data_6MSE # _model_server_result.job_id BfQfsIQ-db-EZVRcHDD40Q _model_server_result.datetime_utc '2024-11-22 16:28:55' _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 6mse # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"ZA","auth_seq_id":501}' # _entry.id 6MSE # _exptl.entry_id 6MSE _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 38 _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 ? 38 ZA N N ? 38 CB 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 AA SG CYS 41 M CYS 41 1_555 AA SG CYS 186 M CYS 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf2 OA SG CYS 41 m CYS 41 1_555 OA SG CYS 186 m CYS 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? metalc ? metalc1 I OE2 GLU 51 c GLU 52 1_555 WA ZN ZN . c ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc2 I NE2 HIS 114 c HIS 115 1_555 WA ZN ZN . c ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? metalc ? metalc3 I OG SER 122 c SER 123 1_555 WA ZN ZN . c ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.643 ? metalc ? metalc4 I OD2 ASP 125 c ASP 126 1_555 WA ZN ZN . c ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc5 WA ZN ZN . c ZN 401 1_555 S O GLY 76 u GLY 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc6 M OG1 THR 223 A THR 223 1_555 YA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.615 ? metalc ? metalc7 XA O2G ATP . A ATP 501 1_555 YA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc8 XA O1B ATP . A ATP 501 1_555 YA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc9 P OG1 THR 213 D THR 213 1_555 BB MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc10 AB O3G ATP . D ATP 501 1_555 BB MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc11 AB O1B ATP . D ATP 501 1_555 BB MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc12 AB O3B ATP . D ATP 501 1_555 BB MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.702 ? metalc ? metalc13 AB O3A ATP . D ATP 501 1_555 BB MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? metalc ? metalc14 R OG1 THR 234 F THR 234 1_555 EB MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? metalc ? metalc15 DB O2B ATP . F ATP 501 1_555 EB MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc16 DB O3B ATP . F ATP 501 1_555 EB MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? # _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 6MSE _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 ATP A 1 501 434 ATP ATP . YA 37 MG A 1 502 435 MG MG . ZA 38 ADP B 1 501 441 ADP ADP . AB 36 ATP D 1 501 419 ATP ATP . BB 37 MG D 1 502 420 MG MG . CB 38 ADP E 1 401 390 ADP ADP . DB 36 ATP F 1 501 440 ATP ATP . EB 37 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 . . . ZA 38 223.52 197.075 165.067 1 146.19 ? PB ADP 501 B 1 HETATM 2 O O1B ADP . . . ZA 38 222.488 197.62 164.124 1 146.19 ? O1B ADP 501 B 1 HETATM 3 O O2B ADP . . . ZA 38 222.976 196.732 166.429 1 146.19 ? O2B ADP 501 B 1 HETATM 4 O O3B ADP . . . ZA 38 224.819 197.839 165.07 1 146.19 ? O3B ADP 501 B 1 HETATM 5 P PA ADP . . . ZA 38 223.807 195.466 162.838 1 146.19 ? PA ADP 501 B 1 HETATM 6 O O1A ADP . . . ZA 38 224.593 196.56 162.178 1 146.19 ? O1A ADP 501 B 1 HETATM 7 O O2A ADP . . . ZA 38 222.363 195.35 162.45 1 146.19 ? O2A ADP 501 B 1 HETATM 8 O O3A ADP . . . ZA 38 223.907 195.653 164.428 1 146.19 ? O3A ADP 501 B 1 HETATM 9 O O5' ADP . . . ZA 38 224.488 194.041 162.538 1 146.19 ? O5' ADP 501 B 1 HETATM 10 C C5' ADP . . . ZA 38 223.64 193.089 161.907 1 146.19 ? C5' ADP 501 B 1 HETATM 11 C C4' ADP . . . ZA 38 224.023 191.634 162.138 1 146.19 ? C4' ADP 501 B 1 HETATM 12 O O4' ADP . . . ZA 38 222.964 190.834 161.61 1 146.19 ? O4' ADP 501 B 1 HETATM 13 C C3' ADP . . . ZA 38 225.29 191.237 161.41 1 146.19 ? C3' ADP 501 B 1 HETATM 14 O O3' ADP . . . ZA 38 226.168 190.558 162.307 1 146.19 ? O3' ADP 501 B 1 HETATM 15 C C2' ADP . . . ZA 38 224.86 190.276 160.325 1 146.19 ? C2' ADP 501 B 1 HETATM 16 O O2' ADP . . . ZA 38 225.578 189.047 160.435 1 146.19 ? O2' ADP 501 B 1 HETATM 17 C C1' ADP . . . ZA 38 223.371 190.042 160.498 1 146.19 ? C1' ADP 501 B 1 HETATM 18 N N9 ADP . . . ZA 38 222.657 190.588 159.324 1 146.19 ? N9 ADP 501 B 1 HETATM 19 C C8 ADP . . . ZA 38 221.728 191.556 159.396 1 146.19 ? C8 ADP 501 B 1 HETATM 20 N N7 ADP . . . ZA 38 221.239 191.865 158.175 1 146.19 ? N7 ADP 501 B 1 HETATM 21 C C5 ADP . . . ZA 38 221.862 191.08 157.29 1 146.19 ? C5 ADP 501 B 1 HETATM 22 C C6 ADP . . . ZA 38 221.803 190.907 155.829 1 146.19 ? C6 ADP 501 B 1 HETATM 23 N N6 ADP . . . ZA 38 220.962 191.662 155.086 1 146.19 ? N6 ADP 501 B 1 HETATM 24 N N1 ADP . . . ZA 38 222.61 189.983 155.272 1 146.19 ? N1 ADP 501 B 1 HETATM 25 C C2 ADP . . . ZA 38 223.442 189.241 156.023 1 146.19 ? C2 ADP 501 B 1 HETATM 26 N N3 ADP . . . ZA 38 223.548 189.346 157.357 1 146.19 ? N3 ADP 501 B 1 HETATM 27 C C4 ADP . . . ZA 38 222.788 190.228 158.045 1 146.19 ? C4 ADP 501 B 1 # _model_server_stats.io_time_ms 42 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 138 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 27 #