data_3BG5 # _model_server_result.job_id TRQ6F2hDgLODvQeCNljynQ _model_server_result.datetime_utc '2024-11-13 17:16:50' _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 3bg5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":2100}' # _entry.id 3BG5 # _exptl.entry_id 3BG5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _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 109.47 _cell.angle_gamma 90 _cell.entry_id 3BG5 _cell.length_a 96.428 _cell.length_b 256.083 _cell.length_c 126.01 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3BG5 _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 PISA tetrameric 4 author_and_software_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 PISA dimeric 2 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R 1 1 A,C,E,F,G,H,L,M,N,O 2 1 B,D,I,J,K,P,Q,R 3 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 ? 5 H N N ? 5 O 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 SER 305 A SER 315 1_555 A N GLY 306 A GLY 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 A C PRO 505 A PRO 513 1_555 A N ASN 506 A ASN 515 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale3 A C VAL 757 A VAL 763 1_555 A N ASP 758 A ASP 765 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale4 A C GLU 842 A GLU 849 1_555 A N SER 843 A SER 852 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale5 A NZ LYS 1135 A LYS 1144 1_555 F C11 BTI . A BTI 2000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale6 B C SER 305 B SER 315 1_555 B N GLY 306 B GLY 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale7 B C PRO 505 B PRO 513 1_555 B N ASN 506 B ASN 515 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale8 B C VAL 757 B VAL 763 1_555 B N ASP 758 B ASP 765 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale9 B C GLU 842 B GLU 849 1_555 B N SER 843 B SER 852 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale10 B NZ LYS 1135 B LYS 1144 1_555 J C11 BTI . B BTI 2000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale11 C C SER 305 C SER 315 1_555 C N GLY 306 C GLY 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale12 C C PRO 505 C PRO 513 1_555 C N ASN 506 C ASN 515 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale13 C C VAL 757 C VAL 763 1_555 C N ASP 758 C ASP 765 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale14 C C GLU 842 C GLU 849 1_555 C N SER 843 C SER 852 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale15 C NZ LYS 1135 C LYS 1144 1_555 M C11 BTI . C BTI 2000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale16 D C SER 305 D SER 315 1_555 D N GLY 306 D GLY 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale17 D C PRO 505 D PRO 513 1_555 D N ASN 506 D ASN 515 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale18 D C VAL 757 D VAL 763 1_555 D N ASP 758 D ASP 765 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale19 D C GLU 842 D GLU 849 1_555 D N SER 843 D SER 852 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale20 D NZ LYS 1135 D LYS 1144 1_555 Q C11 BTI . D BTI 2000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? metalc ? metalc1 B OD1 ASP 565 B ASP 572 1_555 I MN MN . B MN 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? metalc ? metalc2 D OD1 ASP 565 D ASP 572 1_555 P MN MN . D MN 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id ATP _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-5'-TRIPHOSPHATE" _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 PG O1G ATP doub 70 n n PG O2G ATP sing 71 n n PG O3G ATP sing 72 n n PG O3B ATP sing 73 n n O2G HOG2 ATP sing 74 n n O3G HOG3 ATP sing 75 n n PB O1B ATP doub 76 n n PB O2B ATP sing 77 n n PB O3B ATP sing 78 n n PB O3A ATP sing 79 n n O2B HOB2 ATP sing 80 n n PA O1A ATP doub 81 n n PA O2A ATP sing 82 n n PA O3A ATP sing 83 n n PA O5' ATP sing 84 n n O2A HOA2 ATP sing 85 n n O5' C5' ATP sing 86 n n C5' C4' ATP sing 87 n n C5' "H5'1" ATP sing 88 n n C5' "H5'2" ATP sing 89 n n C4' O4' ATP sing 90 n n C4' C3' ATP sing 91 n n C4' H4' ATP sing 92 n n O4' C1' ATP sing 93 n n C3' O3' ATP sing 94 n n C3' C2' ATP sing 95 n n C3' H3' ATP sing 96 n n O3' HO3' ATP sing 97 n n C2' O2' ATP sing 98 n n C2' C1' ATP sing 99 n n C2' H2' ATP sing 100 n n O2' HO2' ATP sing 101 n n C1' N9 ATP sing 102 n n C1' H1' ATP sing 103 n n N9 C8 ATP sing 104 n y N9 C4 ATP sing 105 n y C8 N7 ATP doub 106 n y C8 H8 ATP sing 107 n n N7 C5 ATP sing 108 n y C5 C6 ATP sing 109 n y C5 C4 ATP doub 110 n y C6 N6 ATP sing 111 n n C6 N1 ATP doub 112 n y N6 HN61 ATP sing 113 n n N6 HN62 ATP sing 114 n n N1 C2 ATP sing 115 n y C2 N3 ATP doub 116 n y C2 H2 ATP sing 117 n n N3 C4 ATP sing 118 n y # _atom_sites.entry_id 3BG5 _atom_sites.fract_transf_matrix[1][1] 0.01037 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003666 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.003905 _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] 0.008417 _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 E 2 MN A 1 2002 2002 MN MN . F 3 BTI A 1 2000 2000 BTI BTI . G 4 PYR A 1 2001 2001 PYR PYR . H 5 ATP A 1 2100 2100 ATP ATP . I 2 MN B 1 2002 2002 MN MN . J 3 BTI B 1 2000 2000 BTI BTI . K 4 PYR B 1 2001 2001 PYR PYR . L 2 MN C 1 2002 2002 MN MN . M 3 BTI C 1 2000 2000 BTI BTI . N 4 PYR C 1 2001 2001 PYR PYR . O 5 ATP C 1 2100 2100 ATP ATP . P 2 MN D 1 2002 2002 MN MN . Q 3 BTI D 1 2000 2000 BTI BTI . R 4 PYR D 1 2001 2001 PYR PYR . # 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 ATP . . . O 5 38.606 62.835 -18.701 1 95.5 ? PG ATP 2100 C 1 HETATM 2 O O1G ATP . . . O 5 37.996 62.586 -17.333 1 95.07 ? O1G ATP 2100 C 1 HETATM 3 O O2G ATP . . . O 5 39.909 63.62 -18.663 1 94.42 ? O2G ATP 2100 C 1 HETATM 4 O O3G ATP . . . O 5 38.671 61.602 -19.583 1 94.83 ? O3G ATP 2100 C 1 HETATM 5 P PB ATP . . . O 5 35.957 63.551 -19.678 1 89.9 ? PB ATP 2100 C 1 HETATM 6 O O1B ATP . . . O 5 35.622 64.068 -21.051 1 89.87 ? O1B ATP 2100 C 1 HETATM 7 O O2B ATP . . . O 5 35.137 64.042 -18.511 1 89.95 ? O2B ATP 2100 C 1 HETATM 8 O O3B ATP . . . O 5 37.54 63.83 -19.431 1 93.21 ? O3B ATP 2100 C 1 HETATM 9 P PA ATP . . . O 5 34.445 61.242 -19.986 1 89.04 ? PA ATP 2100 C 1 HETATM 10 O O1A ATP . . . O 5 34.699 60.081 -20.915 1 89.09 ? O1A ATP 2100 C 1 HETATM 11 O O2A ATP . . . O 5 33.441 62.309 -20.342 1 89.96 ? O2A ATP 2100 C 1 HETATM 12 O O3A ATP . . . O 5 35.856 61.951 -19.695 1 89.63 ? O3A ATP 2100 C 1 HETATM 13 O O5' ATP . . . O 5 34.01 60.664 -18.554 1 87.24 ? O5' ATP 2100 C 1 HETATM 14 C C5' ATP . . . O 5 34.933 59.883 -17.81 1 85.18 ? C5' ATP 2100 C 1 HETATM 15 C C4' ATP . . . O 5 34.201 59.232 -16.654 1 83.37 ? C4' ATP 2100 C 1 HETATM 16 O O4' ATP . . . O 5 32.806 59.538 -16.655 1 82.19 ? O4' ATP 2100 C 1 HETATM 17 C C3' ATP . . . O 5 34.301 57.728 -16.751 1 82.83 ? C3' ATP 2100 C 1 HETATM 18 O O3' ATP . . . O 5 35.477 57.286 -16.074 1 84.16 ? O3' ATP 2100 C 1 HETATM 19 C C2' ATP . . . O 5 33.022 57.248 -16.099 1 82.27 ? C2' ATP 2100 C 1 HETATM 20 O O2' ATP . . . O 5 33.168 57.106 -14.683 1 81.93 ? O2' ATP 2100 C 1 HETATM 21 C C1' ATP . . . O 5 32.034 58.366 -16.376 1 81.61 ? C1' ATP 2100 C 1 HETATM 22 N N9 ATP . . . O 5 31.188 58.014 -17.551 1 81.43 ? N9 ATP 2100 C 1 HETATM 23 C C8 ATP . . . O 5 31.189 58.654 -18.738 1 81.16 ? C8 ATP 2100 C 1 HETATM 24 N N7 ATP . . . O 5 30.311 58.094 -19.602 1 80.89 ? N7 ATP 2100 C 1 HETATM 25 C C5 ATP . . . O 5 29.721 57.069 -18.966 1 81.15 ? C5 ATP 2100 C 1 HETATM 26 C C6 ATP . . . O 5 28.693 56.053 -19.302 1 81.11 ? C6 ATP 2100 C 1 HETATM 27 N N6 ATP . . . O 5 28.114 56.038 -20.524 1 81.13 ? N6 ATP 2100 C 1 HETATM 28 N N1 ATP . . . O 5 28.358 55.149 -18.35 1 81.24 ? N1 ATP 2100 C 1 HETATM 29 C C2 ATP . . . O 5 28.936 55.157 -17.131 1 81.16 ? C2 ATP 2100 C 1 HETATM 30 N N3 ATP . . . O 5 29.873 56.05 -16.757 1 81.15 ? N3 ATP 2100 C 1 HETATM 31 C C4 ATP . . . O 5 30.302 57.014 -17.614 1 81.19 ? C4 ATP 2100 C 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 37 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 31 #