data_6WB5 # _model_server_result.job_id cytXoduj6ci9sai4FCmDfg _model_server_result.datetime_utc '2024-11-09 23:17:45' _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 6wb5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":302}' # _entry.id 6WB5 # _exptl.entry_id 6WB5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _entity.id 3 _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 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 6WB5 _cell.length_a 86.551 _cell.length_b 86.551 _cell.length_c 164.334 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6WB5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _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 _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 ? 3 E N N ? 3 G N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 GLC GLC C1 O1 . O4 HO4 . sing 2 ? 2 3 2 AC1 GLC C1 O1 . O4 HO4 . 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 2 n C GLC 1 C 1 GLC A 301 ACR 2 n C GLC 2 C 2 GLC A 301 ACR 2 n C AC1 3 C 3 AC1 A 301 ACR 2 n D GLC 1 D 1 GLC B 301 ACR 2 n D GLC 2 D 2 GLC B 301 ACR 2 n D AC1 3 D 3 AC1 B 301 ACR # 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 C O4 GLC . C GLC 1 1_555 C C1 GLC . C GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 sing covale ? covale2 C O4 GLC . C GLC 2 1_555 C C1 AC1 . C AC1 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 sing covale ? covale3 D O4 GLC . D GLC 1 1_555 D C1 GLC . D GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 sing covale ? covale4 D O4 GLC . D GLC 2 1_555 D C1 AC1 . D AC1 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 sing metalc ? metalc1 A ND1 HIS 182 A HIS 162 1_555 F MN MN . A MN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc2 E PG ANP . A ANP 302 1_555 F MN MN . A MN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? metalc ? metalc3 E O2G ANP . A ANP 302 1_555 F MN MN . A MN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc4 E O3G ANP . A ANP 302 1_555 F MN MN . A MN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? metalc ? metalc5 E O2B ANP . A ANP 302 1_555 F MN MN . A MN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.438 ? metalc ? metalc6 B ND1 HIS 182 B HIS 162 1_555 H MN MN . B MN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc7 G O2G ANP . B ANP 302 1_555 H MN MN . B MN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc8 G O2B ANP . B ANP 302 1_555 H MN MN . B MN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? # _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 59 n n PG O2G ANP sing 60 n n PG O3G ANP sing 61 n n PG N3B ANP sing 62 n n O2G HOG2 ANP sing 63 n n O3G HOG3 ANP sing 64 n n PB O1B ANP doub 65 n n PB O2B ANP sing 66 n n PB N3B ANP sing 67 n n PB O3A ANP sing 68 n n O2B HOB2 ANP sing 69 n n N3B HNB1 ANP sing 70 n n PA O1A ANP doub 71 n n PA O2A ANP sing 72 n n PA O3A ANP sing 73 n n PA O5' ANP sing 74 n n O2A HOA2 ANP sing 75 n n O5' C5' ANP sing 76 n n C5' C4' ANP sing 77 n n C5' "H5'1" ANP sing 78 n n C5' "H5'2" ANP sing 79 n n C4' O4' ANP sing 80 n n C4' C3' ANP sing 81 n n C4' H4' ANP sing 82 n n O4' C1' ANP sing 83 n n C3' O3' ANP sing 84 n n C3' C2' ANP sing 85 n n C3' H3' ANP sing 86 n n O3' HO3' ANP sing 87 n n C2' O2' ANP sing 88 n n C2' C1' ANP sing 89 n n C2' H2' ANP sing 90 n n O2' HO2' ANP sing 91 n n C1' N9 ANP sing 92 n n C1' H1' ANP sing 93 n n N9 C8 ANP sing 94 n y N9 C4 ANP sing 95 n y C8 N7 ANP doub 96 n y C8 H8 ANP sing 97 n n N7 C5 ANP sing 98 n y C5 C6 ANP sing 99 n y C5 C4 ANP doub 100 n y C6 N6 ANP sing 101 n n C6 N1 ANP doub 102 n y N6 HN61 ANP sing 103 n n N6 HN62 ANP sing 104 n n N1 C2 ANP sing 105 n y C2 N3 ANP doub 106 n y C2 H2 ANP sing 107 n n N3 C4 ANP sing 108 n y # _atom_sites.entry_id 6WB5 _atom_sites.fract_transf_matrix[1][1] 0.011554 _atom_sites.fract_transf_matrix[1][2] 0.006671 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013341 _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] 0.006085 _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 E 3 ANP A 1 302 401 ANP ANP . F 4 MN A 1 303 402 MN MN . G 3 ANP B 1 302 401 ANP ANP . H 4 MN B 1 303 402 MN MN . # 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 . . . E 3 20.575 41.444 9.118 1 260.5 ? PG ANP 302 A 1 HETATM 2 O O1G ANP . . . E 3 20.04 40.784 10.349 1 258.48 ? O1G ANP 302 A 1 HETATM 3 O O2G ANP . . . E 3 22.152 41.382 9.135 1 219.52 ? O2G ANP 302 A 1 HETATM 4 O O3G ANP . . . E 3 20.029 40.699 7.833 1 92.05 ? O3G ANP 302 A 1 HETATM 5 P PB ANP . . . E 3 21.037 43.924 8.011 1 187.54 ? PB ANP 302 A 1 HETATM 6 O O1B ANP . . . E 3 21.979 44.797 8.774 1 188.68 ? O1B ANP 302 A 1 HETATM 7 O O2B ANP . . . E 3 21.843 42.946 7.106 1 156.34 ? O2B ANP 302 A 1 HETATM 8 N N3B ANP . . . E 3 20.071 43.059 9.071 1 52.8 ? N3B ANP 302 A 1 HETATM 9 P PA ANP . . . E 3 20.048 46.354 7.414 1 112.26 ? PA ANP 302 A 1 HETATM 10 O O1A ANP . . . E 3 20.999 47.063 6.527 1 112.77 ? O1A ANP 302 A 1 HETATM 11 O O2A ANP . . . E 3 20.288 46.54 8.917 1 111.66 ? O2A ANP 302 A 1 HETATM 12 O O3A ANP . . . E 3 20.116 44.805 7.126 1 133.43 ? O3A ANP 302 A 1 HETATM 13 O O5' ANP . . . E 3 18.577 46.769 7.011 1 70.24 ? O5' ANP 302 A 1 HETATM 14 C C5' ANP . . . E 3 17.724 45.905 6.228 1 72.36 ? C5' ANP 302 A 1 HETATM 15 C C4' ANP . . . E 3 16.823 46.758 5.367 1 76.52 ? C4' ANP 302 A 1 HETATM 16 O O4' ANP . . . E 3 15.714 47.246 6.155 1 77.39 ? O4' ANP 302 A 1 HETATM 17 C C3' ANP . . . E 3 17.477 48.003 4.78 1 72.66 ? C3' ANP 302 A 1 HETATM 18 O O3' ANP . . . E 3 18.139 47.712 3.554 1 73.28 ? O3' ANP 302 A 1 HETATM 19 C C2' ANP . . . E 3 16.285 48.942 4.598 1 64.81 ? C2' ANP 302 A 1 HETATM 20 O O2' ANP . . . E 3 15.585 48.678 3.389 1 63.35 ? O2' ANP 302 A 1 HETATM 21 C C1' ANP . . . E 3 15.421 48.589 5.813 1 72.63 ? C1' ANP 302 A 1 HETATM 22 N N9 ANP . . . E 3 15.681 49.433 6.977 1 76.69 ? N9 ANP 302 A 1 HETATM 23 C C8 ANP . . . E 3 16.608 49.218 7.963 1 74.21 ? C8 ANP 302 A 1 HETATM 24 N N7 ANP . . . E 3 16.632 50.151 8.884 1 82.29 ? N7 ANP 302 A 1 HETATM 25 C C5 ANP . . . E 3 15.657 51.047 8.473 1 87.61 ? C5 ANP 302 A 1 HETATM 26 C C6 ANP . . . E 3 15.187 52.257 9.018 1 87.61 ? C6 ANP 302 A 1 HETATM 27 N N6 ANP . . . E 3 15.66 52.796 10.145 1 96.26 ? N6 ANP 302 A 1 HETATM 28 N N1 ANP . . . E 3 14.199 52.904 8.358 1 75.88 ? N1 ANP 302 A 1 HETATM 29 C C2 ANP . . . E 3 13.721 52.368 7.231 1 76.8 ? C2 ANP 302 A 1 HETATM 30 N N3 ANP . . . E 3 14.084 51.235 6.623 1 84.84 ? N3 ANP 302 A 1 HETATM 31 C C4 ANP . . . E 3 15.062 50.617 7.297 1 85.66 ? C4 ANP 302 A 1 # _model_server_stats.io_time_ms 79 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 31 #