data_6VFX # _model_server_result.job_id zh95138n93FMuriXV4A2NA _model_server_result.datetime_utc '2025-07-06 15:43:33' _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 6vfx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"BA","auth_seq_id":501}' # _entry.id 6VFX # _exptl.entry_id 6VFX _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 6 _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 21-meric _pdbx_struct_assembly.oligomeric_count 21 _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 _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 6 _struct_asym.id BA _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 metalc ? metalc1 A OG1 THR 126 C THR 126 1_555 W MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc2 A OD2 ASP 184 C ASP 184 1_555 W MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? metalc ? metalc3 V O3G ATP . C ATP 501 1_555 W MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc4 V O1B ATP . C ATP 501 1_555 W MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.974 ? metalc ? metalc5 B OG1 THR 126 B THR 126 1_555 Y MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? metalc ? metalc6 B OD2 ASP 184 B ASP 184 1_555 Y MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.783 ? metalc ? metalc7 X O3G ATP . B ATP 501 1_555 Y MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? metalc ? metalc8 X O1B ATP . B ATP 501 1_555 Y MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? metalc ? metalc9 C OG1 THR 126 E THR 126 1_555 AA MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc10 Z O3G ATP . E ATP 501 1_555 AA MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc11 Z O1B ATP . E ATP 501 1_555 AA MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? metalc ? metalc12 E OG1 THR 126 D THR 126 1_555 DA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc13 E OD2 ASP 184 D ASP 184 1_555 DA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? metalc ? metalc14 CA O3G ATP . D ATP 501 1_555 DA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc15 CA O1B ATP . D ATP 501 1_555 DA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.897 ? metalc ? metalc16 F OG1 THR 126 A THR 126 1_555 FA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc17 F OD2 ASP 184 A ASP 184 1_555 FA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.604 ? metalc ? metalc18 EA O3G ATP . A ATP 501 1_555 FA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc19 EA O1B ATP . A ATP 501 1_555 FA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? # _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 6VFX _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 V 4 ATP C 1 501 1 ATP ATP . W 5 MG C 1 502 2 MG MG . X 4 ATP B 1 501 1 ATP ATP . Y 5 MG B 1 502 1 MG MG . Z 4 ATP E 1 501 1 ATP ATP . AA 5 MG E 1 502 4 MG MG . BA 6 ADP F 1 501 1 ADP ADP . CA 4 ATP D 1 501 1 ATP ATP . DA 5 MG D 1 502 3 MG MG . EA 4 ATP A 1 501 1 ATP ATP . FA 5 MG A 1 502 5 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 . . . BA 6 121.568 157.17 102.473 1 69.07 ? PB ADP 501 F 1 HETATM 2 O O1B ADP . . . BA 6 121.998 157.878 101.211 1 69.07 ? O1B ADP 501 F 1 HETATM 3 O O2B ADP . . . BA 6 120.852 158.054 103.466 1 69.07 ? O2B ADP 501 F 1 HETATM 4 O O3B ADP . . . BA 6 122.624 156.278 103.082 1 69.07 ? O3B ADP 501 F 1 HETATM 5 P PA ADP . . . BA 6 120.666 155.252 100.653 1 69.07 ? PA ADP 501 F 1 HETATM 6 O O1A ADP . . . BA 6 120.265 156.075 99.452 1 69.07 ? O1A ADP 501 F 1 HETATM 7 O O2A ADP . . . BA 6 122.048 154.651 100.738 1 69.07 ? O2A ADP 501 F 1 HETATM 8 O O3A ADP . . . BA 6 120.431 156.144 101.973 1 69.07 ? O3A ADP 501 F 1 HETATM 9 O O5' ADP . . . BA 6 119.593 154.064 100.822 1 69.07 ? O5' ADP 501 F 1 HETATM 10 C C5' ADP . . . BA 6 119.804 152.804 100.187 1 69.07 ? C5' ADP 501 F 1 HETATM 11 C C4' ADP . . . BA 6 118.466 152.097 100.008 1 69.07 ? C4' ADP 501 F 1 HETATM 12 O O4' ADP . . . BA 6 117.592 152.438 101.086 1 69.07 ? O4' ADP 501 F 1 HETATM 13 C C3' ADP . . . BA 6 117.785 152.521 98.717 1 69.07 ? C3' ADP 501 F 1 HETATM 14 O O3' ADP . . . BA 6 117.614 151.384 97.866 1 69.07 ? O3' ADP 501 F 1 HETATM 15 C C2' ADP . . . BA 6 116.432 153.073 99.115 1 69.07 ? C2' ADP 501 F 1 HETATM 16 O O2' ADP . . . BA 6 115.391 152.408 98.393 1 69.07 ? O2' ADP 501 F 1 HETATM 17 C C1' ADP . . . BA 6 116.294 152.79 100.601 1 69.07 ? C1' ADP 501 F 1 HETATM 18 N N9 ADP . . . BA 6 115.813 153.998 101.316 1 69.07 ? N9 ADP 501 F 1 HETATM 19 C C8 ADP . . . BA 6 116.517 154.696 102.226 1 69.07 ? C8 ADP 501 F 1 HETATM 20 N N7 ADP . . . BA 6 115.798 155.743 102.704 1 69.07 ? N7 ADP 501 F 1 HETATM 21 C C5 ADP . . . BA 6 114.6 155.722 102.092 1 69.07 ? C5 ADP 501 F 1 HETATM 22 C C6 ADP . . . BA 6 113.368 156.543 102.133 1 69.07 ? C6 ADP 501 F 1 HETATM 23 N N6 ADP . . . BA 6 113.275 157.622 102.947 1 69.07 ? N6 ADP 501 F 1 HETATM 24 N N1 ADP . . . BA 6 112.342 156.178 101.332 1 69.07 ? N1 ADP 501 F 1 HETATM 25 C C2 ADP . . . BA 6 112.425 155.107 100.521 1 69.07 ? C2 ADP 501 F 1 HETATM 26 N N3 ADP . . . BA 6 113.511 154.319 100.433 1 69.07 ? N3 ADP 501 F 1 HETATM 27 C C4 ADP . . . BA 6 114.613 154.567 101.181 1 69.07 ? C4 ADP 501 F 1 HETATM 28 H "H5'1" ADP . . . BA 6 120.286 152.951 99.218 1 69.07 ? "H5'1" ADP 501 F 1 HETATM 29 H "H5'2" ADP . . . BA 6 120.464 152.189 100.803 1 69.07 ? "H5'2" ADP 501 F 1 HETATM 30 H H4' ADP . . . BA 6 118.634 151.011 99.985 1 69.07 ? H4' ADP 501 F 1 HETATM 31 H H3' ADP . . . BA 6 118.371 153.304 98.217 1 69.07 ? H3' ADP 501 F 1 HETATM 32 H HO3' ADP . . . BA 6 117.328 151.674 96.989 1 69.07 ? HO3' ADP 501 F 1 HETATM 33 H H2' ADP . . . BA 6 116.409 154.157 98.94 1 69.07 ? H2' ADP 501 F 1 HETATM 34 H HO2' ADP . . . BA 6 115.415 152.68 97.465 1 69.07 ? HO2' ADP 501 F 1 HETATM 35 H H1' ADP . . . BA 6 115.593 151.956 100.746 1 69.07 ? H1' ADP 501 F 1 HETATM 36 H H8 ADP . . . BA 6 117.526 154.455 102.536 1 69.07 ? H8 ADP 501 F 1 HETATM 37 H HN61 ADP . . . BA 6 112.43 158.171 102.963 1 69.07 ? HN61 ADP 501 F 1 HETATM 38 H HN62 ADP . . . BA 6 114.053 157.877 103.537 1 69.07 ? HN62 ADP 501 F 1 HETATM 39 H H2 ADP . . . BA 6 111.568 154.866 99.904 1 69.07 ? H2 ADP 501 F 1 # _model_server_stats.io_time_ms 82 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 72 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 39 #