data_8RV2 # _model_server_result.job_id 7Ta8Fsqa0u0sEPgUMh1MWQ _model_server_result.datetime_utc '2024-11-26 08:20:37' _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 8rv2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":401}' # _entry.id 8RV2 # _exptl.entry_id 8RV2 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _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 90 _cell.entry_id 8RV2 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8RV2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 G N N ? 3 I N N ? 3 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 covale ? covale1 A C GLU 72 A GLU 72 1_555 A N HIC 73 A HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C HIC 73 A HIC 73 1_555 A N GLY 74 A GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 B C GLU 72 B GLU 72 1_555 B N HIC 73 B HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale4 B C HIC 73 B HIC 73 1_555 B N GLY 74 B GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale5 C C GLU 72 C GLU 72 1_555 C N HIC 73 C HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale6 C C HIC 73 C HIC 73 1_555 C N GLY 74 C GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale7 D C GLU 72 D GLU 72 1_555 D N HIC 73 D HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale8 D C HIC 73 D HIC 73 1_555 D N GLY 74 D GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? metalc ? metalc1 G O1B ADP . A ADP 401 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc2 J MG MG . B MG 402 1_555 K O3 PO4 . B PO4 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.53 ? metalc ? metalc3 L O1B ADP . C ADP 401 1_555 M MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.55 ? metalc ? metalc4 N O1G ATP . D ATP 401 1_555 O MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? # _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 8RV2 _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 G 3 ADP A 1 401 376 ADP ADP . H 4 MG A 1 402 377 MG MG . I 3 ADP B 1 401 376 ADP ADP . J 4 MG B 1 402 377 MG MG . K 5 PO4 B 1 403 378 PO4 PO4 . L 3 ADP C 1 401 376 ADP ADP . M 4 MG C 1 402 377 MG MG . N 6 ATP D 1 401 376 ATP ATP . O 4 MG D 1 402 377 MG MG . # 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 3 154.472 147.522 192.06 1 16.15 ? PB ADP 401 B 1 HETATM 2 O O1B ADP . . . I 3 154.452 146.338 191.127 1 10.84 ? O1B ADP 401 B 1 HETATM 3 O O2B ADP . . . I 3 155.48 148.584 191.698 1 14.3 ? O2B ADP 401 B 1 HETATM 4 O O3B ADP . . . I 3 154.442 147.161 193.524 1 14.69 ? O3B ADP 401 B 1 HETATM 5 P PA ADP . . . I 3 151.664 147.506 192.096 1 6.91 ? PA ADP 401 B 1 HETATM 6 O O1A ADP . . . I 3 150.782 147.757 190.9 1 9.05 ? O1A ADP 401 B 1 HETATM 7 O O2A ADP . . . I 3 151.945 146.1 192.561 1 8.26 ? O2A ADP 401 B 1 HETATM 8 O O3A ADP . . . I 3 153.061 148.248 191.803 1 7.52 ? O3A ADP 401 B 1 HETATM 9 O O5' ADP . . . I 3 151.09 148.357 193.335 1 10.31 ? O5' ADP 401 B 1 HETATM 10 C C5' ADP . . . I 3 151.938 149.278 194.015 1 10.83 ? C5' ADP 401 B 1 HETATM 11 C C4' ADP . . . I 3 151.213 150.588 194.303 1 11.78 ? C4' ADP 401 B 1 HETATM 12 O O4' ADP . . . I 3 149.835 150.524 193.941 1 12.49 ? O4' ADP 401 B 1 HETATM 13 C C3' ADP . . . I 3 151.251 150.963 195.775 1 10.9 ? C3' ADP 401 B 1 HETATM 14 O O3' ADP . . . I 3 152.234 151.974 195.998 1 16.53 ? O3' ADP 401 B 1 HETATM 15 C C2' ADP . . . I 3 149.878 151.521 196.082 1 8.45 ? C2' ADP 401 B 1 HETATM 16 O O2' ADP . . . I 3 149.99 152.89 196.473 1 12.3 ? O2' ADP 401 B 1 HETATM 17 C C1' ADP . . . I 3 149.105 151.42 194.779 1 9.25 ? C1' ADP 401 B 1 HETATM 18 N N9 ADP . . . I 3 147.731 150.919 195.025 1 10.52 ? N9 ADP 401 B 1 HETATM 19 C C8 ADP . . . I 3 147.383 149.647 195.289 1 10.18 ? C8 ADP 401 B 1 HETATM 20 N N7 ADP . . . I 3 146.042 149.534 195.462 1 7.63 ? N7 ADP 401 B 1 HETATM 21 C C5 ADP . . . I 3 145.511 150.761 195.308 1 7.74 ? C5 ADP 401 B 1 HETATM 22 C C6 ADP . . . I 3 144.156 151.353 195.359 1 10 ? C6 ADP 401 B 1 HETATM 23 N N6 ADP . . . I 3 143.068 150.59 195.618 1 10.35 ? N6 ADP 401 B 1 HETATM 24 N N1 ADP . . . I 3 144.041 152.68 195.141 1 8.84 ? N1 ADP 401 B 1 HETATM 25 C C2 ADP . . . I 3 145.112 153.45 194.882 1 5.9 ? C2 ADP 401 B 1 HETATM 26 N N3 ADP . . . I 3 146.368 152.981 194.82 1 5.71 ? N3 ADP 401 B 1 HETATM 27 C C4 ADP . . . I 3 146.629 151.669 195.022 1 7.75 ? C4 ADP 401 B 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 34 _model_server_stats.query_time_ms 527 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 27 #