data_5MPB # _model_server_result.job_id UIulgPyuonZg9RDoBuNY4g _model_server_result.datetime_utc '2024-11-09 01:52:24' _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 5mpb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"DB","auth_seq_id":501}' # _entry.id 5MPB # _exptl.entry_id 5MPB _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details 47-meric _pdbx_struct_assembly.oligomeric_count 47 _pdbx_struct_assembly.details author_and_software_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 36 _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 metalc ? metalc1 CA OG1 THR 257 H THR 257 1_555 WA MG MG . H MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.709 ? metalc ? metalc2 VA O2G ANP . H ANP 501 1_555 WA MG MG . H MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc3 VA O2B ANP . H ANP 501 1_555 WA MG MG . H MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.498 ? metalc ? metalc4 DA OG1 THR 230 I THR 230 1_555 YA MG MG . I MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc5 XA O1G ANP . I ANP 501 1_555 YA MG MG . I MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc6 XA O1B ANP . I ANP 501 1_555 YA MG MG . I MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc7 EA OG1 THR 220 K THR 220 1_555 AB MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.939 ? metalc ? metalc8 ZA O1G ANP . K ANP 501 1_555 AB MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc9 ZA O1B ANP . K ANP 501 1_555 AB MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.721 ? metalc ? metalc10 FA OG1 THR 229 L THR 229 1_555 CB MG MG . L MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc11 BB O2G ANP . L ANP 501 1_555 CB MG MG . L MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc12 BB O1B ANP . L ANP 501 1_555 CB MG MG . L MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? metalc ? metalc13 GA OG1 THR 229 M THR 229 1_555 EB MG MG . M MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.556 ? metalc ? metalc14 DB O3B ADP . M ADP 501 1_555 EB MG MG . M MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? metalc ? metalc15 HA OG1 THR 196 J THR 196 1_555 GB MG MG . J MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? metalc ? metalc16 FB O1G ANP . J ANP 501 1_555 GB MG MG . J MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc17 FB O1B ANP . J ANP 501 1_555 GB MG MG . J MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? # _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 5MPB _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 VA 34 ANP H 1 501 501 ANP ANP . WA 35 MG H 1 502 502 MG MG . XA 34 ANP I 1 501 501 ANP ANP . YA 35 MG I 1 502 502 MG MG . ZA 34 ANP K 1 501 501 ANP ANP . AB 35 MG K 1 502 502 MG MG . BB 34 ANP L 1 501 501 ANP ANP . CB 35 MG L 1 502 502 MG MG . DB 36 ADP M 1 501 501 ADP ADP . EB 35 MG M 1 502 503 MG MG . FB 34 ANP J 1 501 501 ANP ANP . GB 35 MG J 1 502 502 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 . . . DB 36 182.233 269.478 299.749 1 1 ? PB ADP 501 M 1 HETATM 2 O O1B ADP . . . DB 36 182.886 270.091 298.498 1 1 ? O1B ADP 501 M 1 HETATM 3 O O2B ADP . . . DB 36 183.239 269.213 300.851 1 1 ? O2B ADP 501 M 1 HETATM 4 O O3B ADP . . . DB 36 181.065 270.331 300.231 1 1 ? O3B ADP 501 M 1 HETATM 5 P PA ADP . . . DB 36 180.352 266.831 299.216 1 1 ? PA ADP 501 M 1 HETATM 6 O O1A ADP . . . DB 36 179.517 267.216 298.036 1 1 ? O1A ADP 501 M 1 HETATM 7 O O2A ADP . . . DB 36 179.709 266.635 300.545 1 1 ? O2A ADP 501 M 1 HETATM 8 O O3A ADP . . . DB 36 181.545 267.912 299.44 1 1 ? O3A ADP 501 M 1 HETATM 9 O O5' ADP . . . DB 36 181.146 265.518 298.886 1 1 ? O5' ADP 501 M 1 HETATM 10 C C5' ADP . . . DB 36 181.111 264.918 297.552 1 1 ? C5' ADP 501 M 1 HETATM 11 C C4' ADP . . . DB 36 180.567 263.493 297.592 1 1 ? C4' ADP 501 M 1 HETATM 12 O O4' ADP . . . DB 36 181.626 262.528 297.899 1 1 ? O4' ADP 501 M 1 HETATM 13 C C3' ADP . . . DB 36 179.494 263.131 298.659 1 1 ? C3' ADP 501 M 1 HETATM 14 O O3' ADP . . . DB 36 178.221 263.487 298.008 1 1 ? O3' ADP 501 M 1 HETATM 15 C C2' ADP . . . DB 36 179.681 261.7 299.034 1 1 ? C2' ADP 501 M 1 HETATM 16 O O2' ADP . . . DB 36 179.087 260.869 298.083 1 1 ? O2' ADP 501 M 1 HETATM 17 C C1' ADP . . . DB 36 181.227 261.575 298.91 1 1 ? C1' ADP 501 M 1 HETATM 18 N N9 ADP . . . DB 36 181.885 261.905 300.236 1 1 ? N9 ADP 501 M 1 HETATM 19 C C8 ADP . . . DB 36 182.566 262.987 300.652 1 1 ? C8 ADP 501 M 1 HETATM 20 N N7 ADP . . . DB 36 182.941 262.893 301.879 1 1 ? N7 ADP 501 M 1 HETATM 21 C C5 ADP . . . DB 36 182.583 261.656 302.371 1 1 ? C5 ADP 501 M 1 HETATM 22 C C6 ADP . . . DB 36 182.623 261.11 303.699 1 1 ? C6 ADP 501 M 1 HETATM 23 N N6 ADP . . . DB 36 183.242 261.851 304.64 1 1 ? N6 ADP 501 M 1 HETATM 24 N N1 ADP . . . DB 36 181.918 259.969 303.889 1 1 ? N1 ADP 501 M 1 HETATM 25 C C2 ADP . . . DB 36 181.416 259.427 302.776 1 1 ? C2 ADP 501 M 1 HETATM 26 N N3 ADP . . . DB 36 181.3 259.888 301.524 1 1 ? N3 ADP 501 M 1 HETATM 27 C C4 ADP . . . DB 36 181.894 261.057 301.376 1 1 ? C4 ADP 501 M 1 # _model_server_stats.io_time_ms 39 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 465 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 27 #