data_6MSD # _model_server_result.job_id rWaaCK19FM9vyCp_z3P9rg _model_server_result.datetime_utc '2024-10-18 16:19:42' _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 6msd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"GB","auth_seq_id":501}' # _entry.id 6MSD # _exptl.entry_id 6MSD _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 37 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 6MSD _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6MSD _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 48-meric _pdbx_struct_assembly.oligomeric_count 48 _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,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB _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 ? 37 BB N N ? 37 GB 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 disulf ? disulf1 M SG CYS 236 A CYS 236 1_555 M SG CYS 270 A CYS 270 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 AA SG CYS 41 M CYS 41 1_555 AA SG CYS 186 M CYS 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf3 GA SG CYS 70 S CYS 43 1_555 GA SG CYS 223 S CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf4 OA SG CYS 41 m CYS 41 1_555 OA SG CYS 186 m CYS 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf5 UA SG CYS 70 s CYS 43 1_555 UA SG CYS 223 s CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc1 I OE2 GLU 51 c GLU 52 1_555 WA ZN ZN . c ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc2 I ND1 HIS 112 c HIS 113 1_555 WA ZN ZN . c ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.587 ? metalc ? metalc3 I OD2 ASP 125 c ASP 126 1_555 WA ZN ZN . c ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc4 M OG1 THR 223 A THR 223 1_555 YA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc5 N OG1 THR 233 B THR 233 1_555 AB MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc6 P OG1 THR 213 D THR 213 1_555 DB MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? metalc ? metalc7 Q OG1 THR 195 E THR 181 1_555 FB MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc8 R OD1 ASP 286 F ASP 286 1_555 HB MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.894 ? metalc ? metalc9 R OD2 ASP 286 F ASP 286 1_555 HB MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.879 ? metalc ? metalc10 XA O1G ATP . A ATP 501 1_555 YA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc11 XA O3G ATP . A ATP 501 1_555 YA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc12 XA O2B ATP . A ATP 501 1_555 YA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc13 ZA O1G ATP . B ATP 501 1_555 AB MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? metalc ? metalc14 ZA O1B ATP . B ATP 501 1_555 AB MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc15 ZA O3B ATP . B ATP 501 1_555 AB MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc16 ZA O2A ATP . B ATP 501 1_555 AB MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.593 ? metalc ? metalc17 CB O1G ATP . D ATP 501 1_555 DB MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? metalc ? metalc18 CB O2G ATP . D ATP 501 1_555 DB MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc19 CB O1B ATP . D ATP 501 1_555 DB MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc20 EB O2G ATP . E ATP 401 1_555 FB MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc21 EB O3G ATP . E ATP 401 1_555 FB MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc22 EB O1B ATP . E ATP 401 1_555 FB MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc23 GB O3B ADP . F ADP 501 1_555 HB MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? # _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 ? # _atom_sites.entry_id 6MSD _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 WA 34 ZN c 1 401 401 ZN ZN . XA 35 ATP A 1 501 434 ATP ATP . YA 36 MG A 1 502 435 MG MG . ZA 35 ATP B 1 501 441 ATP ATP . AB 36 MG B 1 502 442 MG MG . BB 37 ADP C 1 501 407 ADP ADP . CB 35 ATP D 1 501 419 ATP ATP . DB 36 MG D 1 502 420 MG MG . EB 35 ATP E 1 401 390 ATP ATP . FB 36 MG E 1 402 391 MG MG . GB 37 ADP F 1 501 440 ADP ADP . HB 36 MG F 1 502 441 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 . . . GB 37 236.703 249.354 192.739 1 108 ? PB ADP 501 F 1 HETATM 2 O O1B ADP . . . GB 37 236.056 248.161 192.09 1 108 ? O1B ADP 501 F 1 HETATM 3 O O2B ADP . . . GB 37 235.934 249.93 193.896 1 108 ? O2B ADP 501 F 1 HETATM 4 O O3B ADP . . . GB 37 238.185 249.236 192.968 1 108 ? O3B ADP 501 F 1 HETATM 5 P PA ADP . . . GB 37 236.195 251.972 192.062 1 108 ? PA ADP 501 F 1 HETATM 6 O O1A ADP . . . GB 37 234.723 252.018 192.374 1 108 ? O1A ADP 501 F 1 HETATM 7 O O2A ADP . . . GB 37 237.213 252.426 193.067 1 108 ? O2A ADP 501 F 1 HETATM 8 O O3A ADP . . . GB 37 236.593 250.491 191.622 1 108 ? O3A ADP 501 F 1 HETATM 9 O O5' ADP . . . GB 37 236.465 252.77 190.705 1 108 ? O5' ADP 501 F 1 HETATM 10 C C5' ADP . . . GB 37 236.473 254.183 190.742 1 108 ? C5' ADP 501 F 1 HETATM 11 C C4' ADP . . . GB 37 235.635 254.679 189.579 1 108 ? C4' ADP 501 F 1 HETATM 12 O O4' ADP . . . GB 37 234.626 255.575 190.037 1 108 ? O4' ADP 501 F 1 HETATM 13 C C3' ADP . . . GB 37 236.473 255.435 188.575 1 108 ? C3' ADP 501 F 1 HETATM 14 O O3' ADP . . . GB 37 236.49 254.703 187.356 1 108 ? O3' ADP 501 F 1 HETATM 15 C C2' ADP . . . GB 37 235.745 256.734 188.341 1 108 ? C2' ADP 501 F 1 HETATM 16 O O2' ADP . . . GB 37 235.523 256.927 186.948 1 108 ? O2' ADP 501 F 1 HETATM 17 C C1' ADP . . . GB 37 234.425 256.585 189.061 1 108 ? C1' ADP 501 F 1 HETATM 18 N N9 ADP . . . GB 37 234.095 257.877 189.682 1 108 ? N9 ADP 501 F 1 HETATM 19 C C8 ADP . . . GB 37 234.481 259.065 189.212 1 108 ? C8 ADP 501 F 1 HETATM 20 N N7 ADP . . . GB 37 234.016 260.074 189.984 1 108 ? N7 ADP 501 F 1 HETATM 21 C C5 ADP . . . GB 37 233.309 259.518 190.97 1 108 ? C5 ADP 501 F 1 HETATM 22 C C6 ADP . . . GB 37 232.561 260.011 192.128 1 108 ? C6 ADP 501 F 1 HETATM 23 N N6 ADP . . . GB 37 232.479 261.328 192.373 1 108 ? N6 ADP 501 F 1 HETATM 24 N N1 ADP . . . GB 37 231.97 259.116 192.926 1 108 ? N1 ADP 501 F 1 HETATM 25 C C2 ADP . . . GB 37 232.055 257.805 192.67 1 108 ? C2 ADP 501 F 1 HETATM 26 N N3 ADP . . . GB 37 232.73 257.279 191.642 1 108 ? N3 ADP 501 F 1 HETATM 27 C C4 ADP . . . GB 37 233.361 258.073 190.765 1 108 ? C4 ADP 501 F 1 # _model_server_stats.io_time_ms 50 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 126 _model_server_stats.query_time_ms 265 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #