data_8V30 # _model_server_result.job_id -mzvVwX0dH9m81VAAedxJg _model_server_result.datetime_utc '2024-10-11 03:13:51' _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":"S","auth_seq_id":401}' # _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 . . . S 3 153.72 145.768 96.997 1 128.32 ? PB ADP 401 E 1 HETATM 2 O O1B ADP . . . S 3 154.75 146.264 96.013 1 126.68 ? O1B ADP 401 E 1 HETATM 3 O O2B ADP . . . S 3 153.511 146.641 98.209 1 125.61 -1 O2B ADP 401 E 1 HETATM 4 O O3B ADP . . . S 3 152.448 145.277 96.353 1 122.53 ? O3B ADP 401 E 1 HETATM 5 P PA ADP . . . S 3 155.646 143.7 97.009 1 129.08 ? PA ADP 401 E 1 HETATM 6 O O1A ADP . . . S 3 155.439 143.467 95.534 1 125.05 -1 O1A ADP 401 E 1 HETATM 7 O O2A ADP . . . S 3 156.877 144.406 97.516 1 127.26 ? O2A ADP 401 E 1 HETATM 8 O O3A ADP . . . S 3 154.339 144.419 97.605 1 129.98 ? O3A ADP 401 E 1 HETATM 9 O O5' ADP . . . S 3 155.486 142.3 97.773 1 120.69 ? O5' ADP 401 E 1 HETATM 10 C C5' ADP . . . S 3 155.058 142.321 99.13 1 118.68 ? C5' ADP 401 E 1 HETATM 11 C C4' ADP . . . S 3 154.179 141.108 99.393 1 118.27 ? C4' ADP 401 E 1 HETATM 12 O O4' ADP . . . S 3 154.89 139.927 99.031 1 123.48 ? O4' ADP 401 E 1 HETATM 13 C C3' ADP . . . S 3 153.817 141.004 100.862 1 120.98 ? C3' ADP 401 E 1 HETATM 14 O O3' ADP . . . S 3 152.398 140.918 100.995 1 126.43 ? O3' ADP 401 E 1 HETATM 15 C C2' ADP . . . S 3 154.437 139.714 101.348 1 121.54 ? C2' ADP 401 E 1 HETATM 16 O O2' ADP . . . S 3 153.458 138.95 102.05 1 126.17 ? O2' ADP 401 E 1 HETATM 17 C C1' ADP . . . S 3 154.886 138.982 100.098 1 123.26 ? C1' ADP 401 E 1 HETATM 18 N N9 ADP . . . S 3 156.26 138.462 100.276 1 124.62 ? N9 ADP 401 E 1 HETATM 19 C C8 ADP . . . S 3 157.366 139.21 100.433 1 122 ? C8 ADP 401 E 1 HETATM 20 N N7 ADP . . . S 3 158.467 138.43 100.566 1 121.25 ? N7 ADP 401 E 1 HETATM 21 C C5 ADP . . . S 3 158.064 137.151 100.493 1 122.64 ? C5 ADP 401 E 1 HETATM 22 C C6 ADP . . . S 3 158.711 135.823 100.56 1 122.92 ? C6 ADP 401 E 1 HETATM 23 N N6 ADP . . . S 3 160.048 135.704 100.735 1 125.89 ? N6 ADP 401 E 1 HETATM 24 N N1 ADP . . . S 3 157.925 134.733 100.44 1 122.12 ? N1 ADP 401 E 1 HETATM 25 C C2 ADP . . . S 3 156.596 134.836 100.266 1 120.67 ? C2 ADP 401 E 1 HETATM 26 N N3 ADP . . . S 3 155.942 136.007 100.197 1 120.67 ? N3 ADP 401 E 1 HETATM 27 C C4 ADP . . . S 3 156.608 137.178 100.305 1 123.81 ? C4 ADP 401 E 1 # _model_server_stats.io_time_ms 55 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #