data_9IM5 # _model_server_result.job_id DXOosJK61_YJrHC6Tlz6Qw _model_server_result.datetime_utc '2025-03-07 00:35:59' _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 9im5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"W","auth_seq_id":401}' # _entry.id 9IM5 # _exptl.entry_id 9IM5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 12 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _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 9IM5 _cell.length_a 107.35 _cell.length_b 160.78 _cell.length_c 184.54 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9IM5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,X,Y 1 1 F,W 1 2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 3_545 -x,y-1/2,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 -80.39 92.27 # _struct_asym.details ? _struct_asym.entity_id 12 _struct_asym.id W _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 A OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.458 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.465 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.844 ? metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.653 ? metalc ? metalc8 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc9 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? metalc ? metalc10 B OE1 GLU 111 B GLU 111 1_555 L CA CA . B CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.005 ? metalc ? metalc11 B OE2 GLU 111 B GLU 111 1_555 L CA CA . B CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.594 ? metalc ? metalc12 K MG MG . B MG 501 1_555 P O1A GDP . B GDP 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? metalc ? metalc13 C OD1 ASP 39 C ASP 39 1_555 S CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? metalc ? metalc14 C OD2 ASP 39 C ASP 39 1_555 S CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.454 ? metalc ? metalc15 C O THR 41 C THR 41 1_555 S CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc16 C OG1 THR 41 C THR 41 1_555 S CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? metalc ? metalc17 C O GLY 44 C GLY 44 1_555 S CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? metalc ? metalc18 C OE1 GLU 55 C GLU 55 1_555 S CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.724 ? metalc ? metalc19 C OE2 GLU 55 C GLU 55 1_555 S CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? metalc ? metalc20 Q O1G GTP . C GTP 501 1_555 R MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc21 Q O1B GTP . C GTP 501 1_555 R MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id ACP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE" # 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 ACP doub 49 n n PG O2G ACP sing 50 n n PG O3G ACP sing 51 n n PG C3B ACP sing 52 n n O2G HOG2 ACP sing 53 n n O3G HOG3 ACP sing 54 n n PB O1B ACP doub 55 n n PB O2B ACP sing 56 n n PB C3B ACP sing 57 n n PB O3A ACP sing 58 n n O2B HOB2 ACP sing 59 n n C3B H3B1 ACP sing 60 n n C3B H3B2 ACP sing 61 n n PA O1A ACP doub 62 n n PA O2A ACP sing 63 n n PA O3A ACP sing 64 n n PA O5' ACP sing 65 n n O2A HOA2 ACP sing 66 n n O5' C5' ACP sing 67 n n C5' C4' ACP sing 68 n n C5' "H5'1" ACP sing 69 n n C5' "H5'2" ACP sing 70 n n C4' O4' ACP sing 71 n n C4' C3' ACP sing 72 n n C4' H4' ACP sing 73 n n O4' C1' ACP sing 74 n n C3' O3' ACP sing 75 n n C3' C2' ACP sing 76 n n C3' H3' ACP sing 77 n n O3' HO3' ACP sing 78 n n C2' O2' ACP sing 79 n n C2' C1' ACP sing 80 n n C2' H2' ACP sing 81 n n O2' HO2' ACP sing 82 n n C1' N9 ACP sing 83 n n C1' H1' ACP sing 84 n n N9 C8 ACP sing 85 n y N9 C4 ACP sing 86 n y C8 N7 ACP doub 87 n y C8 H8 ACP sing 88 n n N7 C5 ACP sing 89 n y C5 C6 ACP sing 90 n y C5 