data_3D41 # _model_server_result.job_id AorkNor1Pz_K702p-Y1Axw _model_server_result.datetime_utc '2025-03-04 08:51:31' _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 3d41 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1260}' # _entry.id 3D41 # _exptl.entry_id 3D41 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' _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 3D41 _cell.length_a 85.656 _cell.length_b 85.656 _cell.length_c 78.979 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3D41 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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' 4_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 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 # 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 B MG MG . A MG 267 1_555 C O2G ANP . A ANP 1260 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? metalc ? metalc2 B MG MG . A MG 267 1_555 C O2A ANP . A ANP 1260 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc3 B MG MG . A MG 267 1_555 C O1B ANP . A ANP 1260 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? metalc ? metalc4 B MG MG . A MG 267 1_555 E O HOH . A HOH 4002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.905 ? metalc ? metalc5 B MG MG . A MG 267 1_555 E O HOH . A HOH 4003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc6 B MG MG . A MG 267 1_555 E O HOH . A HOH 4004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.891 ? # _chem_comp.formula 'C10 H17 N6 O12 P3' _chem_comp.formula_weight 506.196 _chem_comp.id ANP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' _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 ANP doub 13 n n PG O2G ANP sing 14 n n PG O3G ANP sing 15 n n PG N3B ANP sing 16 n n O2G HOG2 ANP sing 17 n n O3G HOG3 ANP sing 18 n n PB O1B ANP doub 19 n n PB O2B ANP sing 20 n n PB N3B ANP sing 21 n n PB O3A ANP sing 22 n n O2B HOB2 ANP sing 23 n n N3B HNB1 ANP sing 24 n n PA O1A ANP doub 25 n n PA O2A ANP sing 26 n n PA O3A ANP sing 27 n n PA O5' ANP sing 28 n n O2A HOA2 ANP sing 29 n n O5' C5' ANP sing 30 n n C5' C4' ANP sing 31 n n C5' "H5'1" ANP sing 32 n n C5' "H5'2" ANP sing 33 n n C4' O4' ANP sing 34 n n C4' C3' ANP sing 35 n n C4' H4' ANP sing 36 n n O4' C1' ANP sing 37 n n C3' O3' ANP sing 38 n n C3' C2' ANP sing 39 n n C3' H3' ANP sing 40 n n O3' HO3' ANP sing 41 n n C2' O2' ANP sing 42 n n C2' C1' ANP sing 43 n n C2' H2' ANP sing 44 n n O2' HO2' ANP sing 45 n n C1' N9 ANP sing 46 n n C1' H1' ANP sing 47 n n N9 C8 ANP sing 48 n y N9 C4 ANP sing 49 n y C8 N7 ANP doub 50 n y C8 H8 ANP sing 51 n n N7 C5 ANP sing 52 n y C5 C6 ANP sing 53 n y C5 C4 ANP doub 54 n y C6 N6 ANP sing 55 n n C6 N1 ANP doub 56 n y N6 HN61 ANP sing 57 n n N6 HN62 ANP sing 58 n n N1 C2 ANP sing 59 n y C2 N3 ANP doub 60 n y C2 H2 ANP sing 61 n n N3 C4 ANP sing 62 n y # _atom_sites.entry_id 3D41 _atom_sites.fract_transf_matrix[1][1] 0.011675 _atom_sites.fract_transf_matrix[1][2] 0.00674 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013481 _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] 0.012662 _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 MG A 1 267 26 MG MG . C 3 ANP A 1 1260 1260 ANP ANP . D 4 FCN A 1 4001 4001 FCN FCN . E 5 HOH A 1 4002 1 HOH HOH . E 5 HOH A 2 4003 2 HOH HOH . E 5 HOH A 3 4004 3 HOH HOH . E 5 HOH A 4 4005 4 HOH HOH . E 5 HOH A 5 4006 5 HOH HOH . E 5 HOH A 6 4007 6 HOH HOH . E 5 HOH A 7 4008 7 HOH HOH . E 5 HOH A 8 4009 8 HOH HOH . E 5 HOH A 9 4010 9 HOH HOH . E 5 HOH A 10 4011 10 HOH HOH . E 5 HOH A 11 4012 11 HOH HOH . E 5 HOH A 12 4013 12 HOH HOH . E 5 HOH A 13 4014 13 HOH HOH . E 5 HOH A 14 4015 14 HOH HOH . E 5 HOH A 15 4016 15 HOH HOH . E 5 HOH A 16 4017 16 HOH HOH . E 5 HOH A 17 4018 17 HOH HOH . E 5 HOH A 18 4019 18 HOH HOH . E 5 HOH A 19 4020 19 HOH HOH . E 5 HOH A 20 4021 20 HOH HOH . E 5 HOH A 21 4022 21 HOH HOH . E 5 HOH A 22 4023 22 HOH HOH . E 5 HOH A 23 4024 23 HOH HOH . E 5 HOH A 24 4025 24 HOH HOH . E 5 HOH A 25 4026 25 HOH HOH . E 5 HOH A 26 4027 26 HOH HOH . E 5 HOH A 27 4028 27 HOH HOH . E 5 HOH A 28 4029 28 HOH HOH . E 5 HOH A 29 4030 29 HOH HOH . E 5 HOH A 30 4031 30 HOH HOH . E 5 HOH A 31 4032 31 HOH HOH . E 5 HOH A 32 4033 32 HOH HOH . E 5 HOH A 33 4034 33 HOH HOH . E 5 HOH A 34 4035 34 HOH HOH . E 5 HOH A 35 4036 35 HOH HOH . E 5 HOH A 36 4037 36 HOH HOH . E 5 HOH A 37 4038 37 HOH HOH . E 5 HOH A 38 4039 38 HOH HOH . E 5 HOH A 39 4040 39 HOH HOH . E 5 HOH A 40 4041 40 HOH HOH . E 5 HOH A 41 4042 41 HOH HOH . E 5 HOH A 42 4043 42 HOH HOH . E 5 HOH A 43 4044 43 HOH HOH . E 5 HOH A 44 4045 44 HOH HOH . E 5 HOH A 45 4046 45 HOH HOH . E 5 HOH A 46 4047 46 HOH HOH . E 5 HOH A 47 4048 47 HOH HOH . E 5 HOH A 48 4049 48 HOH HOH . E 5 HOH A 49 4050 49 HOH HOH . E 5 HOH A 50 4051 50 HOH HOH . E 5 HOH A 51 4052 51 HOH HOH . E 5 HOH A 52 4053 52 HOH HOH . E 5 HOH A 53 4054 53 HOH HOH . E 5 HOH A 54 4055 54 HOH HOH . E 5 HOH A 55 4056 55 HOH HOH . E 5 HOH A 56 4057 56 HOH HOH . E 5 HOH A 57 4058 57 HOH HOH . E 5 HOH A 58 4059 58 HOH HOH . E 5 HOH A 59 4060 59 HOH HOH . E 5 HOH A 60 4061 60 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 ANP . . . C 3 27.521 7.3 2.12 1 44.9 ? PG ANP 1260 A 1 HETATM 2 O O1G ANP . . . C 3 26.058 7.03 2.133 1 40.12 ? O1G ANP 1260 A 1 HETATM 3 O O2G ANP . . . C 3 27.96 8.622 1.578 1 46.38 ? O2G ANP 1260 A 1 HETATM 4 O O3G ANP . . . C 3 28.304 6.186 1.457 1 48.92 ? O3G ANP 1260 A 1 HETATM 5 P PB ANP . . . C 3 29.573 8.145 4.157 1 45.66 ? PB ANP 1260 A 1 HETATM 6 O O1B ANP . . . C 3 29.644 9.391 3.332 1 47.9 ? O1B ANP 1260 A 1 HETATM 7 O O2B ANP . . . C 3 29.669 8.428 5.625 1 45.91 ? O2B ANP 1260 A 1 HETATM 8 N N3B ANP . . . C 3 28.089 7.365 3.764 1 43.65 ? N3B ANP 1260 A 1 HETATM 9 P PA ANP . . . C 3 31.536 6.928 2.386 1 45.94 ? PA ANP 1260 A 1 HETATM 10 O O1A ANP . . . C 3 31.227 5.545 1.867 1 45.61 ? O1A ANP 1260 A 1 HETATM 11 O O2A ANP . . . C 3 31.201 7.989 1.4 1 48.04 ? O2A ANP 1260 A 1 HETATM 12 O O3A ANP . . . C 3 30.844 7.208 3.825 1 45.89 ? O3A ANP 1260 A 1 HETATM 13 O O5' ANP . . . C 3 33.048 7.21 2.779 1 44.92 ? O5' ANP 1260 A 1 HETATM 14 C C5' ANP . . . C 3 33.728 6.291 3.643 1 48.84 ? C5' ANP 1260 A 1 HETATM 15 C C4' ANP . . . C 3 34.267 5.1 2.834 1 47.78 ? C4' ANP 1260 A 1 HETATM 16 O O4' ANP . . . C 3 35.542 5.463 2.33 1 47.89 ? O4' ANP 1260 A 1 HETATM 17 C C3' ANP . . . C 3 34.577 3.825 3.622 1 48.48 ? C3' ANP 1260 A 1 HETATM 18 O O3' ANP . . . C 3 33.41 3.003 3.801 1 46.84 ? O3' ANP 1260 A 1 HETATM 19 C C2' ANP . . . C 3 35.674 3.175 2.78 1 48.46 ? C2' ANP 1260 A 1 HETATM 20 O O2' ANP . . . C 3 35.142 2.315 1.789 1 50.43 ? O2' ANP 1260 A 1 HETATM 21 C C1' ANP . . . C 3 36.204 4.286 1.92 1 45.16 ? C1' ANP 1260 A 1 HETATM 22 N N9 ANP . . . C 3 37.617 4.484 2.152 1 43.08 ? N9 ANP 1260 A 1 HETATM 23 C C8 ANP . . . C 3 38.502 4.657 1.163 1 43.02 ? C8 ANP 1260 A 1 HETATM 24 N N7 ANP . . . C 3 39.743 4.843 1.673 1 42.3 ? N7 ANP 1260 A 1 HETATM 25 C C5 ANP . . . C 3 39.652 4.774 3 1 41.89 ? C5 ANP 1260 A 1 HETATM 26 C C6 ANP . . . C 3 40.603 4.865 4.105 1 42.28 ? C6 ANP 1260 A 1 HETATM 27 N N6 ANP . . . C 3 41.917 5.054 3.86 1 43.54 ? N6 ANP 1260 A 1 HETATM 28 N N1 ANP . . . C 3 40.101 4.751 5.35 1 43.23 ? N1 ANP 1260 A 1 HETATM 29 C C2 ANP . . . C 3 38.788 4.534 5.584 1 42.73 ? C2 ANP 1260 A 1 HETATM 30 N N3 ANP . . . C 3 37.856 4.42 4.624 1 43.04 ? N3 ANP 1260 A 1 HETATM 31 C C4 ANP . . . C 3 38.229 4.545 3.325 1 43.28 ? C4 ANP 1260 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 246 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #