data_8IBF # _model_server_result.job_id CdJTTKQVDJQw4F_rIRO-gw _model_server_result.datetime_utc '2025-01-03 01:53:38' _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 8ibf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"HA","auth_seq_id":401}' # _entry.id 8IBF # _exptl.entry_id 8IBF _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 27 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details 24-meric _pdbx_struct_assembly.oligomeric_count 24 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 ? _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 # _struct_asym.details ? _struct_asym.entity_id 27 _struct_asym.id HA _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 disulf ? disulf1 J SG CYS 20 Y CYS 20 1_555 J SG CYS 77 Y CYS 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf2 J SG CYS 97 Y CYS 97 1_555 J SG CYS 117 Y CYS 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? disulf ? disulf3 M SG CYS 33 e CYS 33 1_555 M SG CYS 66 e CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf4 M SG CYS 43 e CYS 43 1_555 M SG CYS 56 e CYS 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf5 W SG CYS 59 o CYS 59 1_555 W SG CYS 90 o CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf6 W SG CYS 69 o CYS 69 1_555 W SG CYS 80 o CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? disulf ? disulf7 X SG CYS 77 p CYS 77 1_555 X SG CYS 84 p CYS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf8 X SG CYS 113 p CYS 113 1_555 X SG CYS 125 p CYS 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? # _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 133 n n PB O2B ADP sing 134 n n PB O3B ADP sing 135 n n PB O3A ADP sing 136 n n O2B HOB2 ADP sing 137 n n O3B HOB3 ADP sing 138 n n PA O1A ADP doub 139 n n PA O2A ADP sing 140 n n PA O3A ADP sing 141 n n PA O5' ADP sing 142 n n O2A HOA2 ADP sing 143 n n O5' C5' ADP sing 144 n n C5' C4' ADP sing 145 n n C5' "H5'1" ADP sing 146 n n C5' "H5'2" ADP sing 147 n n C4' O4' ADP sing 148 n n C4' C3' ADP sing 149 n n C4' H4' ADP sing 150 n n O4' C1' ADP sing 151 n n C3' O3' ADP sing 152 n n C3' C2' ADP sing 153 n n C3' H3' ADP sing 154 n n O3' HO3' ADP sing 155 n n C2' O2' ADP sing 156 n n C2' C1' ADP sing 157 n n C2' H2' ADP sing 158 n n O2' HO2' ADP sing 159 n n C1' N9 ADP sing 160 n n C1' H1' ADP sing 161 n n N9 C8 ADP sing 162 n y N9 C4 ADP sing 163 n y C8 N7 ADP doub 164 n y C8 H8 ADP sing 165 n n N7 C5 ADP sing 166 n y C5 C6 ADP sing 167 n y C5 C4 ADP doub 168 n y C6 N6 ADP sing 169 n n C6 N1 ADP doub 170 n y N6 HN61 ADP sing 171 n n N6 HN62 ADP sing 172 n n N1 C2 ADP sing 173 n y C2 N3 ADP doub 174 n y C2 H2 ADP sing 175 n n N3 C4 ADP sing 176 n y # _atom_sites.entry_id 8IBF _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 Y 25 3PE K 1 101 202 3PE 3PE . Z 25 3PE L 1 701 700 3PE 3PE . AA 25 3PE L 1 702 701 3PE 3PE . BA 25 3PE L 1 703 702 3PE 3PE . CA 26 CDL L 1 704 704 CDL CDL . DA 25 3PE L 1 705 501 3PE 3PE . EA 25 3PE M 1 501 502 3PE 3PE . FA 25 3PE M 1 502 503 3PE 3PE . GA 25 3PE N 1 401 504 3PE 3PE . HA 27 ADP O 1 401 401 ADP ADP . IA 26 CDL X 1 201 507 CDL CDL . JA 25 3PE Y 1 201 706 3PE 3PE . KA 25 3PE d 1 201 505 3PE 3PE . LA 26 CDL h 1 201 705 CDL CDL . MA 25 3PE i 1 201 699 3PE 3PE . NA 25 3PE m 1 201 703 3PE 3PE . OA 25 3PE m 1 202 506 3PE 3PE . PA 25 3PE m 1 203 201 3PE 3PE . QA 28 EHZ n 1 201 201 EHZ EHZ . # 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 . . . HA 27 233.155 260.719 216.55 1 51.98 0 PB ADP 401 O 1 HETATM 2 O O1B ADP . . . HA 27 233.926 259.717 215.726 1 51.98 0 O1B ADP 401 O 1 HETATM 3 O O2B ADP . . . HA 27 232.892 262.028 215.85 1 51.98 -1 O2B ADP 401 O 1 HETATM 4 O O3B ADP . . . HA 27 233.639 260.856 217.973 1 51.98 0 O3B ADP 401 O 1 HETATM 5 P PA ADP . . . HA 27 231.277 259.27 218.03 1 51.98 0 PA ADP 401 O 1 HETATM 6 O O1A ADP . . . HA 27 232.435 258.406 218.468 1 51.98 0 O1A ADP 401 O 1 HETATM 7 O O2A ADP . . . HA 27 230.682 260.266 218.995 1 51.98 -1 O2A ADP 401 O 1 HETATM 8 O O3A ADP . . . HA 27 231.695 260.058 216.693 1 51.98 0 O3A ADP 401 O 1 HETATM 9 O O5' ADP . . . HA 27 230.096 258.308 217.518 1 51.98 0 O5' ADP 401 O 1 HETATM 10 C C5' ADP . . . HA 27 229.637 257.26 218.362 1 51.98 0 C5' ADP 401 O 1 HETATM 11 C C4' ADP . . . HA 27 228.12 257.194 218.317 1 51.98 0 C4' ADP 401 O 1 HETATM 12 O O4' ADP . . . HA 27 227.669 256.65 217.076 1 51.98 0 O4' ADP 401 O 1 HETATM 13 C C3' ADP . . . HA 27 227.565 256.296 219.408 1 51.98 0 C3' ADP 401 O 1 HETATM 14 O O3' ADP . . . HA 27 227.003 257.078 220.463 1 51.98 0 O3' ADP 401 O 1 HETATM 15 C C2' ADP . . . HA 27 226.51 255.45 218.732 1 51.98 0 C2' ADP 401 O 1 HETATM 16 O O2' ADP . . . HA 27 225.233 255.588 219.349 1 51.98 0 O2' ADP 401 O 1 HETATM 17 C C1' ADP . . . HA 27 226.439 255.965 217.311 1 51.98 0 C1' ADP 401 O 1 HETATM 18 N N9 ADP . . . HA 27 226.243 254.821 216.398 1 51.98 0 N9 ADP 401 O 1 HETATM 19 C C8 ADP . . . HA 27 227.006 254.493 215.342 1 51.98 0 C8 ADP 401 O 1 HETATM 20 N N7 ADP . . . HA 27 226.526 253.383 214.73 1 51.98 0 N7 ADP 401 O 1 HETATM 21 C C5 ADP . . . HA 27 225.435 252.987 215.407 1 51.98 0 C5 ADP 401 O 1 HETATM 22 C C6 ADP . . . HA 27 224.451 251.888 215.3 1 51.98 0 C6 ADP 401 O 1 HETATM 23 N N6 ADP . . . HA 27 224.544 250.976 214.308 1 51.98 0 N6 ADP 401 O 1 HETATM 24 N N1 ADP . . . HA 27 223.453 251.841 216.207 1 51.98 0 N1 ADP 401 O 1 HETATM 25 C C2 ADP . . . HA 27 223.349 252.752 217.191 1 51.98 0 C2 ADP 401 O 1 HETATM 26 N N3 ADP . . . HA 27 224.209 253.771 217.347 1 51.98 0 N3 ADP 401 O 1 HETATM 27 C C4 ADP . . . HA 27 225.25 253.941 216.502 1 51.98 0 C4 ADP 401 O 1 # _model_server_stats.io_time_ms 31 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 148 _model_server_stats.query_time_ms 508 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 27 #