data_2D06 # _model_server_result.job_id 5MXRO2dD3eCNBVi43Q9N5w _model_server_result.datetime_utc '2024-11-22 10:35:28' _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 2d06 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":2001}' # _entry.id 2D06 # _exptl.entry_id 2D06 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-3'-5'-DIPHOSPHATE" _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 90 _cell.entry_id 2D06 _cell.length_a 123.64 _cell.length_b 86.07 _cell.length_c 72.95 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2D06 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 2 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 E N N # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id A3P _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-3'-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 P1 O1P A3P doub 1 n n P1 O2P A3P sing 2 n n P1 O3P A3P sing 3 n n P1 O3' A3P sing 4 n n O2P HOP2 A3P sing 5 n n O3P HOP3 A3P sing 6 n n P2 O4P A3P doub 7 n n P2 O5P A3P sing 8 n n P2 O6P A3P sing 9 n n P2 O5' A3P sing 10 n n O5P HOP5 A3P sing 11 n n O6P HOP6 A3P sing 12 n n O5' C5' A3P sing 13 n n C5' C4' A3P sing 14 n n C5' "H5'1" A3P sing 15 n n C5' "H5'2" A3P sing 16 n n C4' O4' A3P sing 17 n n C4' C3' A3P sing 18 n n C4' H4' A3P sing 19 n n O4' C1' A3P sing 20 n n C3' O3' A3P sing 21 n n C3' C2' A3P sing 22 n n C3' H3' A3P sing 23 n n C2' O2' A3P sing 24 n n C2' C1' A3P sing 25 n n C2' H2' A3P sing 26 n n O2' HO2' A3P sing 27 n n C1' N9 A3P sing 28 n n C1' H1' A3P sing 29 n n N9 C8 A3P sing 30 n y N9 C4 A3P sing 31 n y C8 N7 A3P doub 32 n y C8 H8 A3P sing 33 n n N7 C5 A3P sing 34 n y C5 C6 A3P sing 35 n y C5 C4 A3P doub 36 n y C6 N6 A3P sing 37 n n C6 N1 A3P doub 38 n y N6 HN61 A3P sing 39 n n N6 HN62 A3P sing 40 n n N1 C2 A3P sing 41 n y C2 N3 A3P doub 42 n y C2 H2 A3P sing 43 n n N3 C4 A3P sing 44 n y # _atom_sites.entry_id 2D06 _atom_sites.fract_transf_matrix[1][1] 0.008088 _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] 0.011618 _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] 0.013708 _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 A3P A 1 2001 2001 A3P PAP . D 3 EST A 1 304 304 EST EST . E 2 A3P B 1 2002 2002 A3P PAP . F 3 EST B 1 305 305 EST EST . G 4 HOH A 1 3001 3001 HOH HOH . G 4 HOH A 2 3005 3005 HOH HOH . G 4 HOH A 3 3006 3006 HOH HOH . G 4 HOH A 4 3007 3007 HOH HOH . G 4 HOH A 5 3008 3008 HOH HOH . G 4 HOH A 6 3009 3009 HOH HOH . G 4 HOH A 7 3020 3020 HOH HOH . G 4 HOH A 8 3021 3021 HOH HOH . G 4 HOH A 9 3022 3022 HOH HOH . G 4 HOH A 10 3023 3023 HOH HOH . G 4 HOH A 11 3024 3024 HOH HOH . G 4 HOH A 12 3025 3025 HOH HOH . G 4 HOH A 13 3026 3026 HOH HOH . G 4 HOH A 14 3027 3027 HOH HOH . G 4 HOH A 15 3028 3028 HOH HOH . G 4 HOH A 16 3029 3029 HOH HOH . G 4 HOH A 17 3030 3030 HOH HOH . G 4 HOH A 18 3031 3031 HOH HOH . G 4 HOH A 19 3032 3032 HOH HOH . G 4 HOH A 20 3033 3033 HOH HOH . G 4 HOH A 21 3034 3034 HOH HOH . G 4 HOH A 22 3035 3035 HOH HOH . G 4 HOH A 23 3041 3041 HOH HOH . G 4 HOH A 24 3042 3042 HOH HOH . G 4 HOH A 25 3043 3043 HOH HOH . G 4 HOH A 26 3044 3044 HOH HOH . G 4 HOH A 27 3049 3049 HOH HOH . G 4 HOH A 28 3050 3050 HOH HOH . G 4 HOH A 29 3052 3052 HOH HOH . G 4 HOH A 30 3053 3053 HOH HOH . G 4 HOH A 31 3060 3060 HOH HOH . G 4 HOH A 32 3070 3070 HOH HOH . G 4 HOH A 33 3071 3071 HOH HOH . G 4 HOH A 34 3072 3072 HOH HOH . G 4 HOH A 35 3073 3073 HOH HOH . G 4 HOH A 36 3074 3074 HOH HOH . G 4 HOH A 37 3075 3075 HOH HOH . G 4 HOH A 38 3076 3076 HOH HOH . G 4 HOH A 39 3080 3080 HOH HOH . G 4 HOH A 40 3081 3081 HOH HOH . G 4 HOH A 41 3082 3082 HOH HOH . G 4 HOH A 42 3083 3083 HOH HOH . G 4 HOH A 43 3084 3084 HOH HOH . G 4 HOH A 44 3085 3085 HOH HOH . G 4 HOH A 45 3086 3086 HOH HOH . G 4 HOH A 46 3096 3096 HOH HOH . G 4 HOH A 47 3097 3097 HOH HOH . G 4 HOH A 48 3102 3102 HOH HOH . G 4 HOH A 49 3105 3105 HOH HOH . G 4 HOH A 50 3106 3106 HOH HOH . G 4 HOH A 51 3107 3107 HOH HOH . G 4 HOH A 52 3108 3108 HOH HOH . G 4 HOH A 53 3109 3109 HOH HOH . G 4 HOH A 54 3110 3110 HOH HOH . G 4 HOH A 55 3111 3111 HOH HOH . G 4 HOH A 56 3112 3112 HOH HOH . G 4 HOH A 57 3113 3113 HOH HOH . G 4 HOH A 58 3114 3114 HOH HOH . G 4 HOH A 59 3115 3115 HOH HOH . G 4 HOH A 60 3116 3116 HOH HOH . G 4 HOH A 61 3117 3117 HOH HOH . G 4 HOH A 62 3118 3118 HOH HOH . G 4 HOH A 63 3119 3119 HOH HOH . G 4 HOH A 64 3120 3120 HOH HOH . H 4 HOH B 1 3002 3002 HOH HOH . H 4 HOH B 2 3003 3003 HOH HOH . H 4 HOH B 3 3004 3004 HOH HOH . H 4 HOH B 4 3010 3010 HOH HOH . H 4 HOH B 5 3011 3011 HOH HOH . H 4 HOH B 6 3012 3012 HOH HOH . H 4 HOH B 7 3013 3013 HOH HOH . H 4 HOH B 8 3014 3014 HOH HOH . H 4 HOH B 9 3015 3015 HOH HOH . H 4 HOH B 10 3016 3016 HOH HOH . H 4 HOH B 11 3017 3017 HOH HOH . H 4 HOH B 12 3018 3018 HOH HOH . H 4 HOH B 13 3019 3019 HOH HOH . H 4 HOH B 14 3036 3036 HOH HOH . H 4 HOH B 15 3037 3037 HOH HOH . H 4 HOH B 16 3038 3038 HOH HOH . H 4 HOH B 17 3039 3039 HOH HOH . H 4 HOH B 18 3040 3040 HOH HOH . H 4 HOH B 19 3045 3045 HOH HOH . H 4 HOH B 20 3046 3046 HOH HOH . H 4 HOH B 21 3047 3047 HOH HOH . H 4 HOH B 22 3048 3048 HOH HOH . H 4 HOH B 23 3051 3051 HOH HOH . H 4 HOH B 24 3054 3054 HOH HOH . H 4 HOH B 25 3055 3055 HOH HOH . H 4 HOH B 26 3056 3056 HOH HOH . H 4 HOH B 27 3057 3057 HOH HOH . H 4 HOH B 28 3058 3058 HOH HOH . H 4 HOH B 29 3059 3059 HOH HOH . H 4 HOH B 30 3061 3061 HOH HOH . H 4 HOH B 31 3062 3062 HOH HOH . H 4 HOH B 32 3063 3063 HOH HOH . H 4 HOH B 33 3064 3064 HOH HOH . H 4 HOH B 34 3065 3065 HOH HOH . H 4 HOH B 35 3066 3066 HOH HOH . H 4 HOH B 36 3067 3067 HOH HOH . H 4 HOH B 37 3068 3068 HOH HOH . H 4 HOH