data_4AYX # _model_server_result.job_id CRpD4KPYe1lpbGBVSmKq8w _model_server_result.datetime_utc '2024-11-13 05:04:37' _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 4ayx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":900}' # _entry.id 4AYX # _exptl.entry_id 4AYX _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 90 _cell.angle_gamma 120 _cell.entry_id 4AYX _cell.length_a 180.136 _cell.length_b 180.136 _cell.length_c 50.565 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4AYX _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 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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 6_555 -x,-x+y,-z+1/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 16.855 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 OG SER 384 A SER 534 1_555 C MG MG . A MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.539 ? metalc ? metalc2 A OE1 GLN 425 A GLN 575 1_555 C MG MG . A MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.692 ? metalc ? metalc3 C MG MG . A MG 801 1_555 D O2B ACP . A ACP 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.848 ? metalc ? metalc4 C MG MG . A MG 801 1_555 D O3G ACP . A ACP 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.67 ? # _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 4AYX _atom_sites.fract_transf_matrix[1][1] 0.005551 _atom_sites.fract_transf_matrix[1][2] 0.003205 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00641 _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] 0.019777 _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 GLY A 1 1717 1717 GLY GLY . C 3 MG A 1 801 801 MG MG . D 4 ACP A 1 900 900 ACP ACP . E 5 LMT A 1 1720 1720 LMT LMT . F 6 CDL A 1 1721 1721 CDL CDL . G 5 LMT A 1 1724 1724 LMT LMT . H 6 CDL A 1 1726 1726 CDL CDL . I 7 HOH A 1 2001 2001 HOH HOH . I 7 HOH A 2 2002 2002 HOH HOH . I 7 HOH A 3 2003 2003 HOH HOH . I 7 HOH A 4 2004 2004 HOH HOH . I 7 HOH A 5 2005 2005 HOH HOH . I 7 HOH A 6 2006 2006 HOH HOH . I 7 HOH A 7 2007 2007 HOH HOH . I 7 HOH A 8 2008 2008 HOH HOH . I 7 HOH A 9 2009 2009 HOH HOH . I 7 HOH A 10 2010 2010 HOH HOH . I 7 HOH A 11 2011 2011 HOH HOH . I 7 HOH A 12 2012 2012 HOH HOH . I 7 HOH A 13 2013 2013 HOH HOH . I 7 HOH A 14 2014 2014 HOH HOH . I 7 HOH A 15 2015 2015 HOH HOH . I 7 HOH A 16 2016 2016 HOH HOH . I 7 HOH A 17 2017 2017 HOH HOH . I 7 HOH A 18 2018 2018 HOH HOH . I 7 HOH A 19 2019 2019 HOH HOH . I 7 HOH A 20 2020 2020 HOH HOH . I 7 HOH A 21 2021 2021 HOH HOH . I 7 HOH A 22 2022 2022 HOH HOH . I 7 HOH A 23 2023 2023 HOH HOH . I 7 HOH A 24 2024 2024 HOH HOH . I 7 HOH A 25 2025 2025 HOH HOH . I 7 HOH A 26 2026 2026 HOH HOH . I 7 HOH A 27 2027 