data_6MSG # _model_server_result.job_id OF43--nF9V6vba_FObkZgg _model_server_result.datetime_utc '2025-02-05 16:59:43' _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 6msg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"EB","auth_seq_id":501}' # _entry.id 6MSG # _exptl.entry_id 6MSG _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 36 _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 ? # _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 _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 ? 36 XA N N ? 36 EB 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 A SG CYS 633 U CYS 633 1_555 A SG CYS 659 U CYS 659 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 M SG CYS 236 A CYS 236 1_555 M SG CYS 270 A CYS 270 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 AA SG CYS 41 M CYS 41 1_555 AA SG CYS 186 M CYS 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf4 GA SG CYS 70 S CYS 43 1_555 GA SG CYS 223 S CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 OA SG CYS 41 m CYS 41 1_555 OA SG CYS 186 m CYS 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf6 UA SG CYS 70 s CYS 43 1_555 UA SG CYS 223 s CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc1 I NE2 HIS 112 c HIS 113 1_555 WA ZN ZN . c ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc2 I NE2 HIS 114 c HIS 115 1_555 WA ZN ZN . c ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc3 I OD2 ASP 125 c ASP 126 1_555 WA ZN ZN . c ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? metalc ? metalc4 YA O1B ATP . C ATP 501 1_555 ZA MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc5 YA O2B ATP . C ATP 501 1_555 ZA MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc6 AB O3G ATP . D ATP 501 1_555 BB MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc7 AB O1B ATP . D ATP 501 1_555 BB MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? metalc ? metalc8 AB O3B ATP . D ATP 501 1_555 BB MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc9 Q OG1 THR 195 E THR 181 1_555 DB MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc10 CB O2G ATP . E ATP 401 1_555 DB MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc11 CB O1B ATP . E ATP 401 1_555 DB MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.483 ? # _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 6MSG _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 35 ZN c 1 401 401 ZN ZN . XA 36 ADP A 1 501 434 ADP ADP . YA 37 ATP C 1 501 407 ATP ATP . ZA 38 MG C 1 502 408 MG MG . AB 37 ATP D 1 501 440 ATP ATP . BB 38 MG D 1 502 441 MG MG . CB 37 ATP E 1 401 390 ATP ATP . DB 38 MG E 1 402 391 MG MG . EB 36 ADP F 1 501 440 ADP ADP . # 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 . . . EB 36 240.872 250.552 214.701 1 139.01 ? PB ADP 501 F 1 HETATM 2 O O1B ADP . . . EB 36 240.381 250.783 213.292 1 139.01 ? O1B ADP 501 F 1 HETATM 3 O O2B ADP . . . EB 36 239.869 249.835 215.567 1 139.01 ? O2B ADP 501 F 1 HETATM 4 O O3B ADP . . . EB 36 242.288 250.046 214.832 1 139.01 ? O3B ADP 501 F 1 HETATM 5 P PA ADP . . . EB 36 242.165 252.983 214.821 1 139.01 ? PA ADP 501 F 1 HETATM 6 O O1A ADP . . . EB 36 242.539 252.579 213.417 1 139.01 ? O1A ADP 501 F 1 HETATM 7 O O2A ADP . . . EB 36 243.194 252.987 215.919 1 139.01 ? O2A ADP 501 F 1 HETATM 8 O O3A ADP . . . EB 36 240.967 252.034 215.31 1 139.01 ? O3A ADP 501 F 1 HETATM 9 O O5' ADP . . . EB 36 241.449 254.416 214.692 1 139.01 ? O5' ADP 501 F 1 HETATM 10 C C5' ADP . . . EB 36 240.985 254.781 213.396 1 139.01 ? C5' ADP 501 F 1 HETATM 11 C C4' ADP . . . EB 36 241.238 256.253 213.122 1 139.01 ? C4' ADP 501 F 1 HETATM 12 O O4' ADP . . . EB 36 240.25 257.083 213.738 1 139.01 ? O4' ADP 501 F 1 HETATM 13 C C3' ADP . . . EB 36 242.581 256.686 213.668 1 139.01 ? C3' ADP 501 F 1 HETATM 14 O O3' ADP . . . EB 36 243.542 256.737 212.615 1 139.01 ? O3' ADP 501 F 1 HETATM 15 C C2' ADP . . . EB 36 242.336 258.071 214.226 1 139.01 ? C2' ADP 501 F 1 HETATM 16 O O2' ADP . . . EB 36 242.967 259.055 213.405 1 139.01 ? O2' ADP 501 F 1 HETATM 17 C C1' ADP . . . EB 36 240.838 258.297 214.203 1 139.01 ? C1' ADP 501 F 1 HETATM 18 N N9 ADP . . . EB 36 240.352 258.541 215.577 1 139.01 ? N9 ADP 501 F 1 HETATM 19 C C8 ADP . . . EB 36 239.412 257.797 216.175 1 139.01 ? C8 ADP 501 F 1 HETATM 20 N N7 ADP . . . EB 36 239.148 258.255 217.422 1 139.01 ? N7 ADP 501 F 1 HETATM 21 C C5 ADP . . . EB 36 239.945 259.306 217.643 1 139.01 ? C5 ADP 501 F 1 HETATM 22 C C6 ADP . . . EB 36 240.166 260.242 218.764 1 139.01 ? C6 ADP 501 F 1 HETATM 23 N N6 ADP . . . EB 36 239.476 260.119 219.92 1 139.01 ? N6 ADP 501 F 1 HETATM 24 N N1 ADP . . . EB 36 241.081 261.216 218.593 1 139.01 ? N1 ADP 501 F 1 HETATM 25 C C2 ADP . . . EB 36 241.774 261.342 217.449 1 139.01 ? C2 ADP 501 F 1 HETATM 26 N N3 ADP . . . EB 36 241.62 260.53 216.391 1 139.01 ? N3 ADP 501 F 1 HETATM 27 C C4 ADP . . . EB 36 240.735 259.505 216.421 1 139.01 ? C4 ADP 501 F 1 # _model_server_stats.io_time_ms 42 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 501 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #