data_3C9T # _model_server_result.job_id Ey8Ytar1or-5YMkkmgxFlA _model_server_result.datetime_utc '2024-11-27 12:11:49' _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 3c9t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":307}' # _entry.id 3C9T # _exptl.entry_id 3C9T _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _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 3C9T _cell.length_a 60.75 _cell.length_b 66.843 _cell.length_c 196.86 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3C9T _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 x,y,z _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 ? 4 I N N ? 4 O 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 A SG CYS 70 A CYS 34 1_555 B SG CYS 70 B CYS 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc1 A OD2 ASP 79 A ASP 43 1_555 D MG MG . A MG 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.438 ? metalc ? metalc2 A OD2 ASP 107 A ASP 71 1_555 D MG MG . A MG 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.471 ? metalc ? metalc3 A OD1 ASP 107 A ASP 71 1_555 F MG MG . A MG 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? metalc ? metalc4 A OD1 ASN 155 A ASN 119 1_555 G MG MG . A MG 314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc5 A OD2 ASP 243 A ASP 207 1_555 F MG MG . A MG 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? metalc ? metalc6 A OD1 ASP 246 A ASP 210 1_555 C MG MG . A MG 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc7 A OD2 ASP 246 A ASP 210 1_555 E MG MG . A MG 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc8 I O3G ACP . A ACP 307 1_555 G MG MG . A MG 314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? metalc ? metalc9 I O3G ACP . A ACP 307 1_555 M MG MG . B MG 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? metalc ? metalc10 H O2 TPS . A TPS 308 1_555 J MG MG . B MG 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? metalc ? metalc11 G MG MG . A MG 314 1_555 B OD1 ASP 79 B ASP 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc12 G MG MG . A MG 314 1_555 P O2 TPS . B TPS 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc13 B OD2 ASP 79 B ASP 43 1_555 M MG MG . B MG 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? metalc ? metalc14 B OD2 ASP 107 B ASP 71 1_555 M MG MG . B MG 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? metalc ? metalc15 B ND2 ASN 155 B ASN 119 1_555 J MG MG . B MG 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.478 ? metalc ? metalc16 B OD1 ASP 243 B ASP 207 1_555 L MG MG . B MG 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc17 B OD2 ASP 246 B ASP 210 1_555 K MG MG . B MG 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? metalc ? metalc18 O O1G ACP . B ACP 307 1_555 J MG MG . B MG 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? # _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 1 n n PG O2G ACP sing 2 n n PG O3G ACP sing 3 n n PG C3B ACP sing 4 n n O2G HOG2 ACP sing 5 n n O3G HOG3 ACP sing 6 n n PB O1B ACP doub 7 n n PB O2B ACP sing 8 n n PB C3B ACP sing 9 n n PB O3A ACP sing 10 n n O2B HOB2 ACP sing 11 n n C3B H3B1 ACP sing 12 n n C3B H3B2 ACP sing 13 n n PA O1A ACP doub 14 n n PA O2A ACP sing 15 n n PA O3A ACP sing 16 n n PA O5' ACP sing 17 n n O2A HOA2 ACP sing 18 n n O5' C5' ACP sing 19 n n C5' C4' ACP sing 20 n n C5' "H5'1" ACP sing 21 n n C5' "H5'2" ACP sing 22 n n C4' O4' ACP sing 23 n n C4' C3' ACP sing 24 n n C4' H4' ACP sing 25 n n O4' C1' ACP sing 26 n n C3' O3' ACP sing 27 n n C3' C2' ACP sing 28 n n C3' H3' ACP sing 29 n n O3' HO3' ACP sing 30 n n C2' O2' ACP sing 31 n n C2' C1' ACP sing 32 n n C2' H2' ACP sing 33 n n O2' HO2' ACP sing 34 n n C1' N9 ACP sing 35 n n C1' H1' ACP sing 36 n n N9 C8 ACP sing 37 n y N9 C4 ACP sing 38 n y C8 N7 ACP doub 39 n y C8 H8 ACP sing 40 n n N7 C5 ACP sing 41 n y C5 C6 ACP sing 42 n y C5 C4 ACP doub 43 n y C6 N6 ACP sing 44 n n C6 N1 ACP doub 45 n y N6 HN61 ACP sing 46 n n N6 HN62 ACP sing 47 n n N1 C2 ACP sing 48 n y C2 N3 ACP doub 49 n y C2 H2 ACP sing 50 n n N3 C4 ACP sing 51 n y # _atom_sites.entry_id 3C9T _atom_sites.fract_transf_matrix[1][1] 0.016461 _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] 0.01496 _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] 0.00508 _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 C 2 MG A 1 309 309 MG MG . D 2 MG A 1 310 310 MG MG . E 2 MG A 1 312 312 MG MG . F 2 MG A 1 313 313 MG MG . G 2 MG A 1 314 309 MG MG . H 3 TPS A 1 308 308 TPS TPS . I 4 ACP A 1 307 307 ACP ACP . J 2 MG B 1 311 311 MG MG . K 2 MG B 1 310 310 MG MG . L 2 MG B 1 312 311 MG MG . M 2 MG B 1 313 312 MG MG . N 2 MG B 1 314 313 MG MG . O 4 ACP B 1 307 307 ACP ACP . P 3 TPS B 1 308 308 TPS TPS . Q 5 HOH A 1 315 2 HOH HOH . Q 5 HOH A 2 316 3 HOH HOH . Q 5 HOH A 3 317 6 HOH HOH . Q 5 HOH A 4 318 7 HOH HOH . Q 5 HOH A 5 319 8 HOH HOH . Q 5 HOH A 6 320 10 HOH HOH . Q 5 HOH A 7 321 12 HOH HOH . Q 5 HOH A 8 322 13 HOH HOH . R 5 HOH B 1 315 1 HOH HOH . R 5 HOH B 2 316 5 HOH HOH . R 5 HOH B 3 317 9 HOH HOH . R 5 HOH B 4 318 11 HOH HOH . R 5 HOH B 5 319 14 HOH HOH . R 5 HOH B 6 320 15 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 . . . I 4 31.159 69.888 125.893 1 60.64 ? PG ACP 307 A 1 HETATM 2 O O1G ACP . . . I 4 31.431 70.42 127.266 1 62.98 ? O1G ACP 307 A 1 HETATM 3 O O2G ACP . . . I 4 32.41 69.849 125.109 1 64.49 ? O2G ACP 307 A 1 HETATM 4 O O3G ACP . . . I 4 30.422 68.561 125.933 1 62.97 ? O3G ACP 307 A 1 HETATM 5 P PB ACP . . . I 4 29.823 70.866 123.496 1 61.13 ? PB ACP 307 A 1 HETATM 6 O O1B ACP . . . I 4 28.595 71.673 123.314 1 65.4 ? O1B ACP 307 A 1 HETATM 7 O O2B ACP . . . I 4 29.729 69.627 122.71 1 64.34 ? O2B ACP 307 A 1 HETATM 8 C C3B ACP . . . I 4 29.886 70.777 125.12 1 63.08 ? C3B ACP 307 A 1 HETATM 9 P PA ACP . . . I 4 31.875 71.946 121.366 1 58.38 ? PA ACP 307 A 1 HETATM 10 O O1A ACP . . . I 4 33.019 70.961 121.486 1 61.36 ? O1A ACP 307 A 1 HETATM 11 O O2A ACP . . . I 4 32.299 73.362 121.269 1 61.63 ? O2A ACP 307 A 1 HETATM 12 O O3A ACP . . . I 4 30.901 71.812 122.653 1 61.9 ? O3A ACP 307 A 1 HETATM 13 O O5' ACP . . . I 4 31.073 71.3 120.12 1 59.48 ? O5' ACP 307 A 1 HETATM 14 C C5' ACP . . . I 4 29.928 72.059 119.739 1 57.16 ? C5' ACP 307 A 1 HETATM 15 C C4' ACP . . . I 4 28.889 71.854 118.595 1 55.51 ? C4' ACP 307 A 1 HETATM 16 O O4' ACP . . . I 4 29.031 70.771 117.703 1 54.78 ? O4' ACP 307 A 1 HETATM 17 C C3' ACP . . . I 4 27.582 71.721 119.326 1 54.44 ? C3' ACP 307 A 1 HETATM 18 O O3' ACP . . . I 4 26.663 72.675 118.823 1 55.54 ? O3' ACP 307 A 1 HETATM 19 C C2' ACP . . . I 4 27.185 70.244 119.155 1 53.41 ? C2' ACP 307 A 1 HETATM 20 O O2' ACP . . . I 4 25.791 70.121 119.048 1 54.04 ? O2' ACP 307 A 1 HETATM 21 C C1' ACP . . . I 4 27.962 69.855 117.96 1 53.47 ? C1' ACP 307 A 1 HETATM 22 N N9 ACP . . . I 4 28.443 68.404 117.866 1 50.18 ? N9 ACP 307 A 1 HETATM 23 C C8 ACP . . . I 4 29.382 67.697 118.521 1 49.13 ? C8 ACP 307 A 1 HETATM 24 N N7 ACP . . . I 4 29.501 66.416 118.156 1 47.2 ? N7 ACP 307 A 1 HETATM 25 C C5 ACP . . . I 4 28.577 66.306 117.209 1 47.79 ? C5 ACP 307 A 1 HETATM 26 C C6 ACP . . . I 4 28.104 65.227 116.348 1 48.5 ? C6 ACP 307 A 1 HETATM 27 N N6 ACP . . . I 4 28.641 63.967 116.417 1 46.73 ? N6 ACP 307 A 1 HETATM 28 N N1 ACP . . . I 4 27.078 65.448 115.421 1 47.21 ? N1 ACP 307 A 1 HETATM 29 C C2 ACP . . . I 4 26.505 66.687 115.314 1 44.77 ? C2 ACP 307 A 1 HETATM 30 N N3 ACP . . . I 4 26.881 67.744 116.077 1 45.04 ? N3 ACP 307 A 1 HETATM 31 C C4 ACP . . . I 4 27.897 67.515 116.99 1 47.48 ? C4 ACP 307 A 1 # _model_server_stats.io_time_ms 87 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #