data_8V30 # _model_server_result.job_id Lw4XYkgkZoRpC1O7QrhQzQ _model_server_result.datetime_utc '2024-10-11 03:20:40' _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 8v30 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":402}' # _entry.id 8V30 # _exptl.entry_id 8V30 _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 5 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details decameric _pdbx_struct_assembly.oligomeric_count 10 _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 _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 K N N ? 3 M N N ? 3 P N N ? 3 Q N N ? 3 S 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 73 A GLU 72 1_555 A N HIC 74 A HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale2 A C HIC 74 A HIC 73 1_555 A N GLY 75 A GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 B C GLU 73 B GLU 72 1_555 B N HIC 74 B HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale4 B C HIC 74 B HIC 73 1_555 B N GLY 75 B GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale5 B O GLY 198 B GLY 197 1_555 F CD2 EEP 2 F EEP 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.376 ? covale ? covale6 C C GLU 73 C GLU 72 1_555 C N HIC 74 C HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale7 C C HIC 74 C HIC 73 1_555 C N GLY 75 C GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale8 C O GLY 198 C GLY 197 1_555 G CD2 EEP 2 G EEP 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? covale ? covale9 D C GLU 73 D GLU 72 1_555 D N HIC 74 D HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale10 D C HIC 74 D HIC 73 1_555 D N GLY 75 D GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale11 D O GLY 198 D GLY 197 1_555 H CD2 EEP 2 H EEP 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? covale ? covale12 E C GLU 73 E GLU 72 1_555 E N HIC 74 E HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale13 E C HIC 74 E HIC 73 1_555 E N GLY 75 E GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale14 E O GLY 198 E GLY 197 1_555 I CD2 EEP 2 I EEP 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? covale ? covale15 F C TRP 1 F TRP 1 1_555 F N EEP 2 F EEP 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.478 ? covale ? covale16 F N TRP 1 F TRP 1 1_555 F C ALA 7 F ALA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.476 ? covale ? covale17 F C EEP 2 F EEP 2 1_555 F N ALA 3 F ALA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.465 ? covale ? covale18 F C ALA 3 F ALA 3 1_555 F N DTH 4 F DTH 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.469 ? covale ? covale19 F C DTH 4 F DTH 4 1_555 F N CYS 5 F CYS 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.473 ? covale ? covale20 F C CYS 5 F CYS 5 1_555 F N HYP 6 F HYP 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.489 ? covale ? covale21 F C HYP 6 F HYP 6 1_555 F N ALA 7 F ALA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.475 ? covale ? covale22 G C TRP 1 G TRP 1 1_555 G N EEP 2 G EEP 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.475 ? covale ? covale23 G N TRP 1 G TRP 1 1_555 G C ALA 7 G ALA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.477 ? covale ? covale24 G C EEP 2 G EEP 2 1_555 G N ALA 3 G ALA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.465 ? covale ? covale25 G C ALA 3 G ALA 3 1_555 G N DTH 4 G DTH 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.468 ? covale ? covale26 G C DTH 4 G DTH 4 1_555 G N CYS 5 G CYS 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.472 ? covale ? covale27 G C CYS 5 G CYS 5 1_555 G N HYP 6 G HYP 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.49 ? covale ? covale28 G C HYP 6 G HYP 6 1_555 G N ALA 7 G ALA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.476 ? covale ? covale29 H C TRP 1 H TRP 1 1_555 H N EEP 2 H EEP 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.475 ? covale ? covale30 H N TRP 1 H TRP 1 1_555 H C ALA 7 H ALA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.476 ? covale ? covale31 H C EEP 2 H EEP 2 1_555 H N ALA 3 H ALA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? covale ? covale32 H C ALA 3 H ALA 3 1_555 H N DTH 4 H DTH 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.469 ? covale ? covale33 H C DTH 4 H DTH 4 1_555 H N CYS 5 H CYS 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.474 ? covale ? covale34 H C CYS 5 H CYS 5 1_555 H N HYP 6 H HYP 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.489 ? covale ? covale35 H C HYP 6 H HYP 6 1_555 H N ALA 7 H ALA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.475 ? covale ? covale36 I C TRP 1 I TRP 1 1_555 I N EEP 2 I EEP 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.475 ? covale ? covale37 I N TRP 1 I TRP 1 1_555 I C ALA 7 I ALA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.477 ? covale ? covale38 I C EEP 2 I EEP 2 1_555 I N ALA 3 I ALA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? covale ? covale39 I C ALA 3 I ALA 3 1_555 I N DTH 4 I DTH 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.468 ? covale ? covale40 I C DTH 4 I DTH 4 1_555 I N CYS 5 I CYS 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.473 ? covale ? covale41 I C CYS 5 I CYS 5 1_555 I N HYP 6 I HYP 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.489 ? covale ? covale42 I C HYP 6 I HYP 6 1_555 I N ALA 7 I ALA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.474 ? covale ? covale43 J C TRP 1 J TRP 1 1_555 J N EEP 2 J EEP 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.48 ? covale ? covale44 J N TRP 1 J TRP 1 1_555 J C ALA 7 J ALA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.476 ? covale ? covale45 J C EEP 2 J EEP 2 1_555 J N ALA 3 J ALA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? covale ? covale46 J C ALA 3 J ALA 3 1_555 J N DTH 4 J DTH 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.469 ? covale ? covale47 J C DTH 4 J DTH 4 1_555 J N CYS 5 J CYS 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.472 ? covale ? covale48 J C CYS 5 J CYS 5 1_555 J N HYP 6 J HYP 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.489 ? covale ? covale49 J C HYP 6 J HYP 6 1_555 J N ALA 7 J ALA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.473 ? metalc ? metalc1 K O1B ADP . A ADP 401 1_555 L MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.447 ? metalc ? metalc2 M O1B ADP . B ADP 401 1_555 N MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.621 ? metalc ? metalc3 O MG MG . C MG 401 1_555 P O1B ADP . C ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.698 ? metalc ? metalc4 Q O1B ADP . D ADP 401 1_555 R MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.597 ? metalc ? metalc5 S O1B ADP . E ADP 401 1_555 T MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? # _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 8V30 _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 K 3 ADP A 1 401 401 ADP ADP . L 4 MG A 1 402 402 MG MG . M 3 ADP B 1 401 401 ADP ADP . N 4 MG B 1 402 402 MG MG . O 4 MG C 1 401 401 MG MG . P 3 ADP C 1 402 402 ADP ADP . Q 3 ADP D 1 401 401 ADP ADP . R 4 MG D 1 402 402 MG MG . S 3 ADP E 1 401 401 ADP ADP . T 4 MG E 1 402 402 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 . . . P 3 148.885 151.78 152.778 1 125.91 ? PB ADP 402 C 1 HETATM 2 O O1B ADP . . . P 3 149.623 152.657 151.799 1 120.73 ? O1B ADP 402 C 1 HETATM 3 O O2B ADP . . . P 3 148.368 152.482 154.008 1 124.19 -1 O2B ADP 402 C 1 HETATM 4 O O3B ADP . . . P 3 147.898 150.841 152.133 1 118.18 ? O3B ADP 402 C 1 HETATM 5 P PA ADP . . . P 3 151.508 150.748 152.809 1 122.61 ? PA ADP 402 C 1 HETATM 6 O O1A ADP . . . P 3 151.488 150.451 151.331 1 121.72 -1 O1A ADP 402 C 1 HETATM 7 O O2A ADP . . . P 3 152.246 151.944 153.354 1 121.92 ? O2A ADP 402 C 1 HETATM 8 O O3A ADP . . . P 3 149.995 150.772 153.345 1 121.49 ? O3A ADP 402 C 1 HETATM 9 O O5' ADP . . . P 3 151.997 149.432 153.58 1 119.07 ? O5' ADP 402 C 1 HETATM 10 C C5' ADP . . . P 3 151.587 149.252 154.93 1 116.8 ? C5' ADP 402 C 1 HETATM 11 C C4' ADP . . . P 3 151.359 147.771 155.179 1 116 ? C4' ADP 402 C 1 HETATM 12 O O4' ADP . . . P 3 152.542 147.049 154.845 1 120.63 ? O4' ADP 402 C 1 HETATM 13 C C3' ADP . . . P 3 151.047 147.502 156.638 1 116.48 ? C3' ADP 402 C 1 HETATM 14 O O3' ADP . . . P 3 149.781 146.85 156.737 1 121.09 ? O3' ADP 402 C 1 HETATM 15 C C2' ADP . . . P 3 152.127 146.566 157.126 1 114.45 ? C2' ADP 402 C 1 HETATM 16 O O2' ADP . . . P 3 151.522 145.429 157.74 1 121.98 ? O2' ADP 402 C 1 HETATM 17 C C1' ADP . . . P 3 152.903 146.151 155.89 1 114.29 ? C1' ADP 402 C 1 HETATM 18 N N9 ADP . . . P 3 154.358 146.262 156.139 1 113.59 ? N9 ADP 402 C 1 HETATM 19 C C8 ADP . . . P 3 155.018 147.396 156.433 1 115.5 ? C8 ADP 402 C 1 HETATM 20 N N7 ADP . . . P 3 156.343 147.16 156.602 1 116.31 ? N7 ADP 402 C 1 HETATM 21 C C5 ADP . . . P 3 156.543 145.844 156.414 1 113.93 ? C5 ADP 402 C 1 HETATM 22 C C6 ADP . . . P 3 157.703 144.927 156.443 1 113.42 ? C6 ADP 402 C 1 HETATM 23 N N6 ADP . . . P 3 158.949 145.382 156.715 1 116.52 ? N6 ADP 402 C 1 HETATM 24 N N1 ADP . . . P 3 157.478 143.621 156.188 1 112.31 ? N1 ADP 402 C 1 HETATM 25 C C2 ADP . . . P 3 156.247 143.155 155.916 1 114.4 ? C2 ADP 402 C 1 HETATM 26 N N3 ADP . . . P 3 155.151 143.929 155.873 1 114.11 ? N3 ADP 402 C 1 HETATM 27 C C4 ADP . . . P 3 155.232 145.258 156.111 1 114.51 ? C4 ADP 402 C 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #