data_3AV0 # _model_server_result.job_id mOxabOJCoMrZFNsiVYy2bg _model_server_result.datetime_utc '2024-12-21 14:24:27' _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 3av0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1006}' # _entry.id 3AV0 # _exptl.entry_id 3AV0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.247 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOTHIOPHOSPHORIC 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 90 _cell.angle_gamma 90 _cell.entry_id 3AV0 _cell.length_a 86.958 _cell.length_b 147.129 _cell.length_c 175.907 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3AV0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_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 _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 6 _struct_asym.id G _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 metalc ? metalc1 B OG SER 39 B SER 39 1_555 H MG MG . B MG 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc2 B OE1 GLN 134 B GLN 134 1_555 H MG MG . B MG 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc3 G O3G AGS . B AGS 1006 1_555 H MG MG . B MG 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? metalc ? metalc4 G O2B AGS . B AGS 1006 1_555 H MG MG . B MG 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc5 H MG MG . B MG 1007 1_555 N O HOH . B HOH 1400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.483 ? metalc ? metalc6 H MG MG . B MG 1007 1_555 N O HOH . B HOH 1401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? # _chem_comp.formula 'C10 H16 N5 O12 P3 S' _chem_comp.formula_weight 523.247 _chem_comp.id AGS _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ATP-GAMMA-S;ADENOSINE 5'-(3-THIOTRIPHOSPHATE);ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE" # 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 S1G AGS doub 1 n n PG O2G AGS sing 2 n n PG O3G AGS sing 3 n n PG O3B AGS sing 4 n n PB O1B AGS doub 5 n n PB O2B AGS sing 6 n n PB O3B AGS sing 7 n n PB O3A AGS sing 8 n n PA O1A AGS doub 9 n n PA O2A AGS sing 10 n n PA O3A AGS sing 11 n n PA O5' AGS sing 12 n n O5' C5' AGS sing 13 n n C5' C4' AGS sing 14 n n C4' O4' AGS sing 15 n n C4' C3' AGS sing 16 n n O4' C1' AGS sing 17 n n C3' O3' AGS sing 18 n n C3' C2' AGS sing 19 n n C2' O2' AGS sing 20 n n C2' C1' AGS sing 21 n n C1' N9 AGS sing 22 n n N9 C8 AGS sing 23 n y N9 C4 AGS sing 24 n y C8 N7 AGS doub 25 n y N7 C5 AGS sing 26 n y C5 C6 AGS sing 27 n y C5 C4 AGS doub 28 n y C6 N6 AGS sing 29 n n C6 N1 AGS doub 30 n y N1 C2 AGS sing 31 n y C2 N3 AGS doub 32 n y N3 C4 AGS sing 33 n y O2G HOG2 AGS sing 34 n n O3G H21 AGS sing 35 n n O2B HOB2 AGS sing 36 n n O2A HOA2 AGS sing 37 n n C5' "H5'1" AGS sing 38 n n C5' "H5'2" AGS sing 39 n n C4' H4' AGS sing 40 n n C3' H3' AGS sing 41 n n O3' HO3' AGS sing 42 n n C2' H2' AGS sing 43 n n O2' HO2' AGS sing 44 n n C1' H1' AGS sing 45 n n C8 H8 AGS sing 46 n n N6 HN61 AGS sing 47 n n N6 HN62 AGS sing 48 n n C2 H2 AGS sing 49 n n # _atom_sites.entry_id 3AV0 _atom_sites.fract_transf_matrix[1][1] 0.0115 _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] 0.006797 _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] 0.005685 _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 GOL A 1 500 500 GOL GOL . D 4 IPA A 1 600 600 IPA IPA . E 5 SO4 A 1 400 400 SO4 SO4 . F 4 IPA B 1 601 601 IPA IPA . G 6 AGS B 1 1006 1006 AGS AGS . H 7 MG B 1 1007 1007 MG MG . I 3 GOL B 1 1200 1200 GOL GOL . J 3 GOL B 1 1201 1201 GOL GOL . K 3 GOL B 1 1202 1202 GOL GOL . L 4 IPA B 1 1300 1300 IPA IPA . M 8 HOH A 1 701 701 HOH HOH . M 8 HOH A 2 702 702 HOH HOH . M 8 HOH A 3 703 703 HOH HOH . M 8 HOH A 4 704 704 HOH HOH . M 8 HOH A 5 705 705 HOH HOH . M 8 HOH A 6 706 706 HOH HOH . M 8 HOH A 7 707 707 HOH HOH . M 8 HOH A 8 708 708 HOH HOH . M 8 HOH A 9 709 709 HOH HOH . M 8 HOH A 10 711 711 HOH HOH . N 8 HOH B 1 710 710 HOH HOH . N 8 HOH B 2 1400 1400 HOH HOH . N 8 HOH B 3 1401 1401 HOH HOH . N 8 HOH B 4 1402 1402 HOH HOH . N 8 HOH B 5 1403 1403 HOH HOH . N 8 HOH B 6 1404 1404 HOH HOH . N 8 HOH B 7 1405 1405 HOH HOH . N 8 HOH B 8 1406 1406 HOH HOH . N 8 HOH B 9 1407 1407 HOH HOH . N 8 HOH B 10 1408 1408 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 AGS . . . G 6 33.342 13.354 40.902 1 75.38 ? PG AGS 1006 B 1 HETATM 2 S S1G AGS . . . G 6 34.616 15.015 40.562 1 88.19 ? S1G AGS 1006 B 1 HETATM 3 O O2G AGS . . . G 6 33.289 13.122 42.542 1 71.62 ? O2G AGS 1006 B 1 HETATM 4 O O3G AGS . . . G 6 33.853 12.135 40.277 1 74.62 ? O3G AGS 1006 B 1 HETATM 5 P PB AGS . . . G 6 31.364 13.133 38.798 1 66.71 ? PB AGS 1006 B 1 HETATM 6 O O1B AGS . . . G 6 30.473 14.322 38.115 1 64.56 ? O1B AGS 1006 B 1 HETATM 7 O O2B AGS . . . G 6 32.403 12.731 37.871 1 50.9 ? O2B AGS 1006 B 1 HETATM 8 O O3B AGS . . . G 6 31.821 13.598 40.309 1 65.09 ? O3B AGS 1006 B 1 HETATM 9 P PA AGS . . . G 6 29.661 10.809 38.228 1 60.94 ? PA AGS 1006 B 1 HETATM 10 O O1A AGS . . . G 6 29.967 10.921 36.621 1 50.81 ? O1A AGS 1006 B 1 HETATM 11 O O2A AGS . . . G 6 30.133 9.487 38.646 1 71.02 ? O2A AGS 1006 B 1 HETATM 12 O O3A AGS . . . G 6 30.422 11.854 39.24 1 69.18 ? O3A AGS 1006 B 1 HETATM 13 O O5' AGS . . . G 6 28.11 11.055 38.678 1 49.68 ? O5' AGS 1006 B 1 HETATM 14 C C5' AGS . . . G 6 28.041 11.017 40.057 1 52.69 ? C5' AGS 1006 B 1 HETATM 15 C C4' AGS . . . G 6 26.668 11.466 40.479 1 57.99 ? C4' AGS 1006 B 1 HETATM 16 O O4' AGS . . . G 6 25.678 10.755 39.725 1 54.94 ? O4' AGS 1006 B 1 HETATM 17 C C3' AGS . . . G 6 26.552 11.093 41.939 1 62.32 ? C3' AGS 1006 B 1 HETATM 18 O O3' AGS . . . G 6 26.019 12.18 42.657 1 69.6 ? O3' AGS 1006 B 1 HETATM 19 C C2' AGS . . . G 6 25.569 10.004 41.978 1 65.71 ? C2' AGS 1006 B 1 HETATM 20 O O2' AGS . . . G 6 24.717 10.32 43.038 1 76.01 ? O2' AGS 1006 B 1 HETATM 21 C C1' AGS . . . G 6 24.769 10.18 40.706 1 68.64 ? C1' AGS 1006 B 1 HETATM 22 N N9 AGS . . . G 6 24.449 8.812 40.356 1 72.04 ? N9 AGS 1006 B 1 HETATM 23 C C8 AGS . . . G 6 25.413 7.691 40.238 1 71.07 ? C8 AGS 1006 B 1 HETATM 24 N N7 AGS . . . G 6 24.649 6.505 39.885 1 75.04 ? N7 AGS 1006 B 1 HETATM 25 C C5 AGS . . . G 6 23.236 6.878 39.809 1 75.93 ? C5 AGS 1006 B 1 HETATM 26 C C6 AGS . . . G 6 22.004 6.068 39.508 1 76.68 ? C6 AGS 1006 B 1 HETATM 27 N N6 AGS . . . G 6 22.104 4.642 39.248 1 80.04 ? N6 AGS 1006 B 1 HETATM 28 N N1 AGS . . . G 6 20.718 6.733 39.517 1 73.77 ? N1 AGS 1006 B 1 HETATM 29 C C2 AGS . . . G 6 20.623 8.205 39.823 1 75.97 ? C2 AGS 1006 B 1 HETATM 30 N N3 AGS . . . G 6 21.833 9.003 40.128 1 69.77 ? N3 AGS 1006 B 1 HETATM 31 C C4 AGS . . . G 6 23.127 8.319 40.112 1 70.86 ? C4 AGS 1006 B 1 # _model_server_stats.io_time_ms 82 _model_server_stats.parse_time_ms 33 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 1275 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 31 #