data_2XND # _model_server_result.job_id bIlFZT5vtikNpHr-tLOgPg _model_server_result.datetime_utc '2025-02-22 22:36:13' _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 2xnd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Y","auth_seq_id":600}' # _entry.id 2XND # _exptl.entry_id 2XND _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' _entity.pdbx_number_of_molecules 5 _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 90 _cell.entry_id 2XND _cell.length_a 155.74 _cell.length_b 157.1 _cell.length_c 247.27 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2XND _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details heptadecameric _pdbx_struct_assembly.oligomeric_count 17 _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,X,Y,Z,AA,BA,CA _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 ? 7 R N N ? 7 T N N ? 7 W N N ? 7 Y N N ? 7 BA 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 OG1 THR 158 A THR 176 1_555 S MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc2 R O2B ANP . A ANP 600 1_555 S MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc3 R O2G ANP . A ANP 600 1_555 S MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? metalc ? metalc4 B OG1 THR 158 B THR 176 1_555 U MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc5 T O2G ANP . B ANP 600 1_555 U MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc6 T O2B ANP . B ANP 600 1_555 U MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc7 C OG1 THR 158 C THR 176 1_555 X MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? metalc ? metalc8 W O2B ANP . C ANP 600 1_555 X MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc9 W O2G ANP . C ANP 600 1_555 X MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? metalc ? metalc10 D OG1 THR 155 D THR 163 1_555 Z MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc11 D OE1 GLU 180 D GLU 188 1_555 Z MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.878 ? metalc ? metalc12 Y O2G ANP . D ANP 600 1_555 Z MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc13 Y O2B ANP . D ANP 600 1_555 Z MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc14 F OG1 THR 155 F THR 163 1_555 CA MG MG . F MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc15 BA O2G ANP . F ANP 600 1_555 CA MG MG . F MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc16 BA O2B ANP . F ANP 600 1_555 CA MG MG . F MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? # _chem_comp.formula 'C10 H17 N6 O12 P3' _chem_comp.formula_weight 506.196 _chem_comp.id ANP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 ANP doub 13 n n PG O2G ANP sing 14 n n PG O3G ANP sing 15 n n PG N3B ANP sing 16 n n O2G HOG2 ANP sing 17 n n O3G HOG3 ANP sing 18 n n PB O1B ANP doub 19 n n PB O2B ANP sing 20 n n PB N3B ANP sing 21 n n PB O3A ANP sing 22 n n O2B HOB2 ANP sing 23 n n N3B HNB1 ANP sing 24 n n PA O1A ANP doub 25 n n PA O2A ANP sing 26 n n PA O3A ANP sing 27 n n PA O5' ANP sing 28 n n O2A HOA2 ANP sing 29 n n O5' C5' ANP sing 30 n n C5' C4' ANP sing 31 n n C5' "H5'1" ANP sing 32 n n C5' "H5'2" ANP sing 33 n n C4' O4' ANP sing 34 n n C4' C3' ANP sing 35 n n C4' H4' ANP sing 36 n n O4' C1' ANP sing 37 n n C3' O3' ANP sing 38 n n C3' C2' ANP sing 39 n n C3' H3' ANP sing 40 n n O3' HO3' ANP sing 41 n n C2' O2' ANP sing 42 n n C2' C1' ANP sing 43 n n C2' H2' ANP sing 44 n n O2' HO2' ANP sing 45 n n C1' N9 ANP sing 46 n n C1' H1' ANP sing 47 n n N9 C8 ANP sing 48 n y N9 C4 ANP sing 49 n y C8 N7 ANP doub 50 n y C8 H8 ANP sing 51 n n N7 C5 ANP sing 52 n y C5 C6 ANP sing 53 n y C5 C4 ANP doub 54 n y C6 N6 ANP sing 55 n n C6 N1 ANP doub 56 n y N6 HN61 ANP sing 57 n n N6 HN62 ANP sing 58 n n N1 C2 ANP sing 59 n y C2 N3 ANP doub 60 n y C2 H2 ANP sing 61 n n N3 C4 ANP sing 62 n y # _atom_sites.entry_id 2XND _atom_sites.fract_transf_matrix[1][1] 0.006421 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006365 _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] 0.004044 _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 R 7 ANP A 1 600 600 ANP ANP . S 8 MG A 1 601 601 MG MG . T 7 ANP B 1 600 600 ANP ANP . U 8 MG B 1 601 601 MG MG . V 9 GOL B 1 701 701 GOL GOL . W 7 ANP C 1 600 600 ANP ANP . X 8 MG C 1 601 601 MG MG . Y 7 ANP D 1 600 600 ANP ANP . Z 8 MG D 1 601 601 MG MG . AA 10 SO4 E 1 630 630 SO4 SO4 . BA 7 ANP F 1 600 600 ANP ANP . CA 8 MG F 1 601 601 MG MG . # 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 ANP . . . Y 7 50.957 -21.057 58.792 1 68.15 ? PG ANP 600 D 1 HETATM 2 O O1G ANP . . . Y 7 52.282 -20.632 59.571 1 67.51 ? O1G ANP 600 D 1 HETATM 3 O O2G ANP . . . Y 7 51.307 -22.15 57.681 1 66.81 ? O2G ANP 600 D 1 HETATM 4 O O3G ANP . . . Y 7 50.312 -19.783 58.081 1 67.94 ? O3G ANP 600 D 1 HETATM 5 P PB ANP . . . Y 7 48.821 -23.126 59.505 1 64.3 ? PB ANP 600 D 1 HETATM 6 O O1B ANP . . . Y 7 47.578 -22.571 58.694 1 64.13 ? O1B ANP 600 D 1 HETATM 7 O O2B ANP . . . Y 7 49.65 -24.177 58.643 1 63.48 ? O2B ANP 600 D 1 HETATM 8 N N3B ANP . . . Y 7 49.822 -21.755 59.931 1 66.05 ? N3B ANP 600 D 1 HETATM 9 P PA ANP . . . Y 7 48.935 -25.059 61.588 1 63.83 ? PA ANP 600 D 1 HETATM 10 O O1A ANP . . . Y 7 48.567 -26.379 60.8 1 63.96 ? O1A ANP 600 D 1 HETATM 11 O O2A ANP . . . Y 7 50.509 -24.903 61.739 1 63.65 ? O2A ANP 600 D 1 HETATM 12 O O3A ANP . . . Y 7 48.263 -23.786 60.862 1 64.23 ? O3A ANP 600 D 1 HETATM 13 O O5' ANP . . . Y 7 48.212 -25.101 63.019 1 63.53 ? O5' ANP 600 D 1 HETATM 14 C C5' ANP . . . Y 7 48.051 -23.905 63.776 1 63.7 ? C5' ANP 600 D 1 HETATM 15 C C4' ANP . . . Y 7 48.024 -24.199 65.274 1 63.91 ? C4' ANP 600 D 1 HETATM 16 O O4' ANP . . . Y 7 46.689 -24.451 65.732 1 63.82 ? O4' ANP 600 D 1 HETATM 17 C C3' ANP . . . Y 7 48.88 -25.395 65.659 1 63.94 ? C3' ANP 600 D 1 HETATM 18 O O3' ANP . . . Y 7 49.937 -24.965 66.494 1 64.31 ? O3' ANP 600 D 1 HETATM 19 C C2' ANP . . . Y 7 47.957 -26.351 66.388 1 63.62 ? C2' ANP 600 D 1 HETATM 20 O O2' ANP . . . Y 7 48.374 -26.543 67.724 1 63.84 ? O2' ANP 600 D 1 HETATM 21 C C1' ANP . . . Y 7 46.584 -25.706 66.405 1 63.39 ? C1' ANP 600 D 1 HETATM 22 N N9 ANP . . . Y 7 45.663 -26.632 65.704 1 63.1 ? N9 ANP 600 D 1 HETATM 23 C C8 ANP . . . Y 7 45.426 -26.737 64.371 1 63.36 ? C8 ANP 600 D 1 HETATM 24 N N7 ANP . . . Y 7 44.515 -27.72 64.062 1 63.3 ? N7 ANP 600 D 1 HETATM 25 C C5 ANP . . . Y 7 44.156 -28.278 65.228 1 62.89 ? C5 ANP 600 D 1 HETATM 26 C C6 ANP . . . Y 7 43.265 -29.346 65.746 1 62.79 ? C6 ANP 600 D 1 HETATM 27 N N6 ANP . . . Y 7 42.507 -30.093 64.909 1 62.36 ? N6 ANP 600 D 1 HETATM 28 N N1 ANP . . . Y 7 43.216 -29.563 67.084 1 63.16 ? N1 ANP 600 D 1 HETATM 29 C C2 ANP . . . Y 7 43.935 -28.865 67.988 1 63 ? C2 ANP 600 D 1 HETATM 30 N N3 ANP . . . Y 7 44.774 -27.879 67.643 1 62.86 ? N3 ANP 600 D 1 HETATM 31 C C4 ANP . . . Y 7 44.905 -27.563 66.248 1 62.85 ? C4 ANP 600 D 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 48 _model_server_stats.query_time_ms 250 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 31 #