C4 ACP doub 91 n y C6 N6 ACP sing 92 n n C6 N1 ACP doub 93 n y N6 HN61 ACP sing 94 n n N6 HN62 ACP sing 95 n n N1 C2 ACP sing 96 n y C2 N3 ACP doub 97 n y C2 H2 ACP sing 98 n n N3 C4 ACP sing 99 n y # _atom_sites.entry_id 9IM5 _atom_sites.fract_transf_matrix[1][1] 0.009315 _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] 0.00622 _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] 0.005419 _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 G 5 GTP A 1 501 501 GTP GTP . H 6 MG A 1 502 502 MG MG . I 7 CA A 1 503 503 CA CA . J 8 CL A 1 504 504 CL CL . K 6 MG B 1 501 502 MG MG . L 7 CA B 1 502 503 CA CA . M 9 MES B 1 503 504 MES MES . N 9 MES B 1 504 505 MES MES . O 10 A1L2T B 1 505 601 A1L2T LIG . P 11 GDP B 1 506 501 GDP GDP . Q 5 GTP C 1 501 501 GTP GTP . R 6 MG C 1 502 502 MG MG . S 7 CA C 1 503 503 CA CA . T 5 GTP D 1 501 501 GTP GTP . U 6 MG D 1 502 502 MG MG . V 10 A1L2T D 1 503 601 A1L2T LIG . W 12 ACP F 1 401 401 ACP ACP . X 13 HOH A 1 601 2 HOH HOH . Y 13 HOH B 1 601 4 HOH HOH . Y 13 HOH B 2 602 1 HOH HOH . Y 13 HOH B 3 603 5 HOH HOH . Y 13 HOH B 4 604 6 HOH HOH . Y 13 HOH B 5 605 3 HOH HOH . # 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 ACP . . . W 12 8.257 50.637 95.022 1 120.93 ? PG ACP 401 F 1 HETATM 2 O O1G ACP . . . W 12 9.542 51.05 94.405 1 114.4 ? O1G ACP 401 F 1 HETATM 3 O O2G ACP . . . W 12 7.502 49.617 94.027 1 112.87 ? O2G ACP 401 F 1 HETATM 4 O O3G ACP . . . W 12 7.315 51.924 95.25 1 105.72 ? O3G ACP 401 F 1 HETATM 5 P PB ACP . . . W 12 10.034 50.444 97.468 1 118.85 ? PB ACP 401 F 1 HETATM 6 O O1B ACP . . . W 12 10.572 51.646 96.789 1 112.42 ? O1B ACP 401 F 1 HETATM 7 O O2B ACP . . . W 12 11.158 49.293 97.4 1 119.67 ? O2B ACP 401 F 1 HETATM 8 C C3B ACP . . . W 12 8.554 49.821 96.616 1 115.46 ? C3B ACP 401 F 1 HETATM 9 P PA ACP . . . W 12 10.508 51.635 100.06 1 118.83 ? PA ACP 401 F 1 HETATM 10 O O1A ACP . . . W 12 9.913 53.021 100.15 1 94.71 ? O1A ACP 401 F 1 HETATM 11 O O2A ACP . . . W 12 11.972 51.481 99.723 1 120.42 ? O2A ACP 401 F 1 HETATM 12 O O3A ACP . . . W 12 9.644 50.737 99.017 1 115.42 ? O3A ACP 401 F 1 HETATM 13 O O5' ACP . . . W 12 10.269 50.92 101.495 1 114.14 ? O5' ACP 401 F 1 HETATM 14 C C5' ACP . . . W 12 9.547 49.689 101.615 1 107.52 ? C5' ACP 401 F 1 HETATM 15 C C4' ACP . . . W 12 8.656 49.595 102.859 1 97.97 ? C4' ACP 401 F 1 HETATM 16 O O4' ACP . . . W 12 9.31 50.032 104.059 1 95.69 ? O4' ACP 401 F 1 HETATM 17 C C3' ACP . . . W 12 7.427 50.475 102.75 1 93.68 ? C3' ACP 401 F 1 HETATM 18 O O3' ACP . . . W 12 6.375 49.727 102.137 1 93.87 ? O3' ACP 401 F 1 HETATM 19 C C2' ACP . . . W 12 7.063 50.737 104.191 1 88.9 ? C2' ACP 401 F 1 HETATM 20 O O2' ACP . . . W 12 6.174 49.727 104.675 1 92.29 ? O2' ACP 401 F 1 HETATM 21 C C1' ACP . . . W 12 8.38 50.68 104.945 1 87.24 ? C1' ACP 401 F 1 HETATM 22 N N9 ACP . . . W 12 8.904 52.011 105.331 1 88.46 ? N9 ACP 401 F 1 HETATM 23 C C8 ACP . . . W 12 9.831 52.723 104.664 1 95.32 ? C8 ACP 401 F 1 HETATM 24 N N7 ACP . . . W 12 10.106 53.888 105.308 1 94.01 ? N7 ACP 401 F 1 HETATM 25 C C5 ACP . . . W 12 9.355 53.925 106.424 1 87.77 ? C5 ACP 401 F 1 HETATM 26 C C6 ACP . . . W 12 9.161 54.868 107.551 1 86.8 ? C6 ACP 401 F 1 HETATM 27 N N6 ACP . . . W 12 9.847 56.036 107.609 1 85.23 ? N6 ACP 401 F 1 HETATM 28 N N1 ACP . . . W 12 8.278 54.522 108.517 1 87.33 ? N1 ACP 401 F 1 HETATM 29 C C2 ACP . . . W 12 7.592 53.363 108.465 1 89.55 ? C2 ACP 401 F 1 HETATM 30 N N3 ACP . . . W 12 7.718 52.463 107.471 1 89.21 ? N3 ACP 401 F 1 HETATM 31 C C4 ACP . . . W 12 8.574 52.677 106.442 1 88.28 ? C4 ACP 401 F 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 345 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #