data_6D5K # _model_server_result.job_id uteaHcf06DrSgbgo9F6kug _model_server_result.datetime_utc '2024-11-22 21:44:24' _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 6d5k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":301}' # _entry.id 6D5K # _exptl.entry_id 6D5K _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 5 _entity.src_method man _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _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 120 _cell.entry_id 6D5K _cell.length_a 112.252 _cell.length_b 112.252 _cell.length_c 117.993 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6D5K _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 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 trimeric 3 author_and_software_defined_assembly 1 PISA hexameric 6 software_defined_assembly 2 # 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,S,T 1 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T 2 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 6_554 -x,-x+y,-z-2/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 -78.662 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id L _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 D C5' 5AD . A 5AD 301 1_555 E CO B12 . A B12 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc2 F CO B12 . A B12 303 1_555 I C5' 5AD . B 5AD 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? metalc ? metalc3 C OD1 ASN 160 C ASN 214 1_555 Q MG MG . C MG 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? metalc ? metalc4 L O1A ATP . C ATP 301 1_555 M MG MG . C MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.679 ? metalc ? metalc5 L O3G ATP . C ATP 301 1_555 Q MG MG . C MG 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? metalc ? metalc6 L O2B ATP . C ATP 301 1_555 Q MG MG . C MG 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.837 ? metalc ? metalc7 L O2A ATP . C ATP 301 1_555 Q MG MG . C MG 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.884 ? metalc ? metalc8 M MG MG . C MG 302 1_555 T O HOH . C HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc9 M MG MG . C MG 302 1_555 T O HOH . C HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.578 ? metalc ? metalc10 M MG MG . C MG 302 1_555 T O HOH . C HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc11 M MG MG . C MG 302 1_555 T O HOH . C HOH 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc12 Q MG MG . C MG 306 1_555 T O HOH . C HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.867 ? metalc ? metalc13 Q MG MG . C MG 306 1_555 T O HOH . C HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? # _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 103 n n PG O2G ATP sing 104 n n PG O3G ATP sing 105 n n PG O3B ATP sing 106 n n O2G HOG2 ATP sing 107 n n O3G HOG3 ATP sing 108 n n PB O1B ATP doub 109 n n PB O2B ATP sing 110 n n PB O3B ATP sing 111 n n PB O3A ATP sing 112 n n O2B HOB2 ATP sing 113 n n PA O1A ATP doub 114 n n PA O2A ATP sing 115 n n PA O3A ATP sing 116 n n PA O5' ATP sing 117 n n O2A HOA2 ATP sing 118 n n O5' C5' ATP sing 119 n n C5' C4' ATP sing 120 n n C5' "H5'1" ATP sing 121 n n C5' "H5'2" ATP sing 122 n n C4' O4' ATP sing 123 n n C4' C3' ATP sing 124 n n C4' H4' ATP sing 125 n n O4' C1' ATP sing 126 n n C3' O3' ATP sing 127 n n C3' C2' ATP sing 128 n n C3' H3' ATP sing 129 n n O3' HO3' ATP sing 130 n n C2' O2' ATP sing 131 n n C2' C1' ATP sing 132 n n C2' H2' ATP sing 133 n n O2' HO2' ATP sing 134 n n C1' N9 ATP sing 135 n n C1' H1' ATP sing 136 n n N9 C8 ATP sing 137 n y N9 C4 ATP sing 138 n y C8 N7 ATP doub 139 n y C8 H8 ATP sing 140 n n N7 C5 ATP sing 141 n y C5 C6 ATP sing 142 n y C5 C4 ATP doub 143 n y C6 N6 ATP sing 144 n n C6 N1 ATP doub 145 n y N6 HN61 ATP sing 146 n n N6 HN62 ATP sing 147 n n N1 C2 ATP sing 148 n y C2 N3 ATP doub 149 n y C2 H2 ATP sing 150 n n N3 C4 ATP sing 151 n y # _atom_sites.entry_id 6D5K _atom_sites.fract_transf_matrix[1][1] 0.008909 _atom_sites.fract_transf_matrix[1][2] 0.005143 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010287 _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] 0.008475 _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 D 2 5AD A 1 301 1 5AD 5AD . E 3 B12 A 1 302 2 B12 B12 . F 3 B12 A 1 303 4 B12 B12 . G 4 SO4 A 1 304 3 SO4 SO4 . H 4 SO4 A 1 305 6 SO4 SO4 . I 2 5AD B 1 301 3 5AD 5AD . J 4 SO4 B 1 302 1 SO4 SO4 . K 4 SO4 B 1 303 5 SO4 SO4 . L 5 ATP C 1 301 1 ATP ATP . M 6 MG C 1 302 1 MG MG . N 7 EPE C 1 303 1 EPE EPE . O 4 SO4 C 1 304 2 SO4 SO4 . P 4 SO4 C 1 305 4 SO4 SO4 . Q 6 MG C 1 306 2 MG MG . R 8 HOH A 1 401 7 HOH HOH . R 8 HOH A 2 402 64 HOH HOH . R 8 HOH A 3 403 58 HOH HOH . R 8 HOH A 4 404 70 HOH HOH . S 8 HOH B 1 401 71 HOH HOH . S 8 HOH B 2 402 54 HOH HOH . S 8 HOH B 3 403 19 HOH HOH . S 8 HOH B 4 404 63 HOH HOH . S 8 HOH B 5 405 44 HOH HOH . S 8 HOH B 6 406 40 HOH HOH . T 8 HOH C 1 401 1 HOH HOH . T 8 HOH C 2 402 5 HOH HOH . T 8 HOH C 3 403 2 HOH HOH . T 8 HOH C 4 404 3 HOH HOH . T 8 HOH C 5 405 6 HOH HOH . T 8 HOH C 6 406 16 HOH HOH . T 8 HOH C 7 407 4 HOH HOH . T 8 HOH C 8 408 13 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 ATP . . . L 5 -36.162 32.243 -33.46 1 69.41 ? PG ATP 301 C 1 HETATM 2 O O1G ATP . . . L 5 -34.987 32.399 -34.394 1 68.58 ? O1G ATP 301 C 1 HETATM 3 O O2G ATP . . . L 5 -36.957 30.978 -33.671 1 71.51 -1 O2G ATP 301 C 1 HETATM 4 O O3G ATP . . . L 5 -35.883 32.515 -32.003 1 64.21 ? O3G ATP 301 C 1 HETATM 5 P PB ATP . . . L 5 -37.834 34.382 -32.873 1 64.95 ? PB ATP 301 C 1 HETATM 6 O O1B ATP . . . L 5 -38.709 35.336 -33.595 1 65.77 -1 O1B ATP 301 C 1 HETATM 7 O O2B ATP . . . L 5 -36.737 34.863 -31.967 1 65.27 ? O2B ATP 301 C 1 HETATM 8 O O3B ATP . . . L 5 -37.159 33.416 -33.935 1 63.3 ? O3B ATP 301 C 1 HETATM 9 P PA ATP . . . L 5 -38.893 33.049 -30.586 1 67.12 ? PA ATP 301 C 1 HETATM 10 O O1A ATP . . . L 5 -39.413 31.628 -30.442 1 64.48 -1 O1A ATP 301 C 1 HETATM 11 O O2A ATP . . . L 5 -37.534 33.42 -30.038 1 67.73 ? O2A ATP 301 C 1 HETATM 12 O O3A ATP . . . L 5 -38.839 33.348 -32.167 1 69.2 ? O3A ATP 301 C 1 HETATM 13 O O5' ATP . . . L 5 -39.966 34.094 -29.998 1 62.91 ? O5' ATP 301 C 1 HETATM 14 C C5' ATP . . . L 5 -41.308 33.666 -29.798 1 55.69 ? C5' ATP 301 C 1 HETATM 15 C C4' ATP . . . L 5 -42.296 34.808 -30.011 1 50.96 ? C4' ATP 301 C 1 HETATM 16 O O4' ATP . . . L 5 -42.099 35.813 -29.033 1 55.84 ? O4' ATP 301 C 1 HETATM 17 C C3' ATP . . . L 5 -42.13 35.509 -31.335 1 58.86 ? C3' ATP 301 C 1 HETATM 18 O O3' ATP . . . L 5 -43.109 35.006 -32.237 1 70.83 ? O3' ATP 301 C 1 HETATM 19 C C2' ATP . . . L 5 -42.381 36.961 -30.995 1 56.74 ? C2' ATP 301 C 1 HETATM 20 O O2' ATP . . . L 5 -43.771 37.086 -30.778 1 51.94 ? O2' ATP 301 C 1 HETATM 21 C C1' ATP . . . L 5 -41.887 37.129 -29.588 1 58.65 ? C1' ATP 301 C 1 HETATM 22 N N9 ATP . . . L 5 -40.444 37.443 -29.359 1 57.67 ? N9 ATP 301 C 1 HETATM 23 C C8 ATP . . . L 5 -39.378 36.957 -30.014 1 63.2 ? C8 ATP 301 C 1 HETATM 24 N N7 ATP . . . L 5 -38.218 37.413 -29.479 1 64.62 ? N7 ATP 301 C 1 HETATM 25 C C5 ATP . . . L 5 -38.53 38.188 -28.435 1 59.85 ? C5 ATP 301 C 1 HETATM 26 C C6 ATP . . . L 5 -37.776 38.971 -27.428 1 60.07 ? C6 ATP 301 C 1 HETATM 27 N N6 ATP . . . L 5 -36.437 39.027 -27.45 1 65.78 ? N6 ATP 301 C 1 HETATM 28 N N1 ATP . . . L 5 -38.468 39.659 -26.516 1 47.31 ? N1 ATP 301 C 1 HETATM 29 C C2 ATP . . . L 5 -39.813 39.616 -26.505 1 52.97 ? C2 ATP 301 C 1 HETATM 30 N N3 ATP . . . L 5 -40.561 38.907 -27.373 1 59.21 ? N3 ATP 301 C 1 HETATM 31 C C4 ATP . . . L 5 -39.993 38.2 -28.365 1 53.11 ? C4 ATP 301 C 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 35 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #