data_3PUY # _model_server_result.job_id VwoXHOzsCEqhLz9FS7B3dQ _model_server_result.datetime_utc '2024-11-18 15:35:48' _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 3puy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":2501}' # _entry.id 3PUY # _exptl.entry_id 3PUY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _entity.id 8 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC 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 86.91 _cell.angle_beta 80.87 _cell.angle_gamma 74.32 _cell.entry_id 3PUY _cell.length_a 76.55 _cell.length_b 96.283 _cell.length_c 112.283 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3PUY _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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 _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 ? 8 I N N ? 8 K N N # _pdbx_entity_branch.entity_id 5 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 5 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 GLC _pdbx_entity_branch_link.comp_id_2 GLC _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 5 n F GLC 1 C 1 GLC X 2001 MAL 5 n F GLC 2 C 2 GLC X 2001 MAL # 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 covale ? covale1 F O4 GLC . C GLC 1 1_555 F C1 GLC . C GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 sing metalc ? metalc1 D OG SER 43 A SER 43 1_555 H MG MG . A MG 1501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? metalc ? metalc2 D OE1 GLN 82 A GLN 82 1_555 H MG MG . A MG 1501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc3 M O HOH . A HOH 382 1_555 H MG MG . A MG 1501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.907 ? metalc ? metalc4 M O HOH . A HOH 383 1_555 H MG MG . A MG 1501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.922 ? metalc ? metalc5 H MG MG . A MG 1501 1_555 I O2B ANP . A ANP 2501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc6 H MG MG . A MG 1501 1_555 I O1G ANP . A ANP 2501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc7 E OG SER 43 B SER 43 1_555 J MG MG . B MG 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.981 ? metalc ? metalc8 E OE1 GLN 82 B GLN 82 1_555 J MG MG . B MG 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? metalc ? metalc9 N O HOH . B HOH 382 1_555 J MG MG . B MG 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.915 ? metalc ? metalc10 N O HOH . B HOH 383 1_555 J MG MG . B MG 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.868 ? metalc ? metalc11 J MG MG . B MG 1502 1_555 K O2B ANP . B ANP 2502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc12 J MG MG . B MG 1502 1_555 K O1G ANP . B ANP 2502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? # _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 3PUY _atom_sites.fract_transf_matrix[1][1] 0.013063 _atom_sites.fract_transf_matrix[1][2] -0.003667 _atom_sites.fract_transf_matrix[1][3] -0.002057 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010787 _atom_sites.fract_transf_matrix[2][3] -0.000125 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.009021 _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 G 6 PGV F 1 4001 4001 PGV PGV . H 7 MG A 1 1501 1501 MG MG . I 8 ANP A 1 2501 2501 ANP ANP . J 7 MG B 1 1502 1502 MG MG . K 8 ANP B 1 2502 2502 ANP ANP . L 9 HOH F 1 515 10 HOH HOH . L 9 HOH F 2 516 11 HOH HOH . M 9 HOH A 1 382 1 HOH HOH . M 9 HOH A 2 383 2 HOH HOH . M 9 HOH A 3 384 6 HOH HOH . M 9 HOH A 4 385 7 HOH HOH . M 9 HOH A 5 386 8 HOH HOH . M 9 HOH A 6 387 9 HOH HOH . N 9 HOH B 1 382 3 HOH HOH . N 9 HOH B 2 383 4 HOH HOH . N 9 HOH B 3 384 5 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 ANP . . . I 8 62.448 3.333 7.294 1 52.38 ? PG ANP 2501 A 1 HETATM 2 O O1G ANP . . . I 8 62.606 3.845 8.7 1 52.13 ? O1G ANP 2501 A 1 HETATM 3 O O2G ANP . . . I 8 61.929 4.352 6.324 1 53.52 ? O2G ANP 2501 A 1 HETATM 4 O O3G ANP . . . I 8 63.641 2.576 6.775 1 52.58 ? O3G ANP 2501 A 1 HETATM 5 P PB ANP . . . I 8 60.591 1.364 8.75 1 53.25 ? PB ANP 2501 A 1 HETATM 6 O O1B ANP . . . I 8 60.519 -0.106 8.435 1 53.45 ? O1B ANP 2501 A 1 HETATM 7 O O2B ANP . . . I 8 61.41 1.82 9.931 1 53.66 ? O2B ANP 2501 A 1 HETATM 8 N N3B ANP . . . I 8 61.146 2.177 7.312 1 52.88 ? N3B ANP 2501 A 1 HETATM 9 P PA ANP . . . I 8 58.551 2.062 10.512 1 54.13 ? PA ANP 2501 A 1 HETATM 10 O O1A ANP . . . I 8 59.075 3.367 11.035 1 53.71 ? O1A ANP 2501 A 1 HETATM 11 O O2A ANP . . . I 8 58.789 0.795 11.279 1 54.24 ? O2A ANP 2501 A 1 HETATM 12 O O3A ANP . . . I 8 59.089 1.839 9.024 1 54.07 ? O3A ANP 2501 A 1 HETATM 13 O O5' ANP . . . I 8 56.978 2.228 10.246 1 57.89 ? O5' ANP 2501 A 1 HETATM 14 C C5' ANP . . . I 8 56.295 1.304 9.396 1 61.73 ? C5' ANP 2501 A 1 HETATM 15 C C4' ANP . . . I 8 54.96 1.862 8.908 1 64.86 ? C4' ANP 2501 A 1 HETATM 16 O O4' ANP . . . I 8 54.121 2.272 9.996 1 66.81 ? O4' ANP 2501 A 1 HETATM 17 C C3' ANP . . . I 8 55.158 3.061 8.005 1 65.07 ? C3' ANP 2501 A 1 HETATM 18 O O3' ANP . . . I 8 54.587 2.751 6.735 1 65.62 ? O3' ANP 2501 A 1 HETATM 19 C C2' ANP . . . I 8 54.417 4.201 8.676 1 66.53 ? C2' ANP 2501 A 1 HETATM 20 O O2' ANP . . . I 8 53.592 4.886 7.737 1 67.82 ? O2' ANP 2501 A 1 HETATM 21 C C1' ANP . . . I 8 53.556 3.559 9.751 1 68.23 ? C1' ANP 2501 A 1 HETATM 22 N N9 ANP . . . I 8 53.561 4.359 11.006 1 69.73 ? N9 ANP 2501 A 1 HETATM 23 C C8 ANP . . . I 8 54.65 4.747 11.706 1 69.37 ? C8 ANP 2501 A 1 HETATM 24 N N7 ANP . . . I 8 54.315 5.461 12.813 1 69.95 ? N7 ANP 2501 A 1 HETATM 25 C C5 ANP . . . I 8 52.975 5.534 12.833 1 71.57 ? C5 ANP 2501 A 1 HETATM 26 C C6 ANP . . . I 8 51.963 6.143 13.725 1 73.51 ? C6 ANP 2501 A 1 HETATM 27 N N6 ANP . . . I 8 52.333 6.831 14.836 1 73.61 ? N6 ANP 2501 A 1 HETATM 28 N N1 ANP . . . I 8 50.66 5.991 13.381 1 75.46 ? N1 ANP 2501 A 1 HETATM 29 C C2 ANP . . . I 8 50.276 5.312 12.278 1 75.4 ? C2 ANP 2501 A 1 HETATM 30 N N3 ANP . . . I 8 51.142 4.73 11.429 1 73.56 ? N3 ANP 2501 A 1 HETATM 31 C C4 ANP . . . I 8 52.479 4.808 11.645 1 71.65 ? C4 ANP 2501 A 1 # _model_server_stats.io_time_ms 39 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 31 #