 64 HOH HOH . G 6 HOH B 20 68 68 HOH HOH . G 6 HOH B 21 72 72 HOH HOH . G 6 HOH B 22 75 75 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 PG ACP . . . D 4 -35.525 33.865 43.542 1 95.23 ? PG ACP 775 A 1 HETATM 2 O O1G ACP . . . D 4 -35.209 32.795 44.707 1 94.29 ? O1G ACP 775 A 1 HETATM 3 O O2G ACP . . . D 4 -34.295 34.906 43.536 1 94.57 ? O2G ACP 775 A 1 HETATM 4 O O3G ACP . . . D 4 -36.826 34.539 43.755 1 95.86 ? O3G ACP 775 A 1 HETATM 5 P PB ACP . . . D 4 -33.836 32.179 41.737 1 95.12 ? PB ACP 775 A 1 HETATM 6 O O1B ACP . . . D 4 -32.826 33.136 42.201 1 95.55 ? O1B ACP 775 A 1 HETATM 7 O O2B ACP . . . D 4 -33.879 30.83 42.36 1 95.22 ? O2B ACP 775 A 1 HETATM 8 C C3B ACP . . . D 4 -35.463 32.945 41.985 1 95.39 ? C3B ACP 775 A 1 HETATM 9 P PA ACP . . . D 4 -32.885 30.889 39.415 1 91.29 ? PA ACP 775 A 1 HETATM 10 O O1A ACP . . . D 4 -32.252 30.047 40.479 1 90.35 ? O1A ACP 775 A 1 HETATM 11 O O2A ACP . . . D 4 -32.008 31.538 38.438 1 89.4 ? O2A ACP 775 A 1 HETATM 12 O O3A ACP . . . D 4 -33.751 32.042 40.129 1 93.14 ? O3A ACP 775 A 1 HETATM 13 O O5' ACP . . . D 4 -33.979 30.001 38.638 1 89.27 ? O5' ACP 775 A 1 HETATM 14 C C5' ACP . . . D 4 -34.97 29.243 39.34 1 87.36 ? C5' ACP 775 A 1 HETATM 15 C C4' ACP . . . D 4 -35.453 28.061 38.495 1 85.64 ? C4' ACP 775 A 1 HETATM 16 O O4' ACP . . . D 4 -35.946 28.459 37.199 1 84.88 ? O4' ACP 775 A 1 HETATM 17 C C3' ACP . . . D 4 -34.355 27.047 38.203 1 85.05 ? C3' ACP 775 A 1 HETATM 18 O O3' ACP . . . D 4 -34.193 26.193 39.347 1 84.36 ? O3' ACP 775 A 1 HETATM 19 C C2' ACP . . . D 4 -35.065 26.262 37.1 1 84.1 ? C2' ACP 775 A 1 HETATM 20 O O2' ACP . . . D 4 -36.15 25.521 37.649 1 85.88 ? O2' ACP 775 A 1 HETATM 21 C C1' ACP . . . D 4 -35.596 27.428 36.257 1 82.4 ? C1' ACP 775 A 1 HETATM 22 N N9 ACP . . . D 4 -34.549 27.948 35.354 1 78.29 ? N9 ACP 775 A 1 HETATM 23 C C8 ACP . . . D 4 -33.747 28.994 35.61 1 76.52 ? C8 ACP 775 A 1 HETATM 24 N N7 ACP . . . D 4 -32.964 29.207 34.558 1 75.28 ? N7 ACP 775 A 1 HETATM 25 C C5 ACP . . . D 4 -33.24 28.29 33.62 1 74.04 ? C5 ACP 775 A 1 HETATM 26 C C6 ACP . . . D 4 -32.77 28.003 32.377 1 72.61 ? C6 ACP 775 A 1 HETATM 27 N N6 ACP . . . D 4 -31.79 28.742 31.832 1 70.51 ? N6 ACP 775 A 1 HETATM 28 N N1 ACP . . . D 4 -33.283 26.968 31.669 1 71.03 ? N1 ACP 775 A 1 HETATM 29 C C2 ACP . . . D 4 -34.253 26.242 32.199 1 71.77 ? C2 ACP 775 A 1 HETATM 30 N N3 ACP . . . D 4 -34.739 26.484 33.385 1 72.76 ? N3 ACP 775 A 1 HETATM 31 C C4 ACP . . . D 4 -34.258 27.502 34.148 1 75.33 ? C4 ACP 775 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #