data_6MSB # _model_server_result.job_id SklSZ4eQgEK9ej5-l_ho4g _model_server_result.datetime_utc '2025-07-07 09:44:07' _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 6msb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"GB","auth_seq_id":501}' # _entry.id 6MSB # _exptl.entry_id 6MSB _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 6MSB _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6MSB _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? disulf ? disulf2 AA SG CYS 41 M CYS 41 1_555 AA SG CYS 186 M CYS 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf3 GA SG CYS 70 S CYS 43 1_555 GA SG CYS 223 S CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf4 OA SG CYS 41 m CYS 41 1_555 OA SG CYS 186 m CYS 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf5 UA SG CYS 70 s CYS 43 1_555 UA SG CYS 223 s CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc1 I OE2 GLU 51 c GLU 52 1_555 WA ZN ZN . c ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc2 I OD1 ASP 125 c ASP 126 1_555 WA ZN ZN . c ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.691 ? metalc ? metalc3 I OD2 ASP 125 c ASP 126 1_555 WA ZN ZN . c ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc4 M OG1 THR 223 A THR 223 1_555 YA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc5 XA O1G ATP . A ATP 501 1_555 YA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc6 XA O3G ATP . A ATP 501 1_555 YA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc7 XA O2B ATP . A ATP 501 1_555 YA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc8 N OG1 THR 233 B THR 233 1_555 AB MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc9 ZA O1G ATP . B ATP 501 1_555 AB MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc10 ZA O1B ATP . B ATP 501 1_555 AB MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc11 ZA O3B ATP . B ATP 501 1_555 AB MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? metalc ? metalc12 ZA O2A ATP . B ATP 501 1_555 AB MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.618 ? metalc ? metalc13 P OG1 THR 213 D THR 213 1_555 DB MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc14 CB O1G ATP . D ATP 501 1_555 DB MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc15 CB O2G ATP . D ATP 501 1_555 DB MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc16 CB O1B ATP . D ATP 501 1_555 DB MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc17 Q OG1 THR 195 E THR 181 1_555 FB MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc18 EB O2G ATP . E ATP 401 1_555 FB MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? metalc ? metalc19 EB O3G ATP . E ATP 401 1_555 FB MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? metalc ? metalc20 EB O1B ATP . E ATP 401 1_555 FB MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc21 R OG1 THR 234 F THR 234 1_555 HB MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.804 ? metalc ? metalc22 R OD1 ASP 286 F ASP 286 1_555 HB MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.899 ? metalc ? metalc23 R OD2 ASP 286 F ASP 286 1_555 HB MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.978 ? metalc ? metalc24 GB O3B ADP . F ADP 501 1_555 HB MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? # _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 6MSB _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 37 235.684 247.914 194.053 1 110.13 ? PB ADP 501 F 1 HETATM 2 O O1B ADP . . . GB 37 235.041 246.68 193.483 1 110.13 ? O1B ADP 501 F 1 HETATM 3 O O2B ADP . . . GB 37 234.898 248.557 195.162 1 110.13 ? O2B ADP 501 F 1 HETATM 4 O O3B ADP . . . GB 37 237.163 247.796 194.297 1 110.13 ? O3B ADP 501 F 1 HETATM 5 P PA ADP . . . GB 37 235.234 250.501 193.254 1 110.13 ? PA ADP 501 F 1 HETATM 6 O O1A ADP . . . GB 37 233.757 250.574 193.518 1 110.13 ? O1A ADP 501 F 1 HETATM 7 O O2A ADP . . . GB 37 236.231 250.992 194.261 1 110.13 ? O2A ADP 501 F 1 HETATM 8 O O3A ADP . . . GB 37 235.608 248.997 192.882 1 110.13 ? O3A ADP 501 F 1 HETATM 9 O O5' ADP . . . GB 37 235.534 251.256 191.884 1 110.13 ? O5' ADP 501 F 1 HETATM 10 C C5' ADP . . . GB 37 235.62 252.665 191.903 1 110.13 ? C5' ADP 501 F 1 HETATM 11 C C4' ADP . . . GB 37 234.752 253.199 190.777 1 110.13 ? C4' ADP 501 F 1 HETATM 12 O O4' ADP . . . GB 37 233.717 254.03 191.297 1 110.13 ? O4' ADP 501 F 1 HETATM 13 C C3' ADP . . . GB 37 235.545 254.055 189.818 1 110.13 ? C3' ADP 501 F 1 HETATM 14 O O3' ADP . . . GB 37 235.645 253.373 188.575 1 110.13 ? O3' ADP 501 F 1 HETATM 15 C C2' ADP . . . GB 37 234.724 255.295 189.604 1 110.13 ? C2' ADP 501 F 1 HETATM 16 O O2' ADP . . . GB 37 234.42 255.398 188.222 1 110.13 ? O2' ADP 501 F 1 HETATM 17 C C1' ADP . . . GB 37 233.447 255.079 190.379 1 110.13 ? C1' ADP 501 F 1 HETATM 18 N N9 ADP . . . GB 37 233.105 256.326 191.086 1 110.13 ? N9 ADP 501 F 1 HETATM 19 C C8 ADP . . . GB 37 233.464 257.556 190.705 1 110.13 ? C8 ADP 501 F 1 HETATM 20 N N7 ADP . . . GB 37 232.991 258.499 191.548 1 110.13 ? N7 ADP 501 F 1 HETATM 21 C C5 ADP . . . GB 37 232.307 257.856 192.493 1 110.13 ? C5 ADP 501 F 1 HETATM 22 C C6 ADP . . . GB 37 231.558 258.248 193.69 1 110.13 ? C6 ADP 501 F 1 HETATM 23 N N6 ADP . . . GB 37 231.453 259.541 194.035 1 110.13 ? N6 ADP 501 F 1 HETATM 24 N N1 ADP . . . GB 37 230.984 257.283 194.421 1 110.13 ? N1 ADP 501 F 1 HETATM 25 C C2 ADP . . . GB 37 231.09 255.996 194.071 1 110.13 ? C2 ADP 501 F 1 HETATM 26 N N3 ADP . . . GB 37 231.764 255.563 193 1 110.13 ? N3 ADP 501 F 1 HETATM 27 C C4 ADP . . . GB 37 232.376 256.432 192.183 1 110.13 ? C4 ADP 501 F 1 # _model_server_stats.io_time_ms 44 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 140 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 27 #