2027 HOH HOH . I 7 HOH A 28 2028 2028 HOH HOH . I 7 HOH A 29 2029 2029 HOH HOH . I 7 HOH A 30 2030 2030 HOH HOH . I 7 HOH A 31 2031 2031 HOH HOH . I 7 HOH A 32 2032 2032 HOH HOH . I 7 HOH A 33 2033 2033 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 . . . D 4 -19.877 21.39 5.217 1 150.48 ? PG ACP 900 A 1 HETATM 2 O O1G ACP . . . D 4 -19.405 19.99 4.982 1 151.27 ? O1G ACP 900 A 1 HETATM 3 O O2G ACP . . . D 4 -18.722 22.353 5.569 1 151.3 ? O2G ACP 900 A 1 HETATM 4 O O3G ACP . . . D 4 -20.95 21.494 6.325 1 150.57 ? O3G ACP 900 A 1 HETATM 5 P PB ACP . . . D 4 -21.718 20.893 3.097 1 143.44 ? PB ACP 900 A 1 HETATM 6 O O1B ACP . . . D 4 -21.165 19.722 2.304 1 142.51 ? O1B ACP 900 A 1 HETATM 7 O O2B ACP . . . D 4 -22.868 20.598 4.111 1 144.13 ? O2B ACP 900 A 1 HETATM 8 C C3B ACP . . . D 4 -20.596 21.986 3.76 1 147.15 ? C3B ACP 900 A 1 HETATM 9 P PA ACP . . . D 4 -23.81 22.461 1.759 1 138.04 ? PA ACP 900 A 1 HETATM 10 O O1A ACP . . . D 4 -24.064 23.429 2.852 1 137.13 ? O1A ACP 900 A 1 HETATM 11 O O2A ACP . . . D 4 -24.953 21.552 1.301 1 139.11 ? O2A ACP 900 A 1 HETATM 12 O O3A ACP . . . D 4 -22.528 21.525 1.869 1 140.53 ? O3A ACP 900 A 1 HETATM 13 O O5' ACP . . . D 4 -23.732 23.235 0.341 1 135.83 ? O5' ACP 900 A 1 HETATM 14 C C5' ACP . . . D 4 -22.883 22.904 -0.777 1 134.56 ? C5' ACP 900 A 1 HETATM 15 C C4' ACP . . . D 4 -22.528 24.185 -1.489 1 134.32 ? C4' ACP 900 A 1 HETATM 16 O O4' ACP . . . D 4 -23.723 24.969 -1.704 1 134.32 ? O4' ACP 900 A 1 HETATM 17 C C3' ACP . . . D 4 -21.521 25.092 -0.777 1 134.83 ? C3' ACP 900 A 1 HETATM 18 O O3' ACP . . . D 4 -20.47 25.489 -1.653 1 135.12 ? O3' ACP 900 A 1 HETATM 19 C C2' ACP . . . D 4 -22.388 26.244 -0.244 1 134.61 ? C2' ACP 900 A 1 HETATM 20 O O2' ACP . . . D 4 -21.699 27.486 -0.135 1 133.97 ? O2' ACP 900 A 1 HETATM 21 C C1' ACP . . . D 4 -23.507 26.302 -1.287 1 134.5 ? C1' ACP 900 A 1 HETATM 22 N N9 ACP . . . D 4 -24.776 26.855 -0.808 1 134 ? N9 ACP 900 A 1 HETATM 23 C C8 ACP . . . D 4 -25.458 26.504 0.328 1 133.25 ? C8 ACP 900 A 1 HETATM 24 N N7 ACP . . . D 4 -26.556 27.193 0.529 1 132.91 ? N7 ACP 900 A 1 HETATM 25 C C5 ACP . . . D 4 -26.603 28.058 -0.556 1 133.63 ? C5 ACP 900 A 1 HETATM 26 C C6 ACP . . . D 4 -27.522 29.061 -0.933 1 133.54 ? C6 ACP 900 A 1 HETATM 27 N N6 ACP . . . D 4 -28.583 29.407 -0.199 1 133.51 ? N6 ACP 900 A 1 HETATM 28 N N1 ACP . . . D 4 -27.288 29.729 -2.089 1 133.07 ? N1 ACP 900 A 1 HETATM 29 C C2 ACP . . . D 4 -26.2 29.418 -2.804 1 133.03 ? C2 ACP 900 A 1 HETATM 30 N N3 ACP . . . D 4 -25.259 28.504 -2.543 1 133.74 ? N3 ACP 900 A 1 HETATM 31 C C4 ACP . . . D 4 -25.518 27.854 -1.394 1 134.14 ? C4 ACP 900 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #