data_4UXX # _model_server_result.job_id '_VaO2hDDTSnysH0shwVKIA' _model_server_result.datetime_utc '2024-11-08 14:54:14' _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 4uxx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Q","auth_seq_id":1123}' # _entry.id 4UXX # _exptl.entry_id 4UXX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 8 _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 120 _cell.entry_id 4UXX _cell.length_a 72.94 _cell.length_b 72.94 _cell.length_c 195.76 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4UXX _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,S,T,U,V,W _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 8 _struct_asym.id Q _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 OE1 GLU 37 A GLU 28 1_555 E NA NA . A NA 1122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.504 ? metalc ? metalc2 A OE2 GLU 37 A GLU 28 1_555 E NA NA . A NA 1122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? metalc ? metalc3 A OE1 GLU 85 A GLU 76 1_555 E NA NA . A NA 1122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.525 ? metalc ? metalc4 E NA NA . A NA 1122 1_555 F O ACT . A ACT 1123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.837 ? metalc ? metalc5 E NA NA . A NA 1122 1_555 F OXT ACT . A ACT 1123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.471 ? metalc ? metalc6 B OE1 GLU 37 B GLU 28 1_555 N NA NA . B NA 1126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? metalc ? metalc7 B OE2 GLU 85 B GLU 76 1_555 N NA NA . B NA 1126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? metalc ? metalc8 B OE1 GLU 85 B GLU 76 1_555 N NA NA . B NA 1126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc9 M OXT ACT . B ACT 1125 1_555 N NA NA . B NA 1126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.698 ? metalc ? metalc10 M O ACT . B ACT 1125 1_555 N NA NA . B NA 1126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc11 C OE2 GLU 37 C GLU 28 1_555 O ZN ZN . C ZN 1121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc12 C OE1 GLU 85 C GLU 76 1_555 O ZN ZN . C ZN 1121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? metalc ? metalc13 C OE2 GLU 85 C GLU 76 1_555 P ZN ZN . C ZN 1122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? metalc ? metalc14 C OE1 GLU 97 C GLU 88 4_645 T NA NA . C NA 1126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc15 C OE1 GLU 97 C GLU 88 1_555 T NA NA . C NA 1126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.43 ? metalc ? metalc16 O ZN ZN . C ZN 1121 1_555 Q O1B ACP . C ACP 1123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc17 O ZN ZN . C ZN 1121 1_555 Q O3G ACP . C ACP 1123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc18 P ZN ZN . C ZN 1122 1_555 Q O1A ACP . C ACP 1123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc19 P ZN ZN . C ZN 1122 1_555 Q O1G ACP . C ACP 1123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? # _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 4UXX _atom_sites.fract_transf_matrix[1][1] 0.01371 _atom_sites.fract_transf_matrix[1][2] 0.007915 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015831 _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] 0.005108 _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 D 2 CL A 1 1121 1121 CL CL . E 3 NA A 1 1122 1122 NA NA . F 4 ACT A 1 1123 1123 ACT ACT . G 5 OLC A 1 1124 1124 OLC OLC . H 5 OLC A 1 1125 1125 OLC OLC . I 4 ACT A 1 1126 1126 ACT ACT . J 6 MPD B 1 1122 1122 MPD MPD . K 5 OLC B 1 1123 1123 OLC OLC . L 5 OLC B 1 1124 1124 OLC OLC . M 4 ACT B 1 1125 1125 ACT ACT . N 3 NA B 1 1126 1126 NA NA . O 7 ZN C 1 1121 1121 ZN ZN . P 7 ZN C 1 1122 1122 ZN ZN . Q 8 ACP C 1 1123 1123 ACP ACP . R 5 OLC C 1 1124 1124 OLC OLC . S 5 OLC C 1 1125 1125 OLC OLC . T 3 NA C 1 1126 1126 NA NA . U 9 HOH A 1 2001 2001 HOH HOH . U 9 HOH A 2 2002 2002 HOH HOH . U 9 HOH A 3 2003 2003 HOH HOH . U 9 HOH A 4 2004 2004 HOH HOH . U 9 HOH A 5 2005 2005 HOH HOH . U 9 HOH A 6 2006 2006 HOH HOH . V 9 HOH B 1 2001 2001 HOH HOH . V 9 HOH B 2 2002 2002 HOH HOH . V 9 HOH B 3 2003 2003 HOH HOH . W 9 HOH C 1 2001 2001 HOH HOH . W 9 HOH C 2 2002 2002 HOH HOH . W 9 HOH C 3 2003 2003 HOH HOH . W 9 HOH C 4 2004 2004 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 . . . Q 8 34.808 -29.859 11.797 0.85 174.76 ? PG ACP 1123 C 1 HETATM 2 O O1G ACP . . . Q 8 36.25 -30.232 11.663 0.85 176.23 ? O1G ACP 1123 C 1 HETATM 3 O O2G ACP . . . Q 8 34.193 -30.343 13.129 0.85 167.24 ? O2G ACP 1123 C 1 HETATM 4 O O3G ACP . . . Q 8 34.587 -28.332 11.713 0.85 174.27 ? O3G ACP 1123 C 1 HETATM 5 P PB ACP . . . Q 8 33.955 -29.869 8.864 0.85 139.81 ? PB ACP 1123 C 1 HETATM 6 O O1B ACP . . . Q 8 34.19 -28.374 8.793 0.85 140.1 ? O1B ACP 1123 C 1 HETATM 7 O O2B ACP . . . Q 8 32.576 -30.186 8.214 0.85 131.3 ? O2B ACP 1123 C 1 HETATM 8 C C3B ACP . . . Q 8 33.791 -30.582 10.504 0.85 147.06 ? C3B ACP 1123 C 1 HETATM 9 P PA ACP . . . Q 8 36.224 -30.461 7.11 0.85 104.07 ? PA ACP 1123 C 1 HETATM 10 O O1A ACP . . . Q 8 37.483 -30.601 7.971 0.85 129.36 ? O1A ACP 1123 C 1 HETATM 11 O O2A ACP . . . Q 8 36.12 -29.193 6.352 0.85 91.47 ? O2A ACP 1123 C 1 HETATM 12 O O3A ACP . . . Q 8 35.014 -30.795 8.103 0.85 163.44 ? O3A ACP 1123 C 1 HETATM 13 O O5' ACP . . . Q 8 36.199 -31.743 6.183 0.85 87.79 ? O5' ACP 1123 C 1 HETATM 14 C C5' ACP . . . Q 8 35.88 -33.002 6.807 0.85 87.49 ? C5' ACP 1123 C 1 HETATM 15 C C4' ACP . . . Q 8 36.945 -34.01 6.455 0.85 90.45 ? C4' ACP 1123 C 1 HETATM 16 O O4' ACP . . . Q 8 36.902 -34.286 5.038 0.85 92.17 ? O4' ACP 1123 C 1 HETATM 17 C C3' ACP . . . Q 8 38.38 -33.583 6.746 0.85 97.68 ? C3' ACP 1123 C 1 HETATM 18 O O3' ACP . . . Q 8 38.752 -33.92 8.078 0.85 107.86 ? O3' ACP 1123 C 1 HETATM 19 C C2' ACP . . . Q 8 39.172 -34.376 5.707 0.85 87.23 ? C2' ACP 1123 C 1 HETATM 20 O O2' ACP . . . Q 8 39.409 -35.714 6.129 0.85 88.6 ? O2' ACP 1123 C 1 HETATM 21 C C1' ACP . . . Q 8 38.216 -34.348 4.511 0.85 86.06 ? C1' ACP 1123 C 1 HETATM 22 N N9 ACP . . . Q 8 38.403 -33.211 3.618 0.85 84.62 ? N9 ACP 1123 C 1 HETATM 23 C C8 ACP . . . Q 8 37.73 -32.017 3.645 0.85 75.87 ? C8 ACP 1123 C 1 HETATM 24 N N7 ACP . . . Q 8 38.093 -31.174 2.709 0.85 69.6 ? N7 ACP 1123 C 1 HETATM 25 C C5 ACP . . . Q 8 39.079 -31.864 2.014 0.85 74.75 ? C5 ACP 1123 C 1 HETATM 26 C C6 ACP . . . Q 8 39.87 -31.518 0.902 0.85 80.09 ? C6 ACP 1123 C 1 HETATM 27 N N6 ACP . . . Q 8 39.785 -30.35 0.262 0.85 90.48 ? N6 ACP 1123 C 1 HETATM 28 N N1 ACP . . . Q 8 40.765 -32.432 0.463 0.85 83.22 ? N1 ACP 1123 C 1 HETATM 29 C C2 ACP . . . Q 8 40.851 -33.605 1.097 0.85 83.96 ? C2 ACP 1123 C 1 HETATM 30 N N3 ACP . . . Q 8 40.155 -34.042 2.15 0.85 82.81 ? N3 ACP 1123 C 1 HETATM 31 C C4 ACP . . . Q 8 39.279 -33.116 2.564 0.85 84.34 ? C4 ACP 1123 C 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #