data_3N8G # _model_server_result.job_id Pr5nP_T1LJyNoEODNurYJg _model_server_result.datetime_utc '2024-11-27 18:10:22' _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 3n8g # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1001}' # _entry.id 3N8G # _exptl.entry_id 3N8G _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 108 _cell.angle_gamma 90 _cell.entry_id 3N8G _cell.length_a 162 _cell.length_b 76 _cell.length_c 151 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3N8G _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id F _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 O VAL 304 A VAL 304 1_555 C CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.747 ? metalc ? metalc2 A O ALA 305 A ALA 305 1_555 C CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.644 ? metalc ? metalc3 A O ILE 307 A ILE 307 1_555 C CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.511 ? metalc ? metalc4 A OE1 GLU 309 A GLU 309 1_555 C CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.618 ? metalc ? metalc5 A OE2 GLU 309 A GLU 309 1_555 C CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.936 ? metalc ? metalc6 A OD2 ASP 351 A ASP 351 1_555 B CA CA . A CA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? metalc ? metalc7 A O THR 353 A THR 353 1_555 B CA CA . A CA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? metalc ? metalc8 A OD2 ASP 703 A ASP 703 1_555 B CA CA . A CA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.58 ? metalc ? metalc9 A O LEU 711 A LEU 711 1_555 E K K . A K 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.136 ? metalc ? metalc10 A O LYS 712 A LYS 712 1_555 E K K . A K 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.234 ? metalc ? metalc11 A O ALA 714 A ALA 714 1_555 E K K . A K 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.068 ? metalc ? metalc12 A OE1 GLU 732 A GLU 732 1_555 E K K . A K 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.216 ? metalc ? metalc13 A OE2 GLU 732 A GLU 732 1_555 E K K . A K 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.411 ? metalc ? metalc14 A OD1 ASN 768 A ASN 768 1_555 D CA CA . A CA 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.559 ? metalc ? metalc15 A OE2 GLU 771 A GLU 771 1_555 D CA CA . A CA 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.731 ? metalc ? metalc16 A OD1 ASN 796 A ASN 796 1_555 C CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? metalc ? metalc17 A OG1 THR 799 A THR 799 1_555 D CA CA . A CA 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.64 ? metalc ? metalc18 A OD2 ASP 800 A ASP 800 1_555 C CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.806 ? metalc ? metalc19 A OD1 ASP 800 A ASP 800 1_555 D CA CA . A CA 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? metalc ? metalc20 A OD2 ASP 800 A ASP 800 1_555 D CA CA . A CA 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.967 ? metalc ? metalc21 G O HOH . A HOH 995 1_555 B CA CA . A CA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.132 ? metalc ? metalc22 F O3G ACP . A ACP 1001 1_555 B CA CA . A CA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.425 ? metalc ? metalc23 B CA CA . A CA 1002 1_555 G O HOH . A HOH 1023 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.452 ? metalc ? metalc24 B CA CA . A CA 1002 1_555 G O HOH . A HOH 1025 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.732 ? metalc ? metalc25 E K K . A K 1006 1_555 G O HOH . A HOH 1028 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.404 ? metalc ? metalc26 E K K . A K 1006 1_555 G O HOH . A HOH 1091 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.431 ? # _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 3N8G _atom_sites.fract_transf_matrix[1][1] 0.006173 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002006 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013158 _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] 0.006963 _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 B 2 CA A 1 1002 1002 CA CA . C 2 CA A 1 1003 1003 CA CA . D 2 CA A 1 1004 1004 CA CA . E 3 K A 1 1006 1006 K K . F 4 ACP A 1 1001 1001 ACP ACP . G 5 HOH A 1 995 1 HOH HOH . G 5 HOH A 2 996 2 HOH HOH . G 5 HOH A 3 997 3 HOH HOH . G 5 HOH A 4 998 4 HOH HOH . G 5 HOH A 5 999 5 HOH HOH . G 5 HOH A 6 1000 6 HOH HOH . G 5 HOH A 7 1005 7 HOH HOH . G 5 HOH A 8 1007 8 HOH HOH . G 5 HOH A 9 1008 9 HOH HOH . G 5 HOH A 10 1009 10 HOH HOH . G 5 HOH A 11 1010 11 HOH HOH . G 5 HOH A 12 1011 12 HOH HOH . G 5 HOH A 13 1012 13 HOH HOH . G 5 HOH A 14 1013 14 HOH HOH . G 5 HOH A 15 1014 15 HOH HOH . G 5 HOH A 16 1015 16 HOH HOH . G 5 HOH A 17 1016 17 HOH HOH . G 5 HOH A 18 1017 18 HOH HOH . G 5 HOH A 19 1018 19 HOH HOH . G 5 HOH A 20 1019 20 HOH HOH . G 5 HOH A 21 1020 21 HOH HOH . G 5 HOH A 22 1021 22 HOH HOH . G 5 HOH A 23 1022 23 HOH HOH . G 5 HOH A 24 1023 24 HOH HOH . G 5 HOH A 25 1024 25 HOH HOH . G 5 HOH A 26 1025 26 HOH HOH . G 5 HOH A 27 1026 27 HOH HOH . G 5 HOH A 28 1027 28 HOH HOH . G 5 HOH A 29 1028 29 HOH HOH . G 5 HOH A 30 1029 30 HOH HOH . G 5 HOH A 31 1030 31 HOH HOH . G 5 HOH A 32 1031 32 HOH HOH . G 5 HOH A 33 1032 33 HOH HOH . G 5 HOH A 34 1033 34 HOH HOH . G 5 HOH A 35 1034 35 HOH HOH . G 5 HOH A 36 1035 36 HOH HOH . G 5 HOH A 37 1036 37 HOH HOH . G 5 HOH A 38 1037 38 HOH HOH . G 5 HOH A 39 1038 39 HOH HOH . G 5 HOH A 40 1039 40 HOH HOH . G 5 HOH A 41 1040 41 HOH HOH . G 5 HOH A 42 1041 42 HOH HOH . G 5 HOH A 43 1042 43 HOH HOH . G 5 HOH A 44 1043 44 HOH HOH . G 5 HOH A 45 1044 45 HOH HOH . G 5 HOH A 46 1045 46 HOH HOH . G 5 HOH A 47 1046 47 HOH HOH . G 5 HOH A 48 1047 48 HOH HOH . G 5 HOH A 49 1048 49 HOH HOH . G 5 HOH A 50 1049 50 HOH HOH . G 5 HOH A 51 1050 51 HOH HOH . G 5 HOH A 52 1051 52 HOH HOH . G 5 HOH A 53 1052 53 HOH HOH . G 5 HOH A 54 1053 54 HOH HOH . G 5 HOH A 55 1054 55 HOH HOH . G 5 HOH A 56 1055 56 HOH HOH . G 5 HOH A 57 1056 57 HOH HOH . G 5 HOH A 58 1057 58 HOH HOH . G 5 HOH A 59 1058 59 HOH HOH . G 5 HOH A 60 1059 60 HOH HOH . G 5 HOH A 61 1060 61 HOH HOH . G 5 HOH A 62 1061 62 HOH HOH . G 5 HOH A 63 1062 63 HOH HOH . G 5 HOH A 64 1063 64 HOH HOH . G 5 HOH A 65 1064 65 HOH HOH . G 5 HOH A 66 1065 67 HOH HOH . G 5 HOH A 67 1066 68 HOH HOH . G 5 HOH A 68 1067 70 HOH HOH . G 5 HOH A 69 1068 71 HOH HOH . G 5 HOH A 70 1069 73 HOH HOH . G 5 HOH A 71 1070 74 HOH HOH . G 5 HOH A 72 1071 76 HOH HOH . G 5 HOH A 73 1072 81 HOH HOH . G 5 HOH A 74 1073 82 HOH HOH . G 5 HOH A 75 1074 83 HOH HOH . G 5 HOH A 76 1075 84 HOH HOH . G 5 HOH A 77 1076 86 HOH HOH . G 5 HOH A 78 1077 87 HOH HOH . G 5 HOH A 79 1078 89 HOH HOH . G 5 HOH A 80 1079 90 HOH HOH . G 5 HOH A 81 1080 91 HOH HOH . G 5 HOH A 82 1081 92 HOH HOH . G 5 HOH A 83 1082 93 HOH HOH . G 5 HOH A 84 1083 94 HOH HOH . G 5 HOH A 85 1084 96 HOH HOH . G 5 HOH A 86 1085 97 HOH HOH . G 5 HOH A 87 1086 98 HOH HOH . G 5 HOH A 88 1087 99 HOH HOH . G 5 HOH A 89 1088 100 HOH HOH . G 5 HOH A 90 1089 101 HOH HOH . G 5 HOH A 91 1090 102 HOH HOH . G 5 HOH A 92 1091 104 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 . . . F 4 -15.629 2.809 15.436 1 48.62 ? PG ACP 1001 A 1 HETATM 2 O O1G ACP . . . F 4 -15.961 4.35 15.32 1 58.37 ? O1G ACP 1001 A 1 HETATM 3 O O2G ACP . . . F 4 -14.045 2.743 15.299 1 35.07 ? O2G ACP 1001 A 1 HETATM 4 O O3G ACP . . . F 4 -15.92 2.268 16.765 1 52.8 ? O3G ACP 1001 A 1 HETATM 5 P PB ACP . . . F 4 -16.144 2.085 12.503 1 42.48 ? PB ACP 1001 A 1 HETATM 6 O O1B ACP . . . F 4 -15.888 3.55 11.968 1 68.39 ? O1B ACP 1001 A 1 HETATM 7 O O2B ACP . . . F 4 -17.267 1.377 11.861 1 44.28 ? O2B ACP 1001 A 1 HETATM 8 C C3B ACP . . . F 4 -16.142 1.896 14.166 1 41.16 ? C3B ACP 1001 A 1 HETATM 9 P PA ACP . . . F 4 -14.142 0.097 11.525 1 49.78 ? PA ACP 1001 A 1 HETATM 10 O O1A ACP . . . F 4 -15.074 -0.958 12.193 1 35.01 ? O1A ACP 1001 A 1 HETATM 11 O O2A ACP . . . F 4 -12.681 -0.061 11.698 1 50.66 ? O2A ACP 1001 A 1 HETATM 12 O O3A ACP . . . F 4 -14.808 1.367 12.109 1 54.55 ? O3A ACP 1001 A 1 HETATM 13 O O5' ACP . . . F 4 -14.747 0.247 10.055 1 44.64 ? O5' ACP 1001 A 1 HETATM 14 C C5' ACP . . . F 4 -14.06 0.978 9.071 1 36.22 ? C5' ACP 1001 A 1 HETATM 15 C C4' ACP . . . F 4 -15.052 1.619 8.086 1 41.43 ? C4' ACP 1001 A 1 HETATM 16 O O4' ACP . . . F 4 -15.585 0.563 7.327 1 36.94 ? O4' ACP 1001 A 1 HETATM 17 C C3' ACP . . . F 4 -16.278 2.324 8.742 1 46.88 ? C3' ACP 1001 A 1 HETATM 18 O O3' ACP . . . F 4 -15.951 3.62 9.126 1 46.86 ? O3' ACP 1001 A 1 HETATM 19 C C2' ACP . . . F 4 -17.224 2.35 7.511 1 44.9 ? C2' ACP 1001 A 1 HETATM 20 O O2' ACP . . . F 4 -16.818 3.254 6.54 1 36.72 ? O2' ACP 1001 A 1 HETATM 21 C C1' ACP . . . F 4 -16.851 0.956 6.884 1 42.31 ? C1' ACP 1001 A 1 HETATM 22 N N9 ACP . . . F 4 -17.75 -0.065 7.336 1 35.54 ? N9 ACP 1001 A 1 HETATM 23 C C8 ACP . . . F 4 -18.175 -0.436 8.635 1 44.59 ? C8 ACP 1001 A 1 HETATM 24 N N7 ACP . . . F 4 -18.984 -1.503 8.612 1 49.47 ? N7 ACP 1001 A 1 HETATM 25 C C5 ACP . . . F 4 -19.091 -1.834 7.254 1 48.66 ? C5 ACP 1001 A 1 HETATM 26 C C6 ACP . . . F 4 -19.801 -2.838 6.581 1 46.85 ? C6 ACP 1001 A 1 HETATM 27 N N6 ACP . . . F 4 -20.581 -3.681 7.291 1 46.3 ? N6 ACP 1001 A 1 HETATM 28 N N1 ACP . . . F 4 -19.734 -2.94 5.208 1 47.9 ? N1 ACP 1001 A 1 HETATM 29 C C2 ACP . . . F 4 -18.948 -2.02 4.573 1 50.92 ? C2 ACP 1001 A 1 HETATM 30 N N3 ACP . . . F 4 -18.227 -0.998 5.089 1 56.04 ? N3 ACP 1001 A 1 HETATM 31 C C4 ACP . . . F 4 -18.337 -0.952 6.451 1 47.75 ? C4 ACP 1001 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 260 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #