data_4NH1 # _model_server_result.job_id kAuqD25qgdNr9EqkPkzUwg _model_server_result.datetime_utc '2024-11-06 01:31:17' _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 4nh1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":403}' # _entry.id 4NH1 # _exptl.entry_id 4NH1 _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 118.54 _cell.angle_gamma 90 _cell.entry_id 4NH1 _cell.length_a 210.537 _cell.length_b 57.441 _cell.length_c 139.394 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4NH1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 G N N ? 4 K 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 OD1 ASN 161 A ASN 161 1_555 E MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? metalc ? metalc2 A OD2 ASP 175 A ASP 175 1_555 E MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? metalc ? metalc3 A OD1 ASP 175 A ASP 175 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? metalc ? metalc4 A OD2 ASP 175 A ASP 175 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc5 E MG MG . A MG 401 1_555 G O3G ACP . A ACP 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc6 E MG MG . A MG 401 1_555 G O2A ACP . A ACP 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc7 E MG MG . A MG 401 1_555 N O HOH . A HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc8 F MG MG . A MG 402 1_555 G O1B ACP . A ACP 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? metalc ? metalc9 F MG MG . A MG 402 1_555 G O2G ACP . A ACP 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc10 B OD1 ASN 161 B ASN 161 1_555 I MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? metalc ? metalc11 B OD1 ASP 175 B ASP 175 1_555 H MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? metalc ? metalc12 B OD2 ASP 175 B ASP 175 1_555 H MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? metalc ? metalc13 B OD2 ASP 175 B ASP 175 1_555 I MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc14 H MG MG . B MG 401 1_555 K O1B ACP . B ACP 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.953 ? metalc ? metalc15 H MG MG . B MG 401 1_555 K O2G ACP . B ACP 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc16 H MG MG . B MG 401 1_555 O O HOH . B HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc17 I MG MG . B MG 402 1_555 K O3G ACP . B ACP 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc18 I MG MG . B MG 402 1_555 K O2A ACP . B ACP 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc19 I MG MG . B MG 402 1_555 O O HOH . B HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc20 C SG CYS 109 C CYS 109 1_555 L ZN ZN . C ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? metalc ? metalc21 C SG CYS 114 C CYS 114 1_555 L ZN ZN . C ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc22 C SG CYS 137 C CYS 137 1_555 L ZN ZN . C ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? metalc ? metalc23 C SG CYS 140 C CYS 140 1_555 L ZN ZN . C ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc24 D SG CYS 109 D CYS 109 1_555 M ZN ZN . D ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc25 D SG CYS 114 D CYS 114 1_555 M ZN ZN . D ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc26 D SG CYS 137 D CYS 137 1_555 M ZN ZN . D ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc27 D SG CYS 140 D CYS 140 1_555 M ZN ZN . D ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? # _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 4NH1 _atom_sites.fract_transf_matrix[1][1] 0.00475 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002583 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017409 _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] 0.008166 _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 E 3 MG A 1 401 4 MG MG . F 3 MG A 1 402 5 MG MG . G 4 ACP A 1 403 9 ACP ACP . H 3 MG B 1 401 3 MG MG . I 3 MG B 1 402 6 MG MG . J 5 GOL B 1 403 7 GOL GOL . K 4 ACP B 1 404 8 ACP ACP . L 6 ZN C 1 301 1 ZN ZN . M 6 ZN D 1 301 2 ZN ZN . N 7 HOH A 1 501 1 HOH HOH . N 7 HOH A 2 502 9 HOH HOH . N 7 HOH A 3 503 15 HOH HOH . O 7 HOH B 1 501 2 HOH HOH . O 7 HOH B 2 502 8 HOH HOH . O 7 HOH B 3 503 11 HOH HOH . O 7 HOH B 4 504 16 HOH HOH . O 7 HOH B 5 505 17 HOH HOH . O 7 HOH B 6 506 18 HOH HOH . O 7 HOH B 7 507 19 HOH HOH . O 7 HOH B 8 508 20 HOH HOH . O 7 HOH B 9 509 21 HOH HOH . P 7 HOH C 1 401 10 HOH HOH . P 7 HOH C 2 402 12 HOH HOH . P 7 HOH C 3 403 13 HOH HOH . Q 7 HOH D 1 401 3 HOH HOH . Q 7 HOH D 2 402 4 HOH HOH . Q 7 HOH D 3 403 5 HOH HOH . Q 7 HOH D 4 404 6 HOH HOH . Q 7 HOH D 5 405 14 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 . . . G 4 36.931 -9.39 76.326 0.92 245.63 ? PG ACP 403 A 1 HETATM 2 O O1G ACP . . . G 4 35.718 -10.144 75.926 0.92 245.99 ? O1G ACP 403 A 1 HETATM 3 O O2G ACP . . . G 4 36.578 -8.17 77.323 0.92 141.35 ? O2G ACP 403 A 1 HETATM 4 O O3G ACP . . . G 4 37.955 -10.331 77.157 0.92 112.54 ? O3G ACP 403 A 1 HETATM 5 P PB ACP . . . G 4 39 -7.356 75.386 0.92 191.05 ? PB ACP 403 A 1 HETATM 6 O O1B ACP . . . G 4 39.067 -7.1 76.843 0.92 172.49 ? O1B ACP 403 A 1 HETATM 7 O O2B ACP . . . G 4 38.443 -6.055 74.595 0.92 104.1 ? O2B ACP 403 A 1 HETATM 8 C C3B ACP . . . G 4 37.847 -8.713 74.9 0.92 223.11 ? C3B ACP 403 A 1 HETATM 9 P PA ACP . . . G 4 41.749 -7.929 75.592 0.92 129.42 ? PA ACP 403 A 1 HETATM 10 O O1A ACP . . . G 4 42.306 -6.637 76.069 0.92 97.23 ? O1A ACP 403 A 1 HETATM 11 O O2A ACP . . . G 4 41.345 -8.903 76.829 0.92 185.6 ? O2A ACP 403 A 1 HETATM 12 O O3A ACP . . . G 4 40.405 -7.726 74.706 0.92 78 ? O3A ACP 403 A 1 HETATM 13 O O5' ACP . . . G 4 42.737 -8.739 74.618 0.92 104.1 ? O5' ACP 403 A 1 HETATM 14 C C5' ACP . . . G 4 43.245 -10.025 74.972 0.92 106.45 ? C5' ACP 403 A 1 HETATM 15 C C4' ACP . . . G 4 44.443 -10.32 74.076 0.92 113.55 ? C4' ACP 403 A 1 HETATM 16 O O4' ACP . . . G 4 45.406 -9.322 74.401 0.92 116.94 ? O4' ACP 403 A 1 HETATM 17 C C3' ACP . . . G 4 45.104 -11.616 74.486 0.92 124.51 ? C3' ACP 403 A 1 HETATM 18 O O3' ACP . . . G 4 44.686 -12.665 73.599 0.92 129.99 ? O3' ACP 403 A 1 HETATM 19 C C2' ACP . . . G 4 46.584 -11.337 74.278 0.92 124.45 ? C2' ACP 403 A 1 HETATM 20 O O2' ACP . . . G 4 47.06 -12.093 73.153 0.92 111.78 ? O2' ACP 403 A 1 HETATM 21 C C1' ACP . . . G 4 46.654 -9.85 73.956 0.92 123.46 ? C1' ACP 403 A 1 HETATM 22 N N9 ACP . . . G 4 47.66 -9.158 74.786 0.92 120.47 ? N9 ACP 403 A 1 HETATM 23 C C8 ACP . . . G 4 47.361 -8.164 75.616 0.92 107.96 ? C8 ACP 403 A 1 HETATM 24 N N7 ACP . . . G 4 48.485 -7.77 76.205 0.92 107.93 ? N7 ACP 403 A 1 HETATM 25 C C5 ACP . . . G 4 49.48 -8.52 75.741 0.92 115.3 ? C5 ACP 403 A 1 HETATM 26 C C6 ACP . . . G 4 50.782 -8.518 76.016 0.92 119.01 ? C6 ACP 403 A 1 HETATM 27 N N6 ACP . . . G 4 51.191 -7.619 76.908 0.92 106.48 ? N6 ACP 403 A 1 HETATM 28 N N1 ACP . . . G 4 51.632 -9.37 75.43 0.92 140.44 ? N1 ACP 403 A 1 HETATM 29 C C2 ACP . . . G 4 51.131 -10.286 74.504 0.92 147.15 ? C2 ACP 403 A 1 HETATM 30 N N3 ACP . . . G 4 49.76 -10.267 74.233 0.92 143.23 ? N3 ACP 403 A 1 HETATM 31 C C4 ACP . . . G 4 48.97 -9.383 74.859 0.92 128.97 ? C4 ACP 403 A 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #