data_5IUL # _model_server_result.job_id YBFRLpfFBt5kJvoP5raV3A _model_server_result.datetime_utc '2024-11-15 23:00:27' _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 5iul # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":401}' # _entry.id 5IUL # _exptl.entry_id 5IUL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 117.1 _cell.angle_gamma 90 _cell.entry_id 5IUL _cell.length_a 88.186 _cell.length_b 116.68 _cell.length_c 91.877 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5IUL _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,G,H,I,J,K,L,M,S,T,U 1 1 D,E,F,N,O,P,Q,R,V,W,X 2 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 ? 3 G N N ? 3 I N N ? 3 N N N ? 3 P 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 A OE2 GLU 137 A GLU 289 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc2 A OD1 ASN 141 A ASN 293 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc3 G O3G ACP . A ACP 401 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc4 G O2B ACP . A ACP 401 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc5 G O2A ACP . A ACP 401 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc6 H MG MG . A MG 402 1_555 S O HOH . A HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? metalc ? metalc7 B OE2 GLU 137 B GLU 289 1_555 J MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? metalc ? metalc8 B OD1 ASN 141 B ASN 293 1_555 J MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc9 I O1G ACP . B ACP 401 1_555 J MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc10 I O1B ACP . B ACP 401 1_555 J MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? metalc ? metalc11 I O2A ACP . B ACP 401 1_555 J MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc12 J MG MG . B MG 402 1_555 T O HOH . B HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc13 C OD1 ASP 13 C ASP 9 1_555 K MG MG . C MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc14 C O ASN 26 C ASN 22 1_555 L K K . C K 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.085 ? metalc ? metalc15 C O GLU 28 C GLU 24 1_555 L K K . C K 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.926 ? metalc ? metalc16 C O MET 31 C MET 27 1_555 L K K . C K 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.838 ? metalc ? metalc17 C OD2 ASP 58 C ASP 54 1_555 K MG MG . C MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc18 C O GLU 60 C GLU 56 1_555 K MG MG . C MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? metalc ? metalc19 C O LYS 74 C LYS 70 1_555 M K K . C K 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.604 ? metalc ? metalc20 C O THR 76 C THR 72 1_555 M K K . C K 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.004 ? metalc ? metalc21 K MG MG . C MG 201 1_555 U O HOH . C HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc22 K MG MG . C MG 201 1_555 U O HOH . C HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? metalc ? metalc23 K MG MG . C MG 201 1_555 U O HOH . C HOH 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? metalc ? metalc24 D OE2 GLU 137 D GLU 289 1_555 O MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? metalc ? metalc25 D OD1 ASN 141 D ASN 293 1_555 O MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc26 N O1G ACP . D ACP 401 1_555 O MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc27 N O2B ACP . D ACP 401 1_555 O MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc28 N O2A ACP . D ACP 401 1_555 O MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc29 O MG MG . D MG 402 1_555 V O HOH . D HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc30 E OE2 GLU 137 E GLU 289 1_555 Q MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc31 E OD1 ASN 141 E ASN 293 1_555 Q MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc32 P O1G ACP . E ACP 401 1_555 Q MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc33 P O1B ACP . E ACP 401 1_555 Q MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc34 P O1A ACP . E ACP 401 1_555 Q MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc35 Q MG MG . E MG 402 1_555 W O HOH . E HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc36 F OD1 ASP 13 F ASP 9 1_555 R MG MG . F MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc37 