data_1Y8P # _model_server_result.job_id 5PbTWoaHy8iyGALJ4WkwMw _model_server_result.datetime_utc '2024-11-04 23:22:17' _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 1y8p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":504}' # _entry.id 1Y8P # _exptl.entry_id 1Y8P _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 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 1Y8P _cell.length_a 120.904 _cell.length_b 120.904 _cell.length_c 240.085 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1Y8P _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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' 11_455 -x+y-1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 -120.904 0 120.0425 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id F _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 A O SER 33 A SER 20 1_555 D K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.631 ? metalc ? metalc2 A O PHE 35 A PHE 22 1_555 D K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.822 ? metalc ? metalc3 A OD1 ASN 72 A ASN 59 1_555 D K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.964 ? metalc ? metalc4 A OD1 ASN 264 A ASN 251 1_555 C MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? metalc ? metalc5 A O LEU 313 A LEU 300 1_555 E K K . A K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.647 ? metalc ? metalc6 A O ASN 315 A ASN 302 1_555 E K K . A K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.019 ? metalc ? metalc7 A O TYR 318 A TYR 305 1_555 E K K . A K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.077 ? metalc ? metalc8 A O GLY 338 A GLY 325 1_555 E K K . A K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.916 ? metalc ? metalc9 A O PHE 385 A PHE 372 1_555 D K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? metalc ? metalc10 C MG MG . A MG 501 1_555 F O2B ATP . A ATP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.892 ? metalc ? metalc11 C MG MG . A MG 501 1_555 F O1G ATP . A ATP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc12 C MG MG . A MG 501 1_555 F O2A ATP . A ATP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? metalc ? metalc13 C MG MG . A MG 501 1_555 H O HOH . A HOH 535 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? metalc ? metalc14 E K K . A K 503 1_555 F O1A ATP . A ATP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.832 ? # _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 1Y8P _atom_sites.fract_transf_matrix[1][1] 0.008271 _atom_sites.fract_transf_matrix[1][2] 0.004775 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009551 _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] 0.004165 _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 MG A 1 501 1 MG MG . D 4 K A 1 502 2 K K . E 4 K A 1 503 3 K K . F 5 ATP A 1 504 1 ATP ATP . G 6 RED B 1 373 173 RED LPA . H 7 HOH A 1 505 1 HOH WAT . H 7 HOH A 2 506 2 HOH WAT . H 7 HOH A 3 507 3 HOH WAT . H 7 HOH A 4 508 4 HOH WAT . H 7 HOH A 5 509 5 HOH WAT . H 7 HOH A 6 510 7 HOH WAT . H 7 HOH A 7 511 8 HOH WAT . H 7 HOH A 8 512 10 HOH WAT . H 7 HOH A 9 513 11 HOH WAT . H 7 HOH A 10 514 12 HOH WAT . H 7 HOH A 11 515 13 HOH WAT . H 7 HOH A 12 516 14 HOH WAT . H 7 HOH A 13 517 15 HOH WAT . H 7 HOH A 14 518 16 HOH WAT . H 7 HOH A 15 519 17 HOH WAT . H 7 HOH A 16 520 18 HOH WAT . H 7 HOH A 17 521 19 HOH WAT . H 7 HOH A 18 522 20 HOH WAT . H 7 HOH A 19 523 21 HOH WAT . H 7 HOH A 20 524 22 HOH WAT . H 7 HOH A 21 525 23 HOH WAT . H 7 HOH A 22 526 24 HOH WAT . H 7 HOH A 23 527 25 HOH WAT . H 7 HOH A 24 528 26 HOH WAT . H 7 HOH A 25 529 27 HOH WAT . H 7 HOH A 26 530 28 HOH WAT . H 7 HOH A 27 531 29 HOH WAT . H 7 HOH A 28 532 30 HOH WAT . H 7 HOH A 29 533 31 HOH WAT . H 7 HOH A 30 534 32 HOH WAT . H 7 HOH A 31 535 33 HOH WAT . H 7 HOH A 32 536 34 HOH WAT . H 7 HOH A 33 537 35 HOH WAT . H 7 HOH A 34 538 36 HOH WAT . H 7 HOH A 35 539 37 HOH WAT . H 7 HOH A 36 540 38 HOH WAT . H 7 HOH A 37 541 39 HOH WAT . H 7 HOH A 38 542 40 HOH WAT . H 7 HOH A 39 543 41 HOH WAT . H 7 HOH A 40 544 42 HOH WAT . H 7 HOH A 41 545 43 HOH WAT . H 7 HOH A 42 546 44 HOH WAT . H 7 HOH A 43 547 45 HOH WAT . H 7 HOH A 44 548 46 HOH WAT . H 7 HOH A 45 549 47 HOH WAT . H 7 HOH A 46 550 48 HOH WAT . H 7 HOH A 47 551 49 HOH WAT . H 7 HOH A 48 552 50 HOH WAT . H 7 HOH A 49 553 51 HOH WAT . H 7 HOH A 50 554 52 HOH WAT . H 7 HOH A 51 555 53 HOH WAT . H 7 HOH A 52 556 55 HOH WAT . H 7 HOH A 53 557 56 HOH WAT . I 7 HOH B 1 6 6 HOH WAT . I 7 HOH B 2 9 9 HOH WAT . I 7 HOH B 3 54 54 HOH WAT . # 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 . . . F 5 -47.855 15.812 76.632 1 55.76 ? PG ATP 504 A 1 HETATM 2 O O1G ATP . . . F 5 -49.031 16.323 75.793 1 56.54 ? O1G ATP 504 A 1 HETATM 3 O O2G ATP . . . F 5 -47.962 14.36 77.093 1 59.6 ? O2G ATP 504 A 1 HETATM 4 O O3G ATP . . . F 5 -47.888 16.48 77.977 1 49.75 ? O3G ATP 504 A 1 HETATM 5 P PB ATP . . . F 5 -46.63 16.276 73.976 1 48.52 ? PB ATP 504 A 1 HETATM 6 O O1B ATP . . . F 5 -45.577 16.009 72.869 1 39.58 ? O1B ATP 504 A 1 HETATM 7 O O2B ATP . . . F 5 -47.295 17.646 73.82 1 45.04 ? O2B ATP 504 A 1 HETATM 8 O O3B ATP . . . F 5 -46.534 15.9 75.591 1 44.91 ? O3B ATP 504 A 1 HETATM 9 P PA ATP . . . F 5 -49.052 15.476 72.742 1 47.25 ? PA ATP 504 A 1 HETATM 10 O O1A ATP . . . F 5 -49.825 14.19 72.719 1 47.85 ? O1A ATP 504 A 1 HETATM 11 O O2A ATP . . . F 5 -49.679 16.694 73.463 1 44.04 ? O2A ATP 504 A 1 HETATM 12 O O3A ATP . . . F 5 -47.67 15.155 73.478 1 48.86 ? O3A ATP 504 A 1 HETATM 13 O O5' ATP . . . F 5 -48.695 15.743 71.203 1 38.68 ? O5' ATP 504 A 1 HETATM 14 C C5' ATP . . . F 5 -47.708 15.016 70.558 1 43.52 ? C5' ATP 504 A 1 HETATM 15 C C4' ATP . . . F 5 -47.102 15.804 69.406 1 48.8 ? C4' ATP 504 A 1 HETATM 16 O O4' ATP . . . F 5 -48.082 16.265 68.482 1 49.93 ? O4' ATP 504 A 1 HETATM 17 C C3' ATP . . . F 5 -46.372 17.101 69.839 1 49.24 ? C3' ATP 504 A 1 HETATM 18 O O3' ATP . . . F 5 -45.086 16.761 70.332 1 53.75 ? O3' ATP 504 A 1 HETATM 19 C C2' ATP . . . F 5 -46.306 17.912 68.578 1 47.01 ? C2' ATP 504 A 1 HETATM 20 O O2' ATP . . . F 5 -45.286 17.43 67.719 1 46.24 ? O2' ATP 504 A 1 HETATM 21 C C1' ATP . . . F 5 -47.581 17.484 67.866 1 47.53 ? C1' ATP 504 A 1 HETATM 22 N N9 ATP . . . F 5 -48.573 18.565 68.039 1 46.02 ? N9 ATP 504 A 1 HETATM 23 C C8 ATP . . . F 5 -49.583 18.507 68.898 1 43.8 ? C8 ATP 504 A 1 HETATM 24 N N7 ATP . . . F 5 -50.315 19.646 68.818 1 44.45 ? N7 ATP 504 A 1 HETATM 25 C C5 ATP . . . F 5 -49.732 20.457 67.898 1 40.23 ? C5 ATP 504 A 1 HETATM 26 C C6 ATP . . . F 5 -49.996 21.792 67.356 1 37.68 ? C6 ATP 504 A 1 HETATM 27 N N6 ATP . . . F 5 -51.053 22.538 67.741 1 38.38 ? N6 ATP 504 A 1 HETATM 28 N N1 ATP . . . F 5 -49.156 22.244 66.437 1 37.65 ? N1 ATP 504 A 1 HETATM 29 C C2 ATP . . . F 5 -48.108 21.524 65.995 1 36.18 ? C2 ATP 504 A 1 HETATM 30 N N3 ATP . . . F 5 -47.81 20.311 66.452 1 38.16 ? N3 ATP 504 A 1 HETATM 31 C C4 ATP . . . F 5 -48.587 19.737 67.388 1 41.29 ? C4 ATP 504 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 261 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #