data_7W3H # _model_server_result.job_id jvBAmvmZDC1oTY-qQib2rw _model_server_result.datetime_utc '2025-07-02 12:32:07' _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 7w3h # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"DB","auth_seq_id":501}' # _entry.id 7W3H # _exptl.entry_id 7W3H _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 1 _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 7W3H _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7W3H _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 49-meric _pdbx_struct_assembly.oligomeric_count 49 _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 _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 38 _struct_asym.id DB _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 disulf ? disulf1 A SG CYS 236 A CYS 236 1_555 A SG CYS 270 A CYS 270 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf2 U SG CYS 633 U CYS 633 1_555 U SG CYS 659 U CYS 659 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc1 A OG1 THR 223 A THR 223 1_555 YA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc2 XA O2G ATP . A ATP 501 1_555 YA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.772 ? metalc ? metalc3 XA O1B ATP . A ATP 501 1_555 YA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? metalc ? metalc4 XA O3B ATP . A ATP 501 1_555 YA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.854 ? metalc ? metalc5 XA O3A ATP . A ATP 501 1_555 YA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.907 ? metalc ? metalc6 B OG1 THR 233 B THR 233 1_555 AB MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.843 ? metalc ? metalc7 ZA O1G ATP . B ATP 501 1_555 AB MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc8 ZA O2B ATP . B ATP 501 1_555 AB MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc9 ZA O3B ATP . B ATP 501 1_555 AB MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? metalc ? metalc10 ZA O3A ATP . B ATP 501 1_555 AB MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.828 ? metalc ? metalc11 BB O2G ATP . C ATP 501 1_555 CB MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.497 ? metalc ? metalc12 BB O1B ATP . C ATP 501 1_555 CB MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc13 F OG1 THR 234 F THR 234 1_555 FB MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc14 EB O2G ATP . F ATP 501 1_555 FB MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? metalc ? metalc15 EB O2B ATP . F ATP 501 1_555 FB MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc16 EB O3B ATP . F ATP 501 1_555 FB MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.966 ? metalc ? metalc17 EB O1A ATP . F ATP 501 1_555 FB MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc18 BA NE2 HIS 113 c HIS 113 1_555 GB ZN ZN . c ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc19 BA NE2 HIS 115 c HIS 115 1_555 GB ZN ZN . c ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc20 BA OD2 ASP 126 c ASP 126 1_555 GB ZN ZN . c ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? # _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 7W3H _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 XA 36 ATP A 1 501 501 ATP ATP . YA 37 MG A 1 502 502 MG MG . ZA 36 ATP B 1 501 501 ATP ATP . AB 37 MG B 1 502 502 MG MG . BB 36 ATP C 1 501 501 ATP ATP . CB 37 MG C 1 502 502 MG MG . DB 38 ADP D 1 501 501 ADP ADP . EB 36 ATP F 1 501 501 ATP ATP . FB 37 MG F 1 502 502 MG MG . GB 39 ZN c 1 401 401 ZN ZN . # 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 . . . DB 38 245.711 206.396 236.263 1 130.95 ? PB ADP 501 D 1 HETATM 2 O O1B ADP . . . DB 38 245.339 205.266 235.341 1 130.95 ? O1B ADP 501 D 1 HETATM 3 O O2B ADP . . . DB 38 246.157 207.647 235.548 1 130.95 ? O2B ADP 501 D 1 HETATM 4 O O3B ADP . . . DB 38 244.726 206.619 237.38 1 130.95 ? O3B ADP 501 D 1 HETATM 5 P PA ADP . . . DB 38 247.08 204.473 237.765 1 130.95 ? PA ADP 501 D 1 HETATM 6 O O1A ADP . . . DB 38 248.179 203.658 237.144 1 130.95 ? O1A ADP 501 D 1 HETATM 7 O O2A ADP . . . DB 38 245.682 203.919 237.815 1 130.95 ? O2A ADP 501 D 1 HETATM 8 O O3A ADP . . . DB 38 247.045 205.884 237 1 130.95 ? O3A ADP 501 D 1 HETATM 9 O O5' ADP . . . DB 38 247.552 204.815 239.257 1 130.95 ? O5' ADP 501 D 1 HETATM 10 C C5' ADP . . . DB 38 246.693 205.513 240.147 1 130.95 ? C5' ADP 501 D 1 HETATM 11 C C4' ADP . . . DB 38 247.165 205.285 241.578 1 130.95 ? C4' ADP 501 D 1 HETATM 12 O O4' ADP . . . DB 38 246.467 204.191 242.174 1 130.95 ? O4' ADP 501 D 1 HETATM 13 C C3' ADP . . . DB 38 248.646 204.959 241.64 1 130.95 ? C3' ADP 501 D 1 HETATM 14 O O3' ADP . . . DB 38 249.355 206.045 242.24 1 130.95 ? O3' ADP 501 D 1 HETATM 15 C C2' ADP . . . DB 38 248.755 203.73 242.513 1 130.95 ? C2' ADP 501 D 1 HETATM 16 O O2' ADP . . . DB 38 249.571 204.006 243.649 1 130.95 ? O2' ADP 501 D 1 HETATM 17 C C1' ADP . . . DB 38 247.348 203.401 242.968 1 130.95 ? C1' ADP 501 D 1 HETATM 18 N N9 ADP . . . DB 38 247.09 201.975 242.689 1 130.95 ? N9 ADP 501 D 1 HETATM 19 C C8 ADP . . . DB 38 246.184 201.502 241.818 1 130.95 ? C8 ADP 501 D 1 HETATM 20 N N7 ADP . . . DB 38 246.191 200.146 241.79 1 130.95 ? N7 ADP 501 D 1 HETATM 21 C C5 ADP . . . DB 38 247.123 199.738 242.661 1 130.95 ? C5 ADP 501 D 1 HETATM 22 C C6 ADP . . . DB 38 247.642 198.438 243.119 1 130.95 ? C6 ADP 501 D 1 HETATM 23 N N6 ADP . . . DB 38 247.148 197.285 242.625 1 130.95 ? N6 ADP 501 D 1 HETATM 24 N N1 ADP . . . DB 38 248.618 198.441 244.045 1 130.95 ? N1 ADP 501 D 1 HETATM 25 C C2 ADP . . . DB 38 249.112 199.587 244.543 1 130.95 ? C2 ADP 501 D 1 HETATM 26 N N3 ADP . . . DB 38 248.686 200.804 244.172 1 130.95 ? N3 ADP 501 D 1 HETATM 27 C C4 ADP . . . DB 38 247.699 200.945 243.262 1 130.95 ? C4 ADP 501 D 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 32 _model_server_stats.create_model_time_ms 174 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 27 #