F OD2 ASP 58 F ASP 54 1_555 R MG MG . F MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc38 F O GLU 60 F GLU 56 1_555 R MG MG . F MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? metalc ? metalc39 R MG MG . F MG 201 1_555 X O HOH . F HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc40 R MG MG . F MG 201 1_555 X O HOH . F HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? metalc ? metalc41 R MG MG . F MG 201 1_555 X O HOH . F HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.447 ? # _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 5IUL _atom_sites.fract_transf_matrix[1][1] 0.01134 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005803 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00857 _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] 0.012226 _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 3 ACP A 1 401 1 ACP ACP . H 4 MG A 1 402 371 MG MG . I 3 ACP B 1 401 1 ACP ACP . J 4 MG B 1 402 371 MG MG . K 4 MG C 1 201 1 MG MG . L 5 K C 1 202 1 K K . M 5 K C 1 203 2 K K . N 3 ACP D 1 401 1 ACP ACP . O 4 MG D 1 402 371 MG MG . P 3 ACP E 1 401 1 ACP ACP . Q 4 MG E 1 402 371 MG MG . R 4 MG F 1 201 2 MG MG . S 6 HOH A 1 501 14 HOH HOH . S 6 HOH A 2 502 21 HOH HOH . S 6 HOH A 3 503 26 HOH HOH . T 6 HOH B 1 501 22 HOH HOH . U 6 HOH C 1 301 9 HOH HOH . U 6 HOH C 2 302 12 HOH HOH . U 6 HOH C 3 303 7 HOH HOH . U 6 HOH C 4 304 10 HOH HOH . U 6 HOH C 5 305 4 HOH HOH . U 6 HOH C 6 306 11 HOH HOH . V 6 HOH D 1 501 23 HOH HOH . V 6 HOH D 2 502 18 HOH HOH . V 6 HOH D 3 503 27 HOH HOH . W 6 HOH E 1 501 24 HOH HOH . X 6 HOH F 1 301 1 HOH HOH . X 6 HOH F 2 302 19 HOH HOH . X 6 HOH F 3 303 25 HOH HOH . X 6 HOH F 4 304 20 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 . . . P 3 -81.242 -4.882 49.772 1 85.27 ? PG ACP 401 E 1 HETATM 2 O O1G ACP . . . P 3 -82.376 -4.605 48.763 1 81.83 ? O1G ACP 401 E 1 HETATM 3 O O2G ACP . . . P 3 -79.888 -4.884 49.03 1 81.27 ? O2G ACP 401 E 1 HETATM 4 O O3G ACP . . . P 3 -81.315 -3.962 50.948 1 88.86 ? O3G ACP 401 E 1 HETATM 5 P PB ACP . . . P 3 -82.596 -7.586 49.56 1 94.06 ? PB ACP 401 E 1 HETATM 6 O O1B ACP . . . P 3 -82.314 -7.401 48.039 1 87.55 ? O1B ACP 401 E 1 HETATM 7 O O2B ACP . . . P 3 -82.472 -8.984 50.023 1 101.08 ? O2B ACP 401 E 1 HETATM 8 C C3B ACP . . . P 3 -81.4 -6.552 50.396 1 92.25 ? C3B ACP 401 E 1 HETATM 9 P PA ACP . . . P 3 -85.248 -6.643 48.91 1 94.75 ? PA ACP 401 E 1 HETATM 10 O O1A ACP . . . P 3 -84.758 -5.962 47.688 1 90.88 ? O1A ACP 401 E 1 HETATM 11 O O2A ACP . . . P 3 -86.264 -5.814 49.705 1 93.38 ? O2A ACP 401 E 1 HETATM 12 O O3A ACP . . . P 3 -84.028 -6.971 49.885 1 96.19 ? O3A ACP 401 E 1 HETATM 13 O O5' ACP . . . P 3 -85.928 -8.018 48.477 1 99.6 ? O5' ACP 401 E 1 HETATM 14 C C5' ACP . . . P 3 -86.493 -8.841 49.515 1 107.56 ? C5' ACP 401 E 1 HETATM 15 C C4' ACP . . . P 3 -86.416 -10.296 49.131 1 111.61 ? C4' ACP 401 E 1 HETATM 16 O O4' ACP . . . P 3 -87.285 -10.554 48.008 1 111.13 ? O4' ACP 401 E 1 HETATM 17 C C3' ACP . . . P 3 -85.053 -10.797 48.68 1 111.48 ? C3' ACP 401 E 1 HETATM 18 O O3' ACP . . . P 3 -84.17 -11.101 49.755 1 116.4 ? O3' ACP 401 E 1 HETATM 19 C C2' ACP . . . P 3 -85.433 -12.035 47.873 1 114.4 ? C2' ACP 401 E 1 HETATM 20 O O2' ACP . . . P 3 -85.742 -13.143 48.714 1 121.33 ? O2' ACP 401 E 1 HETATM 21 C C1' ACP . . . P 3 -86.718 -11.561 47.187 1 112.28 ? C1' ACP 401 E 1 HETATM 22 N N9 ACP . . . P 3 -86.534 -11.025 45.839 1 106.09 ? N9 ACP 401 E 1 HETATM 23 C C8 ACP . . . P 3 -86.573 -9.708 45.457 1 100.94 ? C8 ACP 401 E 1 HETATM 24 N N7 ACP . . . P 3 -86.469 -9.525 44.162 1 99.13 ? N7 ACP 401 E 1 HETATM 25 C C5 ACP . . . P 3 -86.349 -10.811 43.656 1 102.85 ? C5 ACP 401 E 1 HETATM 26 C C6 ACP . . . P 3 -86.197 -11.311 42.341 1 103.67 ? C6 ACP 401 E 1 HETATM 27 N N6 ACP . . . P 3 -86.128 -10.536 41.253 1 100.09 ? N6 ACP 401 E 1 HETATM 28 N N1 ACP . . . P 3 -86.093 -12.652 42.181 1 107.66 ? N1 ACP 401 E 1 HETATM 29 C C2 ACP . . . P 3 -86.131 -13.436 43.267 1 110.5 ? C2 ACP 401 E 1 HETATM 30 N N3 ACP . . . P 3 -86.265 -13.08 44.552 1 110.14 ? N3 ACP 401 E 1 HETATM 31 C C4 ACP . . . P 3 -86.374 -11.746 44.682 1 105.87 ? C4 ACP 401 E 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 31 #