B 38 3069 3069 HOH HOH . H 4 HOH B 39 3077 3077 HOH HOH . H 4 HOH B 40 3078 3078 HOH HOH . H 4 HOH B 41 3079 3079 HOH HOH . H 4 HOH B 42 3087 3087 HOH HOH . H 4 HOH B 43 3088 3088 HOH HOH . H 4 HOH B 44 3089 3089 HOH HOH . H 4 HOH B 45 3090 3090 HOH HOH . H 4 HOH B 46 3091 3091 HOH HOH . H 4 HOH B 47 3092 3092 HOH HOH . H 4 HOH B 48 3093 3093 HOH HOH . H 4 HOH B 49 3094 3094 HOH HOH . H 4 HOH B 50 3095 3095 HOH HOH . H 4 HOH B 51 3099 3099 HOH HOH . H 4 HOH B 52 3100 3100 HOH HOH . H 4 HOH B 53 3101 3101 HOH HOH . H 4 HOH B 54 3103 3103 HOH HOH . H 4 HOH B 55 3104 3104 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 P1 A3P . . . C 2 140.682 -62.673 1.799 1 37.68 ? P1 A3P 2001 A 1 HETATM 2 O O1P A3P . . . C 2 140.098 -61.541 2.541 1 31.81 ? O1P A3P 2001 A 1 HETATM 3 O O2P A3P . . . C 2 141.664 -62.365 0.765 1 48.48 ? O2P A3P 2001 A 1 HETATM 4 O O3P A3P . . . C 2 140.971 -63.836 2.697 1 26.63 ? O3P A3P 2001 A 1 HETATM 5 P P2 A3P . . . C 2 133.671 -62.529 -1.08 1 33.98 ? P2 A3P 2001 A 1 HETATM 6 O O4P A3P . . . C 2 132.948 -61.511 -0.283 1 46.14 ? O4P A3P 2001 A 1 HETATM 7 O O5P A3P . . . C 2 133.725 -62.313 -2.546 1 40.29 ? O5P A3P 2001 A 1 HETATM 8 O O6P A3P . . . C 2 133.19 -64.08 -0.595 1 55.42 ? O6P A3P 2001 A 1 HETATM 9 O O5' A3P . . . C 2 135.205 -62.391 -0.523 1 35.84 ? O5' A3P 2001 A 1 HETATM 10 C C5' A3P . . . C 2 136.197 -63.007 -1.279 1 51.78 ? C5' A3P 2001 A 1 HETATM 11 C C4' A3P . . . C 2 137.407 -63.459 -0.482 1 21.65 ? C4' A3P 2001 A 1 HETATM 12 O O4' A3P . . . C 2 138.15 -64.112 -1.543 1 45.78 ? O4' A3P 2001 A 1 HETATM 13 C C3' A3P . . . C 2 138.447 -62.399 0.054 1 48.95 ? C3' A3P 2001 A 1 HETATM 14 O O3' A3P . . . C 2 139.333 -63.201 0.947 1 38.1 ? O3' A3P 2001 A 1 HETATM 15 C C2' A3P . . . C 2 139.126 -61.989 -1.252 1 44.67 ? C2' A3P 2001 A 1 HETATM 16 O O2' A3P . . . C 2 140.349 -61.246 -1.061 1 52.79 ? O2' A3P 2001 A 1 HETATM 17 C C1' A3P . . . C 2 139.322 -63.37 -1.848 1 43.81 ? C1' A3P 2001 A 1 HETATM 18 N N9 A3P . . . C 2 139.434 -63.475 -3.304 1 41.98 ? N9 A3P 2001 A 1 HETATM 19 C C8 A3P . . . C 2 138.807 -62.633 -4.223 1 40.14 ? C8 A3P 2001 A 1 HETATM 20 N N7 A3P . . . C 2 139.064 -62.928 -5.47 1 29.84 ? N7 A3P 2001 A 1 HETATM 21 C C5 A3P . . . C 2 139.935 -64.06 -5.379 1 35.81 ? C5 A3P 2001 A 1 HETATM 22 C C6 A3P . . . C 2 140.594 -64.887 -6.383 1 44.54 ? C6 A3P 2001 A 1 HETATM 23 N N6 A3P . . . C 2 140.452 -64.654 -7.694 1 53.34 ? N6 A3P 2001 A 1 HETATM 24 N N1 A3P . . . C 2 141.381 -65.929 -5.943 1 44.56 ? N1 A3P 2001 A 1 HETATM 25 C C2 A3P . . . C 2 141.497 -66.127 -4.609 1 47.99 ? C2 A3P 2001 A 1 HETATM 26 N N3 A3P . . . C 2 140.936 -65.431 -3.576 1 34.87 ? N3 A3P 2001 A 1 HETATM 27 C C4 A3P . . . C 2 140.153 -64.401 -4.038 1 26.23 ? C4 A3P 2001 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #