data_5XIP # _model_server_result.job_id AvJeNL24d_64XVb-5sVdFw _model_server_result.datetime_utc '2024-11-28 02:04:13' _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 5xip # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":1001}' # _entry.id 5XIP # _exptl.entry_id 5XIP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' _entity.pdbx_number_of_molecules 4 _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 5XIP _cell.length_a 138.757 _cell.length_b 138.757 _cell.length_c 425.671 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5XIP _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,I,J,Q,R 1 1 C,D,K,L,M,N,O,P,S,T 2 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 ? 2 E N N ? 2 H N N ? 2 K N N ? 2 N 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 E O3G ANP . A ANP 1001 1_555 F MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc2 E O1B ANP . A ANP 1001 1_555 F MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.874 ? metalc ? metalc3 F MG MG . A MG 1002 1_555 Q O HOH . A HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc4 F MG MG . A MG 1002 1_555 Q O HOH . A HOH 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc5 F MG MG . A MG 1002 1_555 Q O HOH . A HOH 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.767 ? metalc ? metalc6 F MG MG . A MG 1002 1_555 Q O HOH . A HOH 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.91 ? metalc ? metalc7 H O1G ANP . B ANP 1001 1_555 I MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? metalc ? metalc8 H O2G ANP . B ANP 1001 1_555 I MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? metalc ? metalc9 H O2B ANP . B ANP 1001 1_555 I MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? metalc ? metalc10 I MG MG . B MG 1002 1_555 R O HOH . B HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? metalc ? metalc11 I MG MG . B MG 1002 1_555 R O HOH . B HOH 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? metalc ? metalc12 I MG MG . B MG 1002 1_555 R O HOH . B HOH 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.852 ? metalc ? metalc13 I MG MG . B MG 1002 1_555 R O HOH . B HOH 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.849 ? metalc ? metalc14 K O1G ANP . C ANP 1001 1_555 L MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.835 ? metalc ? metalc15 K O1B ANP . C ANP 1001 1_555 L MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.809 ? metalc ? metalc16 L MG MG . C MG 1002 1_555 S O HOH . C HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.77 ? metalc ? metalc17 L MG MG . C MG 1002 1_555 S O HOH . C HOH 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.825 ? metalc ? metalc18 L MG MG . C MG 1002 1_555 S O HOH . C HOH 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.77 ? metalc ? metalc19 L MG MG . C MG 1002 1_555 S O HOH . C HOH 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? metalc ? metalc20 N O2G ANP . D ANP 1001 1_555 O MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.778 ? metalc ? metalc21 N O2B ANP . D ANP 1001 1_555 O MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc22 O MG MG . D MG 1002 1_555 T O HOH . D HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.894 ? metalc ? metalc23 O MG MG . D MG 1002 1_555 T O HOH . D HOH 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc24 O MG MG . D MG 1002 1_555 T O HOH . D HOH 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? metalc ? metalc25 O MG MG . D MG 1002 1_555 T O HOH . D HOH 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.808 ? # _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 5XIP _atom_sites.fract_transf_matrix[1][1] 0.007207 _atom_sites.fract_transf_matrix[1][2] 0.004161 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008322 _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] 0.002349 _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 2 ANP A 1 1001 1001 ANP ANP . F 3 MG A 1 1002 1051 MG MG . G 4 HFG A 1 1003 1101 HFG HFG . H 2 ANP B 1 1001 1001 ANP ANP . I 3 MG B 1 1002 1051 MG MG . J 4 HFG B 1 1003 1101 HFG HFG . K 2 ANP C 1 1001 1001 ANP ANP . L 3 MG C 1 1002 1051 MG MG . M 4 HFG C 1 1003 1101 HFG HFG . N 2 ANP D 1 1001 1001 ANP ANP . O 3 MG D 1 1002 1051 MG MG . P 4 HFG D 1 1003 1101 HFG HFG . Q 5 HOH A 1 1101 3 HOH HOH . Q 5 HOH A 2 1102 1 HOH HOH . Q 5 HOH A 3 1103 2 HOH HOH . Q 5 HOH A 4 1104 4 HOH HOH . R 5 HOH B 1 1101 5 HOH HOH . R 5 HOH B 2 1102 7 HOH HOH . R 5 HOH B 3 1103 8 HOH HOH . R 5 HOH B 4 1104 6 HOH HOH . S 5 HOH C 1 1101 10 HOH HOH . S 5 HOH C 2 1102 12 HOH HOH . S 5 HOH C 3 1103 11 HOH HOH . S 5 HOH C 4 1104 9 HOH HOH . T 5 HOH D 1 1101 14 HOH HOH . T 5 HOH D 2 1102 13 HOH HOH . T 5 HOH D 3 1103 16 HOH HOH . T 5 HOH D 4 1104 15 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 . . . H 2 -34.791 171.531 4.458 1 26.74 ? PG ANP 1001 B 1 HETATM 2 O O1G ANP . . . H 2 -33.362 171.5 3.837 1 26.68 ? O1G ANP 1001 B 1 HETATM 3 O O2G ANP . . . H 2 -34.627 171.002 5.915 1 26.35 ? O2G ANP 1001 B 1 HETATM 4 O O3G ANP . . . H 2 -35.357 172.876 4.435 1 27 ? O3G ANP 1001 B 1 HETATM 5 P PB ANP . . . H 2 -35.349 169.035 3.845 1 27.08 ? PB ANP 1001 B 1 HETATM 6 O O1B ANP . . . H 2 -35.433 168.207 2.677 1 26.47 ? O1B ANP 1001 B 1 HETATM 7 O O2B ANP . . . H 2 -34.019 168.846 4.588 1 26.96 ? O2B ANP 1001 B 1 HETATM 8 N N3B ANP . . . H 2 -35.783 170.557 3.621 1 26.26 ? N3B ANP 1001 B 1 HETATM 9 P PA ANP . . . H 2 -37.597 167.418 4.567 1 26.04 ? PA ANP 1001 B 1 HETATM 10 O O1A ANP . . . H 2 -38.313 167.778 3.323 1 24.33 ? O1A ANP 1001 B 1 HETATM 11 O O2A ANP . . . H 2 -37.005 166.067 4.687 1 28.05 ? O2A ANP 1001 B 1 HETATM 12 O O3A ANP . . . H 2 -36.465 168.493 4.83 1 26.24 ? O3A ANP 1001 B 1 HETATM 13 O O5' ANP . . . H 2 -38.579 167.656 5.807 1 24.79 ? O5' ANP 1001 B 1 HETATM 14 C C5' ANP . . . H 2 -39.978 167.626 5.585 1 22.78 ? C5' ANP 1001 B 1 HETATM 15 C C4' ANP . . . H 2 -40.592 168.911 6.068 1 20.99 ? C4' ANP 1001 B 1 HETATM 16 O O4' ANP . . . H 2 -40.266 168.953 7.474 1 19.05 ? O4' ANP 1001 B 1 HETATM 17 C C3' ANP . . . H 2 -39.912 170.122 5.435 1 20.65 ? C3' ANP 1001 B 1 HETATM 18 O O3' ANP . . . H 2 -40.607 170.516 4.239 1 20.79 ? O3' ANP 1001 B 1 HETATM 19 C C2' ANP . . . H 2 -40.06 171.12 6.525 1 20.03 ? C2' ANP 1001 B 1 HETATM 20 O O2' ANP . . . H 2 -41.372 171.712 6.517 1 20.67 ? O2' ANP 1001 B 1 HETATM 21 C C1' ANP . . . H 2 -39.911 170.307 7.801 1 18.67 ? C1' ANP 1001 B 1 HETATM 22 N N9 ANP . . . H 2 -38.554 170.381 8.408 1 17.2 ? N9 ANP 1001 B 1 HETATM 23 C C8 ANP . . . H 2 -37.364 170.04 7.818 1 16.79 ? C8 ANP 1001 B 1 HETATM 24 N N7 ANP . . . H 2 -36.303 170.211 8.604 1 15.79 ? N7 ANP 1001 B 1 HETATM 25 C C5 ANP . . . H 2 -36.849 170.696 9.786 1 15.46 ? C5 ANP 1001 B 1 HETATM 26 C C6 ANP . . . H 2 -36.259 171.077 11.014 1 15.7 ? C6 ANP 1001 B 1 HETATM 27 N N6 ANP . . . H 2 -34.948 171.015 11.23 1 15.85 ? N6 ANP 1001 B 1 HETATM 28 N N1 ANP . . . H 2 -37.055 171.52 12.004 1 15.61 ? N1 ANP 1001 B 1 HETATM 29 C C2 ANP . . . H 2 -38.37 171.582 11.787 1 15.43 ? C2 ANP 1001 B 1 HETATM 30 N N3 ANP . . . H 2 -39.026 171.249 10.671 1 14.99 ? N3 ANP 1001 B 1 HETATM 31 C C4 ANP . . . H 2 -38.232 170.805 9.677 1 15.83 ? C4 ANP 1001 B 1 # _model_server_stats.io_time_ms 73 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #