data_3NYO # _model_server_result.job_id G5uaemcLKkYel8fuynChyQ _model_server_result.datetime_utc '2024-11-01 19:35:29' _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 3nyo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":577}' # _entry.id 3NYO # _exptl.entry_id 3NYO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 347.221 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ADENOSINE MONOPHOSPHATE' _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 90 _cell.angle_gamma 120 _cell.entry_id 3NYO _cell.length_a 154.574 _cell.length_b 154.574 _cell.length_c 208.117 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3NYO _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_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,C,D,E,F,G,H,I,J,K,L,T 1 1 B,M,N,O,P,Q,R,S,U 2 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U 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 ? 2 C N N ? 2 M N 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 19 n n P O2P AMP sing 20 n n P O3P AMP sing 21 n n P O5' AMP sing 22 n n O2P HOP2 AMP sing 23 n n O3P HOP3 AMP sing 24 n n O5' C5' AMP sing 25 n n C5' C4' AMP sing 26 n n C5' "H5'1" AMP sing 27 n n C5' "H5'2" AMP sing 28 n n C4' O4' AMP sing 29 n n C4' C3' AMP sing 30 n n C4' H4' AMP sing 31 n n O4' C1' AMP sing 32 n n C3' O3' AMP sing 33 n n C3' C2' AMP sing 34 n n C3' H3' AMP sing 35 n n O3' HO3' AMP sing 36 n n C2' O2' AMP sing 37 n n C2' C1' AMP sing 38 n n C2' H2' AMP sing 39 n n O2' HO2' AMP sing 40 n n C1' N9 AMP sing 41 n n C1' H1' AMP sing 42 n n N9 C8 AMP sing 43 n y N9 C4 AMP sing 44 n y C8 N7 AMP doub 45 n y C8 H8 AMP sing 46 n n N7 C5 AMP sing 47 n y C5 C6 AMP sing 48 n y C5 C4 AMP doub 49 n y C6 N6 AMP sing 50 n n C6 N1 AMP doub 51 n y N6 HN61 AMP sing 52 n n N6 HN62 AMP sing 53 n n N1 C2 AMP sing 54 n y C2 N3 AMP doub 55 n y C2 H2 AMP sing 56 n n N3 C4 AMP sing 57 n y # _atom_sites.entry_id 3NYO _atom_sites.fract_transf_matrix[1][1] 0.006469 _atom_sites.fract_transf_matrix[1][2] 0.003735 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00747 _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] 0.004805 _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 2 AMP A 1 577 577 AMP AMP . D 3 SO4 A 1 578 578 SO4 SO4 . E 3 SO4 A 1 579 579 SO4 SO4 . F 3 SO4 A 1 580 580 SO4 SO4 . G 3 SO4 A 1 581 581 SO4 SO4 . H 3 SO4 A 1 582 582 SO4 SO4 . I 4 BU3 A 1 583 583 BU3 BU3 . J 3 SO4 A 1 584 584 SO4 SO4 . K 3 SO4 A 1 585 585 SO4 SO4 . L 3 SO4 A 1 586 582 SO4 SO4 . M 2 AMP B 1 577 577 AMP AMP . N 3 SO4 B 1 578 578 SO4 SO4 . O 3 SO4 B 1 579 579 SO4 SO4 . P 3 SO4 B 1 580 580 SO4 SO4 . Q 3 SO4 B 1 581 581 SO4 SO4 . R 4 BU3 B 1 583 583 BU3 BU3 . S 3 SO4 B 1 584 584 SO4 SO4 . T 5 HOH A 1 587 1 HOH HOH . T 5 HOH A 2 588 2 HOH HOH . T 5 HOH A 3 589 3 HOH HOH . T 5 HOH A 4 590 4 HOH HOH . T 5 HOH A 5 591 6 HOH HOH . T 5 HOH A 6 592 7 HOH HOH . U 5 HOH B 1 582 3 HOH HOH . U 5 HOH B 2 585 4 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 . . . M 2 -52.03 59.227 -46.8 1 109.13 ? P AMP 577 B 1 HETATM 2 O O1P AMP . . . M 2 -52.615 60.432 -47.501 1 109.32 ? O1P AMP 577 B 1 HETATM 3 O O2P AMP . . . M 2 -52.876 58.661 -45.684 1 108.94 ? O2P AMP 577 B 1 HETATM 4 O O3P AMP . . . M 2 -51.458 58.164 -47.708 1 108.66 ? O3P AMP 577 B 1 HETATM 5 O O5' AMP . . . M 2 -50.773 59.852 -46.022 1 108.6 ? O5' AMP 577 B 1 HETATM 6 C C5' AMP . . . M 2 -49.597 60.197 -46.738 1 108.05 ? C5' AMP 577 B 1 HETATM 7 C C4' AMP . . . M 2 -48.463 59.353 -46.187 1 107.4 ? C4' AMP 577 B 1 HETATM 8 O O4' AMP . . . M 2 -48.674 59.081 -44.806 1 106.55 ? O4' AMP 577 B 1 HETATM 9 C C3' AMP . . . M 2 -48.377 57.997 -46.859 1 106.9 ? C3' AMP 577 B 1 HETATM 10 O O3' AMP . . . M 2 -47.509 58.046 -47.994 1 108.3 ? O3' AMP 577 B 1 HETATM 11 C C2' AMP . . . M 2 -47.828 57.087 -45.787 1 106.32 ? C2' AMP 577 B 1 HETATM 12 O O2' AMP . . . M 2 -46.421 56.914 -45.915 1 106.47 ? O2' AMP 577 B 1 HETATM 13 C C1' AMP . . . M 2 -48.102 57.815 -44.487 1 106.63 ? C1' AMP 577 B 1 HETATM 14 N N9 AMP . . . M 2 -49.039 56.946 -43.738 1 106.81 ? N9 AMP 577 B 1 HETATM 15 C C8 AMP . . . M 2 -50.39 56.962 -43.782 1 106.34 ? C8 AMP 577 B 1 HETATM 16 N N7 AMP . . . M 2 -50.908 56.001 -42.968 1 105.54 ? N7 AMP 577 B 1 HETATM 17 C C5 AMP . . . M 2 -49.876 55.351 -42.395 1 105.42 ? C5 AMP 577 B 1 HETATM 18 C C6 AMP . . . M 2 -49.693 54.229 -41.443 1 104.91 ? C6 AMP 577 B 1 HETATM 19 N N6 AMP . . . M 2 -50.755 53.591 -40.911 1 104.93 ? N6 AMP 577 B 1 HETATM 20 N N1 AMP . . . M 2 -48.438 53.852 -41.112 1 105.17 ? N1 AMP 577 B 1 HETATM 21 C C2 AMP . . . M 2 -47.36 54.474 -41.622 1 106.41 ? C2 AMP 577 B 1 HETATM 22 N N3 AMP . . . M 2 -47.447 55.498 -42.494 1 107.03 ? N3 AMP 577 B 1 HETATM 23 C C4 AMP . . . M 2 -48.65 55.973 -42.911 1 106.49 ? C4 AMP 577 B 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 23 #