data_1G9X # _model_server_result.job_id hCBjme0GQQEfh4LXgPywOA _model_server_result.datetime_utc '2024-12-08 06:10:12' _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 1g9x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1300}' # _entry.id 1G9X # _exptl.entry_id 1G9X _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 3 _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 1G9X _cell.length_a 117.31 _cell.length_b 117.31 _cell.length_c 42.19 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1G9X _symmetry.cell_setting ? _symmetry.Int_Tables_number 144 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31' # 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 ? monomeric 1 author_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,F,M 1 1 B,G,H,I,N 2 1 C,J,K,L,O 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 ? 4 F N N ? 4 I N N ? 4 L N 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 OG SER 47 A SER 47 1_555 D MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.608 ? metalc ? metalc2 F O1B ADP . A ADP 300 1_555 D MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.658 ? metalc ? metalc3 D MG MG . A MG 301 1_555 M O HOH . A HOH 3038 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc4 B OG SER 47 B SER 1047 1_555 G MG MG . B MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc5 B OE2 GLU 179 B GLU 1179 1_555 G MG MG . B MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.831 ? metalc ? metalc6 G MG MG . B MG 1301 1_555 N O HOH . B HOH 3030 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc7 C OG SER 47 C SER 2047 1_555 J MG MG . C MG 2301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 1G9X _atom_sites.fract_transf_matrix[1][1] 0.008524 _atom_sites.fract_transf_matrix[1][2] 0.004922 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009843 _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] 0.023702 _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 D 2 MG A 1 301 301 MG MG . E 3 MMC A 1 302 31 MMC CMM . F 4 ADP A 1 300 300 ADP ADP . G 2 MG B 1 1301 1301 MG MG . H 3 MMC B 1 1302 1031 MMC CMM . I 4 ADP B 1 1300 1300 ADP ADP . J 2 MG C 1 2301 2301 MG MG . K 3 MMC C 1 2302 2031 MMC CMM . L 4 ADP C 1 2300 2300 ADP ADP . M 5 HOH A 1 3004 3004 HOH TIP . M 5 HOH A 2 3005 3005 HOH TIP . M 5 HOH A 3 3009 3009 HOH TIP . M 5 HOH A 4 3011 3011 HOH TIP . M 5 HOH A 5 3013 3013 HOH TIP . M 5 HOH A 6 3014 3014 HOH TIP . M 5 HOH A 7 3015 3015 HOH TIP . M 5 HOH A 8 3016 3016 HOH TIP . M 5 HOH A 9 3018 3018 HOH TIP . M 5 HOH A 10 3024 3024 HOH TIP . M 5 HOH A 11 3025 3025 HOH TIP . M 5 HOH A 12 3028 3028 HOH TIP . M 5 HOH A 13 3034 3034 HOH TIP . M 5 HOH A 14 3038 3038 HOH TIP . M 5 HOH A 15 3039 3039 HOH TIP . M 5 HOH A 16 3040 3040 HOH TIP . M 5 HOH A 17 3045 3045 HOH TIP . M 5 HOH A 18 3051 3051 HOH TIP . M 5 HOH A 19 3054 3054 HOH TIP . M 5 HOH A 20 3057 3057 HOH TIP . M 5 HOH A 21 3060 3060 HOH TIP . M 5 HOH A 22 3061 3061 HOH TIP . M 5 HOH A 23 3065 3065 HOH TIP . M 5 HOH A 24 3073 3073 HOH TIP . M 5 HOH A 25 3074 3074 HOH TIP . M 5 HOH A 26 3076 3076 HOH TIP . M 5 HOH A 27 3078 3078 HOH TIP . M 5 HOH A 28 3079 3079 HOH TIP . M 5 HOH A 29 3081 3081 HOH TIP . M 5 HOH A 30 3086 3086 HOH TIP . M 5 HOH A 31 3087 3087 HOH TIP . M 5 HOH A 32 3088 3088 HOH TIP . M 5 HOH A 33 3089 3089 HOH TIP . M 5 HOH A 34 3090 3090 HOH TIP . M 5 HOH A 35 3094 3094 HOH TIP . M 5 HOH A 36 3096 3096 HOH TIP . M 5 HOH A 37 3098 3098 HOH TIP . M 5 HOH A 38 3099 3099 HOH TIP . M 5 HOH A 39 3105 3105 HOH TIP . M 5 HOH A 40 3107 3107 HOH TIP . M 5 HOH A 41 3109 3109 HOH TIP . M 5 HOH A 42 3111 3111 HOH TIP . M 5 HOH A 43 3113 3113 HOH TIP . M 5 HOH A 44 3123 3123 HOH TIP . M 5 HOH A 45 3129 3129 HOH TIP . M 5 HOH A 46 3134 3134 HOH TIP . M 5 HOH A 47 3138 3138 HOH TIP . M 5 HOH A 48 3141 3141 HOH TIP . N 5 HOH B 1 3001 3001 HOH TIP . N 5 HOH B 2 3002 3002 HOH TIP . N 5 HOH B 3 3003 3003 HOH TIP . N 5 HOH B 4 3006 3006 HOH TIP . N 5 HOH B 5 3010 3010 HOH TIP . N 5 HOH B 6 3019 3019 HOH TIP . N 5 HOH B 7 3023 3023 HOH TIP . N 5 HOH B 8 3026 3026 HOH TIP . N 5 HOH B 9 3027 3027 HOH TIP . N 5 HOH B 10 3029 3029 HOH TIP . N 5 HOH B 11 3030 3030 HOH TIP . N 5 HOH B 12 3031 3031 HOH TIP . N 5 HOH B 13 3032 3032 HOH TIP . N 5 HOH B 14 3033 3033 HOH TIP . N 5 HOH B 15 3036 3036 HOH TIP . N 5 HOH B 16 3041 3041 HOH TIP . N 5 HOH B 17 3042 3042 HOH TIP . N 5 HOH B 18 3044 3044 HOH TIP . N 5 HOH B 19 3046 3046 HOH TIP . N 5 HOH B 20 3047 3047 HOH TIP . N 5 HOH B 21 3048 3048 HOH TIP . N 5 HOH B 22 3053 3053 HOH TIP . N 5 HOH B 23 3059 3059 HOH TIP . N 5 HOH B 24 3062 3062 HOH TIP . N 5 HOH B 25 3063 3063 HOH TIP . N 5 HOH B 26 3064 3064 HOH TIP . N 5 HOH B 27 3067 3067 HOH TIP . N 5 HOH B 28 3070 3070 HOH TIP . N 5 HOH B 29 3077 3077 HOH TIP . N 5 HOH B 30 3080 3080 HOH TIP . N 5 HOH B 31 3082 3082 HOH TIP . N 5 HOH B 32 3084 3084 HOH TIP . N 5 HOH B 33 3085 3085 HOH TIP . N 5 HOH B 34 3092 3092 HOH TIP . N 5 HOH B 35 3095 3095 HOH TIP . N 5 HOH B 36 3097 3097 HOH TIP . N 5 HOH B 37 3100 3100 HOH TIP . N 5 HOH B 38 3102 3102 HOH TIP . N 5 HOH B 39 3103 3103 HOH TIP . N 5 HOH B 40 3106 3106 HOH TIP . N 5 HOH B 41 3108 3108 HOH TIP . N 5 HOH B 42 3110 3110 HOH TIP . N 5 HOH B 43 3112 3112 HOH TIP . N 5 HOH B 44 3115 3115 HOH TIP . N 5 HOH B 45 3118 3118 HOH TIP . N 5 HOH B 46 3120 3120 HOH TIP . N 5 HOH B 47 3125 3125 HOH TIP . N 5 HOH B 48 3126 3126 HOH TIP . N 5 HOH B 49 3127 3127 HOH TIP . N 5 HOH B 50 3128 3128 HOH TIP . N 5 HOH B 51 3131 3131 HOH TIP . N 5 HOH B 52 3132 3132 HOH TIP . N 5 HOH B 53 3135 3135 HOH TIP . N 5 HOH B 54 3136 3136 HOH TIP . N 5 HOH B 55 3139 3139 HOH TIP . N 5 HOH B 56 3140 3140 HOH TIP . N 5 HOH B 57 3142 3142 HOH TIP . O 5 HOH C 1 3007 3007 HOH TIP . O 5 HOH C 2 3008 3008 HOH TIP . O 5 HOH C 3 3012 3012 HOH TIP . O 5 HOH C 4 3017 3017 HOH TIP . O 5 HOH C 5 3020 3020 HOH TIP . O 5 HOH C 6 3021 3021 HOH TIP . O 5 HOH C 7 3022 3022 HOH TIP . O 5 HOH C 8 3035 3035 HOH TIP . O 5 HOH C 9 3037 3037 HOH TIP . O 5 HOH C 10 3043 3043 HOH TIP . O 5 HOH C 11 3049 3049 HOH TIP . O 5 HOH C 12 3050 3050 HOH TIP . O 5 HOH C 13 3052 3052 HOH TIP . O 5 HOH C 14 3055 3055 HOH TIP . O 5 HOH C 15 3056 3056 HOH TIP . O 5 HOH C 16 3058 3058 HOH TIP . O 5 HOH C 17 3066 3066 HOH TIP . O 5 HOH C 18 3068 3068 HOH TIP . O 5 HOH C 19 3069 3069 HOH TIP . O 5 HOH C 20 3071 3071 HOH TIP . O 5 HOH C 21 3072 3072 HOH TIP . O 5 HOH C 22 3075 3075 HOH TIP . O 5 HOH C 23 3083 3083 HOH TIP . O 5 HOH C 24 3091 3091 HOH TIP . O 5 HOH C 25 3093 3093 HOH TIP . O 5 HOH C 26 3101 3101 HOH TIP . O 5 HOH C 27 3104 3104 HOH TIP . O 5 HOH C 28 3114 3114 HOH TIP . O 5 HOH C 29 3116 3116 HOH TIP . O 5 HOH C 30 3117 3117 HOH TIP . O 5 HOH C 31 3119 3119 HOH TIP . O 5 HOH C 32 3121 3121 HOH TIP . O 5 HOH C 33 3122 3122 HOH TIP . O 5 HOH C 34 3124 3124 HOH TIP . O 5 HOH C 35 3130 3130 HOH TIP . O 5 HOH C 36 3133 3133 HOH TIP . O 5 HOH C 37 3137 3137 HOH TIP . O 5 HOH C 38 3143 3143 HOH TIP . # 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 PB ADP . . . I 4 33.911 76.176 20.824 1 15.59 ? PB ADP 1300 B 1 HETATM 2 O O1B ADP . . . I 4 34.445 77.225 21.713 1 16.6 ? O1B ADP 1300 B 1 HETATM 3 O O2B ADP . . . I 4 34.766 74.794 20.881 1 18.4 ? O2B ADP 1300 B 1 HETATM 4 O O3B ADP . . . I 4 32.502 75.881 21.174 1 17.5 ? O3B ADP 1300 B 1 HETATM 5 P PA ADP . . . I 4 35.233 76.651 18.299 1 19.57 ? PA ADP 1300 B 1 HETATM 6 O O1A ADP . . . I 4 36.372 75.894 18.843 1 18.36 ? O1A ADP 1300 B 1 HETATM 7 O O2A ADP . . . I 4 35.62 78.026 17.975 1 21.57 ? O2A ADP 1300 B 1 HETATM 8 O O3A ADP . . . I 4 34.057 76.651 19.355 1 18.72 ? O3A ADP 1300 B 1 HETATM 9 O O5' ADP . . . I 4 34.581 75.924 17.039 1 21.53 ? O5' ADP 1300 B 1 HETATM 10 C C5' ADP . . . I 4 34.126 74.563 17.138 1 24.54 ? C5' ADP 1300 B 1 HETATM 11 C C4' ADP . . . I 4 34.342 73.888 15.786 1 25.16 ? C4' ADP 1300 B 1 HETATM 12 O O4' ADP . . . I 4 35.329 74.616 15.034 1 25.63 ? O4' ADP 1300 B 1 HETATM 13 C C3' ADP . . . I 4 34.884 72.48 15.913 1 26.93 ? C3' ADP 1300 B 1 HETATM 14 O O3' ADP . . . I 4 34.32 71.617 14.92 1 29.23 ? O3' ADP 1300 B 1 HETATM 15 C C2' ADP . . . I 4 36.379 72.618 15.724 1 26.77 ? C2' ADP 1300 B 1 HETATM 16 O O2' ADP . . . I 4 37.012 71.383 15.341 1 27.84 ? O2' ADP 1300 B 1 HETATM 17 C C1' ADP . . . I 4 36.439 73.736 14.708 1 25.27 ? C1' ADP 1300 B 1 HETATM 18 N N9 ADP . . . I 4 37.739 74.509 14.773 1 23.61 ? N9 ADP 1300 B 1 HETATM 19 C C8 ADP . . . I 4 38.078 75.329 15.766 1 23.11 ? C8 ADP 1300 B 1 HETATM 20 N N7 ADP . . . I 4 39.271 75.853 15.512 1 22.46 ? N7 ADP 1300 B 1 HETATM 21 C C5 ADP . . . I 4 39.708 75.383 14.367 1 23.53 ? C5 ADP 1300 B 1 HETATM 22 C C6 ADP . . . I 4 40.863 75.563 13.594 1 24.05 ? C6 ADP 1300 B 1 HETATM 23 N N6 ADP . . . I 4 41.841 76.396 14.009 1 22.99 ? N6 ADP 1300 B 1 HETATM 24 N N1 ADP . . . I 4 40.993 74.896 12.415 1 23.04 ? N1 ADP 1300 B 1 HETATM 25 C C2 ADP . . . I 4 40.031 74.062 11.977 1 22.42 ? C2 ADP 1300 B 1 HETATM 26 N N3 ADP . . . I 4 38.928 73.886 12.706 1 21.96 ? N3 ADP 1300 B 1 HETATM 27 C C4 ADP . . . I 4 38.724 74.511 13.885 1 22.82 ? C4 ADP 1300 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 336 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #