data_1KYI # _model_server_result.job_id OSssqGncIvMBFx73b1YrGA _model_server_result.datetime_utc '2025-02-27 19:08:37' _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 1kyi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Z","auth_seq_id":451}' # _entry.id 1KYI # _exptl.entry_id 1KYI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 12 _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 1KYI _cell.length_a 208.51 _cell.length_b 219.97 _cell.length_c 242.63 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KYI _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details 24-meric _pdbx_struct_assembly.oligomeric_count 24 _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,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 Y N N ? 3 Z N N ? 3 AA N N ? 3 BA N N ? 3 CA N N ? 3 DA N N ? 3 QA N N ? 3 RA N N ? 3 SA N N ? 3 TA N N ? 3 UA N N ? 3 VA 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 G OG1 THR 1 G THR 1 1_555 EA CS LVS . G LVS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 H OG1 THR 1 H THR 1 1_555 FA CS LVS . H LVS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale3 I OG1 THR 1 I THR 1 1_555 GA CS LVS . I LVS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.285 ? covale ? covale4 J OG1 THR 1 J THR 1 1_555 HA CS LVS . J LVS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.49 ? covale ? covale5 K OG1 THR 1 K THR 1 1_555 IA CS LVS . K LVS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.473 ? covale ? covale6 L OG1 THR 1 L THR 1 1_555 JA CS LVS . L LVS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.31 ? covale ? covale7 M OG1 THR 1 M THR 1 1_555 KA CS LVS . M LVS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.352 ? covale ? covale8 N OG1 THR 1 N THR 1 1_555 LA CS LVS . N LVS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale9 O OG1 THR 1 O THR 1 1_555 MA CS LVS . O LVS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale10 P OG1 THR 1 P THR 1 1_555 NA CS LVS . P LVS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale11 Q OG1 THR 1 Q THR 1 1_555 OA CS LVS . Q LVS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale12 R OG1 THR 1 R THR 1 1_555 PA CS LVS . R LVS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? # _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 1KYI _atom_sites.fract_transf_matrix[1][1] 0.004796 _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] 0.004546 _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] 0.004122 _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 Y 3 ATP A 1 450 450 ATP ATP . Z 3 ATP B 1 451 450 ATP ATP . AA 3 ATP C 1 452 450 ATP ATP . BA 3 ATP D 1 453 450 ATP ATP . CA 3 ATP E 1 454 450 ATP ATP . DA 3 ATP F 1 455 450 ATP ATP . EA 4 LVS G 1 175 174 LVS LEU . FA 4 LVS H 1 175 174 LVS LEU . GA 4 LVS I 1 175 174 LVS LEU . HA 4 LVS J 1 175 174 LVS LEU . IA 4 LVS K 1 175 174 LVS LEU . JA 4 LVS L 1 175 174 LVS LEU . KA 4 LVS M 1 175 174 LVS LEU . LA 4 LVS N 1 175 174 LVS LEU . MA 4 LVS O 1 175 174 LVS LEU . NA 4 LVS P 1 175 174 LVS LEU . OA 4 LVS Q 1 175 174 LVS LEU . PA 4 LVS R 1 175 174 LVS LEU . QA 3 ATP S 1 456 450 ATP ATP . RA 3 ATP T 1 457 450 ATP ATP . SA 3 ATP U 1 458 450 ATP ATP . TA 3 ATP V 1 459 450 ATP ATP . UA 3 ATP W 1 460 450 ATP ATP . VA 3 ATP X 1 461 450 ATP ATP . # 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 . . . Z 3 168.646 53.209 123.08 1 65.08 ? PG ATP 451 B 1 HETATM 2 O O1G ATP . . . Z 3 169.468 53.742 121.888 1 63.83 ? O1G ATP 451 B 1 HETATM 3 O O2G ATP . . . Z 3 168.621 54.073 124.334 1 65.44 ? O2G ATP 451 B 1 HETATM 4 O O3G ATP . . . Z 3 167.333 52.531 122.728 1 64.71 ? O3G ATP 451 B 1 HETATM 5 P PB ATP . . . Z 3 170.49 51.459 124.832 1 45.24 ? PB ATP 451 B 1 HETATM 6 O O1B ATP . . . Z 3 171.614 50.634 124.274 1 45.25 ? O1B ATP 451 B 1 HETATM 7 O O2B ATP . . . Z 3 170.812 52.615 125.747 1 45.7 ? O2B ATP 451 B 1 HETATM 8 O O3B ATP . . . Z 3 169.556 51.919 123.568 1 54.47 ? O3B ATP 451 B 1 HETATM 9 P PA ATP . . . Z 3 169.715 49.575 126.905 1 40.22 ? PA ATP 451 B 1 HETATM 10 O O1A ATP . . . Z 3 169.02 50.044 128.179 1 39.76 ? O1A ATP 451 B 1 HETATM 11 O O2A ATP . . . Z 3 171.191 49.248 126.944 1 36.53 ? O2A ATP 451 B 1 HETATM 12 O O3A ATP . . . Z 3 169.47 50.527 125.635 1 43.32 ? O3A ATP 451 B 1 HETATM 13 O O5' ATP . . . Z 3 168.863 48.343 126.374 1 37.25 ? O5' ATP 451 B 1 HETATM 14 C C5' ATP . . . Z 3 169.441 47.058 126.191 1 36.11 ? C5' ATP 451 B 1 HETATM 15 C C4' ATP . . . Z 3 168.672 46.009 126.978 1 37.64 ? C4' ATP 451 B 1 HETATM 16 O O4' ATP . . . Z 3 169.459 44.794 126.937 1 37.26 ? O4' ATP 451 B 1 HETATM 17 C C3' ATP . . . Z 3 168.539 46.321 128.462 1 38.82 ? C3' ATP 451 B 1 HETATM 18 O O3' ATP . . . Z 3 167.477 45.573 129.035 1 40.35 ? O3' ATP 451 B 1 HETATM 19 C C2' ATP . . . Z 3 169.891 45.883 129.013 1 39.37 ? C2' ATP 451 B 1 HETATM 20 O O2' ATP . . . Z 3 169.775 45.396 130.324 1 39.72 ? O2' ATP 451 B 1 HETATM 21 C C1' ATP . . . Z 3 170.289 44.736 128.081 1 37.98 ? C1' ATP 451 B 1 HETATM 22 N N9 ATP . . . Z 3 171.662 44.925 127.612 1 35.36 ? N9 ATP 451 B 1 HETATM 23 C C8 ATP . . . Z 3 172.051 45.581 126.467 1 36.85 ? C8 ATP 451 B 1 HETATM 24 N N7 ATP . . . Z 3 173.347 45.625 126.292 1 38.55 ? N7 ATP 451 B 1 HETATM 25 C C5 ATP . . . Z 3 173.849 44.946 127.388 1 35.79 ? C5 ATP 451 B 1 HETATM 26 C C6 ATP . . . Z 3 175.161 44.645 127.785 1 35.06 ? C6 ATP 451 B 1 HETATM 27 N N6 ATP . . . Z 3 176.237 44.991 127.089 1 34.93 ? N6 ATP 451 B 1 HETATM 28 N N1 ATP . . . Z 3 175.33 43.961 128.934 1 35.27 ? N1 ATP 451 B 1 HETATM 29 C C2 ATP . . . Z 3 174.238 43.601 129.623 1 35.99 ? C2 ATP 451 B 1 HETATM 30 N N3 ATP . . . Z 3 172.945 43.826 129.35 1 35.14 ? N3 ATP 451 B 1 HETATM 31 C C4 ATP . . . Z 3 172.821 44.509 128.208 1 34.74 ? C4 ATP 451 B 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 59 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #