data_5YFX # _model_server_result.job_id NwKg0EsZARYadHsrRnB1ZA _model_server_result.datetime_utc '2024-11-17 16:42:19' _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 5yfx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 5YFX # _exptl.entry_id 5YFX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 347.221 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ADENOSINE MONOPHOSPHATE' _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 5YFX _cell.length_a 81.13 _cell.length_b 81.13 _cell.length_c 100.18 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YFX _symmetry.cell_setting ? _symmetry.Int_Tables_number 150 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 3 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6 # 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' 2_765 -y+2,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 121.695 70.260641 0 3 'crystal symmetry operation' 3_675 -x+y+1,-x+2,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 140.521282 0 4 'crystal symmetry operation' 4_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 0 5 'crystal symmetry operation' 5_675 x-y+1,-y+2,-z 1 0 0 0 -1 0 0 0 -1 0 140.521282 0 6 'crystal symmetry operation' 6_765 -x+2,-x+y+1,-z -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 121.695 70.260641 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H14 N5 O7 P' _chem_comp.formula_weight 347.221 _chem_comp.id AMP _chem_comp.mon_nstd_flag . _chem_comp.name 'ADENOSINE MONOPHOSPHATE' _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 P O1P AMP doub 13 n n P O2P AMP sing 14 n n P O3P AMP sing 15 n n P O5' AMP sing 16 n n O2P HOP2 AMP sing 17 n n O3P HOP3 AMP sing 18 n n O5' C5' AMP sing 19 n n C5' C4' AMP sing 20 n n C5' "H5'1" AMP sing 21 n n C5' "H5'2" AMP sing 22 n n C4' O4' AMP sing 23 n n C4' C3' AMP sing 24 n n C4' H4' AMP sing 25 n n O4' C1' AMP sing 26 n n C3' O3' AMP sing 27 n n C3' C2' AMP sing 28 n n C3' H3' AMP sing 29 n n O3' HO3' AMP sing 30 n n C2' O2' AMP sing 31 n n C2' C1' AMP sing 32 n n C2' H2' AMP sing 33 n n O2' HO2' AMP sing 34 n n C1' N9 AMP sing 35 n n C1' H1' AMP sing 36 n n N9 C8 AMP sing 37 n y N9 C4 AMP sing 38 n y C8 N7 AMP doub 39 n y C8 H8 AMP sing 40 n n N7 C5 AMP sing 41 n y C5 C6 AMP sing 42 n y C5 C4 AMP doub 43 n y C6 N6 AMP sing 44 n n C6 N1 AMP doub 45 n y N6 HN61 AMP sing 46 n n N6 HN62 AMP sing 47 n n N1 C2 AMP sing 48 n y C2 N3 AMP doub 49 n y C2 H2 AMP sing 50 n n N3 C4 AMP sing 51 n y # _atom_sites.entry_id 5YFX _atom_sites.fract_transf_matrix[1][1] 0.012326 _atom_sites.fract_transf_matrix[1][2] 0.007116 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014233 _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] 0.009982 _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 B 2 RI2 A 1 401 1 RI2 RI2 . C 3 AMP A 1 402 2 AMP AMP . D 4 HOH A 1 501 32 HOH HOH . D 4 HOH A 2 502 27 HOH HOH . D 4 HOH A 3 503 45 HOH HOH . D 4 HOH A 4 504 34 HOH HOH . D 4 HOH A 5 505 40 HOH HOH . D 4 HOH A 6 506 11 HOH HOH . D 4 HOH A 7 507 10 HOH HOH . D 4 HOH A 8 508 37 HOH HOH . D 4 HOH A 9 509 42 HOH HOH . D 4 HOH A 10 510 24 HOH HOH . D 4 HOH A 11 511 39 HOH HOH . D 4 HOH A 12 512 26 HOH HOH . D 4 HOH A 13 513 28 HOH HOH . D 4 HOH A 14 514 9 HOH HOH . D 4 HOH A 15 515 6 HOH HOH . D 4 HOH A 16 516 22 HOH HOH . D 4 HOH A 17 517 13 HOH HOH . D 4 HOH A 18 518 14 HOH HOH . D 4 HOH A 19 519 12 HOH HOH . D 4 HOH A 20 520 18 HOH HOH . D 4 HOH A 21 521 30 HOH HOH . D 4 HOH A 22 522 16 HOH HOH . D 4 HOH A 23 523 17 HOH HOH . D 4 HOH A 24 524 8 HOH HOH . D 4 HOH A 25 525 44 HOH HOH . D 4 HOH A 26 526 35 HOH HOH . D 4 HOH A 27 527 25 HOH HOH . D 4 HOH A 28 528 19 HOH HOH . D 4 HOH A 29 529 15 HOH HOH . D 4 HOH A 30 530 7 HOH HOH . D 4 HOH A 31 531 5 HOH HOH . D 4 HOH A 32 532 23 HOH HOH . D 4 HOH A 33 533 36 HOH HOH . D 4 HOH A 34 534 2 HOH HOH . D 4 HOH A 35 535 41 HOH HOH . D 4 HOH A 36 536 1 HOH HOH . D 4 HOH A 37 537 31 HOH HOH . D 4 HOH A 38 538 4 HOH HOH . D 4 HOH A 39 539 38 HOH HOH . D 4 HOH A 40 540 33 HOH HOH . D 4 HOH A 41 541 21 HOH HOH . D 4 HOH A 42 542 29 HOH HOH . D 4 HOH A 43 543 3 HOH HOH . D 4 HOH A 44 544 20 HOH HOH . D 4 HOH A 45 545 43 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 P AMP . . . C 3 28.526 74.107 8.051 1 53.81 ? P AMP 402 A 1 HETATM 2 O O1P AMP . . . C 3 29.603 73.351 7.258 1 42.81 ? O1P AMP 402 A 1 HETATM 3 O O2P AMP . . . C 3 27.258 73.354 8.419 1 48.66 ? O2P AMP 402 A 1 HETATM 4 O O3P AMP . . . C 3 28.174 75.519 7.638 1 50.22 ? O3P AMP 402 A 1 HETATM 5 O O5' AMP . . . C 3 29.326 74.313 9.421 1 46.28 ? O5' AMP 402 A 1 HETATM 6 C C5' AMP . . . C 3 28.576 74.822 10.488 1 43.4 ? C5' AMP 402 A 1 HETATM 7 C C4' AMP . . . C 3 29.316 74.647 11.767 1 41.53 ? C4' AMP 402 A 1 HETATM 8 O O4' AMP . . . C 3 28.546 75.348 12.703 1 41.5 ? O4' AMP 402 A 1 HETATM 9 C C3' AMP . . . C 3 29.318 73.215 12.239 1 42.16 ? C3' AMP 402 A 1 HETATM 10 O O3' AMP . . . C 3 30.488 73.063 13.068 1 41.57 ? O3' AMP 402 A 1 HETATM 11 C C2' AMP . . . C 3 27.991 73.057 12.965 1 40.74 ? C2' AMP 402 A 1 HETATM 12 O O2' AMP . . . C 3 28.122 72.148 14.062 1 38.47 ? O2' AMP 402 A 1 HETATM 13 C C1' AMP . . . C 3 27.715 74.471 13.451 1 40.49 ? C1' AMP 402 A 1 HETATM 14 N N9 AMP . . . C 3 26.378 75.121 13.321 1 41.03 ? N9 AMP 402 A 1 HETATM 15 C C8 AMP . . . C 3 25.676 75.505 12.224 1 40.15 ? C8 AMP 402 A 1 HETATM 16 N N7 AMP . . . C 3 24.511 76.132 12.581 1 40 ? N7 AMP 402 A 1 HETATM 17 C C5 AMP . . . C 3 24.473 76.202 13.926 1 38.48 ? C5 AMP 402 A 1 HETATM 18 C C6 AMP . . . C 3 23.567 76.736 14.958 1 34.85 ? C6 AMP 402 A 1 HETATM 19 N N6 AMP . . . C 3 22.437 77.336 14.631 1 35.2 ? N6 AMP 402 A 1 HETATM 20 N N1 AMP . . . C 3 23.882 76.609 16.248 1 35.67 ? N1 AMP 402 A 1 HETATM 21 C C2 AMP . . . C 3 25.025 76.002 16.629 1 40.9 ? C2 AMP 402 A 1 HETATM 22 N N3 AMP . . . C 3 25.935 75.483 15.76 1 40.77 ? N3 AMP 402 A 1 HETATM 23 C C4 AMP . . . C 3 25.708 75.548 14.412 1 41.59 ? C4 AMP 402 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 223 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 23 #