data_5MPB # _model_server_result.job_id RCdYMVXmziQ0gI9zK3k6Tg _model_server_result.datetime_utc '2024-11-09 02:16:20' _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":"BB","auth_seq_id":501}' # _entry.id 5MPB # _exptl.entry_id 5MPB _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 506.196 _entity.id 34 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' _entity.pdbx_number_of_molecules 5 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 34 VA N N ? 34 XA N N ? 34 ZA N N ? 34 BB N N ? 34 FB 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 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 H17 N6 O12 P3' _chem_comp.formula_weight 506.196 _chem_comp.id ANP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' _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 PG O1G ANP doub 57 n n PG O2G ANP sing 58 n n PG O3G ANP sing 59 n n PG N3B ANP sing 60 n n O2G HOG2 ANP sing 61 n n O3G HOG3 ANP sing 62 n n PB O1B ANP doub 63 n n PB O2B ANP sing 64 n n PB N3B ANP sing 65 n n PB O3A ANP sing 66 n n O2B HOB2 ANP sing 67 n n N3B HNB1 ANP sing 68 n n PA O1A ANP doub 69 n n PA O2A ANP sing 70 n n PA O3A ANP sing 71 n n PA O5' ANP sing 72 n n O2A HOA2 ANP sing 73 n n O5' C5' ANP sing 74 n n C5' C4' ANP sing 75 n n C5' "H5'1" ANP sing 76 n n C5' "H5'2" ANP sing 77 n n C4' O4' ANP sing 78 n n C4' C3' ANP sing 79 n n C4' H4' ANP sing 80 n n O4' C1' ANP sing 81 n n C3' O3' ANP sing 82 n n C3' C2' ANP sing 83 n n C3' H3' ANP sing 84 n n O3' HO3' ANP sing 85 n n C2' O2' ANP sing 86 n n C2' C1' ANP sing 87 n n C2' H2' ANP sing 88 n n O2' HO2' ANP sing 89 n n C1' N9 ANP sing 90 n n C1' H1' ANP sing 91 n n N9 C8 ANP sing 92 n y N9 C4 ANP sing 93 n y C8 N7 ANP doub 94 n y C8 H8 ANP sing 95 n n N7 C5 ANP sing 96 n y C5 C6 ANP sing 97 n y C5 C4 ANP doub 98 n y C6 N6 ANP sing 99 n n C6 N1 ANP doub 100 n y N6 HN61 ANP sing 101 n n N6 HN62 ANP sing 102 n n N1 C2 ANP sing 103 n y C2 N3 ANP doub 104 n y C2 H2 ANP sing 105 n n N3 C4 ANP sing 106 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 PG ANP . . . BB 34 181.736 295.921 311.984 1 1 ? PG ANP 501 L 1 HETATM 2 O O1G ANP . . . BB 34 183.042 296.221 311.287 1 1 ? O1G ANP 501 L 1 HETATM 3 O O2G ANP . . . BB 34 180.539 296.666 311.475 1 1 ? O2G ANP 501 L 1 HETATM 4 O O3G ANP . . . BB 34 181.472 294.493 312.336 1 1 ? O3G ANP 501 L 1 HETATM 5 P PB ANP . . . BB 34 181.869 297.669 314.881 1 1 ? PB ANP 501 L 1 HETATM 6 O O1B ANP . . . BB 34 180.642 298.531 314.636 1 1 ? O1B ANP 501 L 1 HETATM 7 O O2B ANP . . . BB 34 183.243 298.281 315.132 1 1 ? O2B ANP 501 L 1 HETATM 8 N N3B ANP . . . BB 34 182.039 296.576 313.516 1 1 ? N3B ANP 501 L 1 HETATM 9 P PA ANP . . . BB 34 180.681 295.378 317.001 1 1 ? PA ANP 501 L 1 HETATM 10 O O1A ANP . . . BB 34 180.873 294.06 316.325 1 1 ? O1A ANP 501 L 1 HETATM 11 O O2A ANP . . . BB 34 179.31 295.866 317.069 1 1 ? O2A ANP 501 L 1 HETATM 12 O O3A ANP . . . BB 34 181.552 296.596 316.245 1 1 ? O3A ANP 501 L 1 HETATM 13 O O5' ANP . . . BB 34 181.438 295.303 318.412 1 1 ? O5' ANP 501 L 1 HETATM 14 C C5' ANP . . . BB 34 181.312 294.103 319.167 1 1 ? C5' ANP 501 L 1 HETATM 15 C C4' ANP . . . BB 34 181.191 294.322 320.689 1 1 ? C4' ANP 501 L 1 HETATM 16 O O4' ANP . . . BB 34 182.174 295.256 321.275 1 1 ? O4' ANP 501 L 1 HETATM 17 C C3' ANP . . . BB 34 179.892 294.962 321.164 1 1 ? C3' ANP 501 L 1 HETATM 18 O O3' ANP . . . BB 34 178.806 294.072 321.055 1 1 ? O3' ANP 501 L 1 HETATM 19 C C2' ANP . . . BB 34 180.229 295.274 322.65 1 1 ? C2' ANP 501 L 1 HETATM 20 O O2' ANP . . . BB 34 180.189 294.171 323.554 1 1 ? O2' ANP 501 L 1 HETATM 21 C C1' ANP . . . BB 34 181.658 295.624 322.601 1 1 ? C1' ANP 501 L 1 HETATM 22 N N9 ANP . . . BB 34 181.871 297.065 322.965 1 1 ? N9 ANP 501 L 1 HETATM 23 C C8 ANP . . . BB 34 182.713 298.018 322.316 1 1 ? C8 ANP 501 L 1 HETATM 24 N N7 ANP . . . BB 34 182.781 299.155 322.997 1 1 ? N7 ANP 501 L 1 HETATM 25 C C5 ANP . . . BB 34 182.052 298.958 324.124 1 1 ? C5 ANP 501 L 1 HETATM 26 C C6 ANP . . . BB 34 181.96 299.812 325.221 1 1 ? C6 ANP 501 L 1 HETATM 27 N N6 ANP . . . BB 34 182.587 301.038 325.068 1 1 ? N6 ANP 501 L 1 HETATM 28 N N1 ANP . . . BB 34 181.158 299.385 326.208 1 1 ? N1 ANP 501 L 1 HETATM 29 C C2 ANP . . . BB 34 180.571 298.199 326.081 1 1 ? C2 ANP 501 L 1 HETATM 30 N N3 ANP . . . BB 34 180.741 297.264 325.115 1 1 ? N3 ANP 501 L 1 HETATM 31 C C4 ANP . . . BB 34 181.503 297.693 324.117 1 1 ? C4 ANP 501 L 1 # _model_server_stats.io_time_ms 45 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 157 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #