data_1S26 # _model_server_result.job_id x7HP703Ej1y0_KbqLqPz-w _model_server_result.datetime_utc '2024-11-04 22:15:12' _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 1s26 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":3139}' # _entry.id 1S26 # _exptl.entry_id 1S26 _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 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' _entity.pdbx_number_of_molecules 3 _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 1S26 _cell.length_a 117.555 _cell.length_b 167.605 _cell.length_c 345.346 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1S26 _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 2 2 2' # 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 PISA dimeric 2 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,G,H,M,N 1 1 B,E,I,J,O,P 2 1 C,F,K,L,Q,R 3 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 ? 4 H N N ? 4 J N N ? 4 L 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 OD1 ASP 201 A ASP 491 1_555 G YB YB . A YB 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.281 ? metalc ? metalc2 A OD2 ASP 201 A ASP 491 1_555 G YB YB . A YB 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.916 ? metalc ? metalc3 A OD1 ASP 203 A ASP 493 1_555 G YB YB . A YB 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? metalc ? metalc4 A OD2 ASP 203 A ASP 493 1_555 G YB YB . A YB 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.876 ? metalc ? metalc5 A NE2 HIS 287 A HIS 577 1_555 G YB YB . A YB 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.025 ? metalc ? metalc6 G YB YB . A YB 901 1_555 H O1A APC . A APC 1139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.424 ? metalc ? metalc7 G YB YB . A YB 901 1_555 H O2B APC . A APC 1139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.228 ? metalc ? metalc8 B OD1 ASP 201 B ASP 491 1_555 I YB YB . B YB 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.611 ? metalc ? metalc9 B OD2 ASP 201 B ASP 491 1_555 I YB YB . B YB 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.443 ? metalc ? metalc10 B OD1 ASP 203 B ASP 493 1_555 I YB YB . B YB 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? metalc ? metalc11 B OD2 ASP 203 B ASP 493 1_555 I YB YB . B YB 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc12 C OD1 ASP 201 C ASP 491 1_555 K YB YB . C YB 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.046 ? metalc ? metalc13 C OD2 ASP 201 C ASP 491 1_555 K YB YB . C YB 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.805 ? metalc ? metalc14 C OD1 ASP 203 C ASP 493 1_555 K YB YB . C YB 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc15 C OD2 ASP 203 C ASP 493 1_555 K YB YB . C YB 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.014 ? metalc ? metalc16 C NE2 HIS 287 C HIS 577 1_555 K YB YB . C YB 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.091 ? metalc ? metalc17 D OD1 ASP 93 D ASP 93 1_555 N CA CA . D CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.621 ? metalc ? metalc18 D OD1 ASP 95 D ASP 95 1_555 N CA CA . D CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? metalc ? metalc19 D OD1 ASN 97 D ASN 97 1_555 N CA CA . D CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc20 D O TYR 99 D TYR 99 1_555 N CA CA . D CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc21 D OE1 GLU 104 D GLU 104 1_555 N CA CA . D CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? metalc ? metalc22 D OE2 GLU 104 D GLU 104 1_555 N CA CA . D CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.65 ? metalc ? metalc23 D OD1 ASP 131 D ASP 131 1_555 M CA CA . D CA 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc24 D OD1 ASP 133 D ASP 133 1_555 M CA CA . D CA 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.856 ? metalc ? metalc25 D O GLN 135 D GLN 135 1_555 M CA CA . D CA 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc26 D OE1 GLU 140 D GLU 140 1_555 M CA CA . D CA 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.682 ? metalc ? metalc27 D OE2 GLU 140 D GLU 140 1_555 M CA CA . D CA 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc28 E OD1 ASP 93 E ASP 93 1_555 P CA CA . E CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.636 ? metalc ? metalc29 E OD1 ASP 95 E ASP 95 1_555 P CA CA . E CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? metalc ? metalc30 E OD1 ASN 97 E ASN 97 1_555 P CA CA . E CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc31 E O TYR 99 E TYR 99 1_555 P CA CA . E CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc32 E OE1 GLU 104 E GLU 104 1_555 P CA CA . E CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc33 E OE2 GLU 104 E GLU 104 1_555 P CA CA . E CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.586 ? metalc ? metalc34 E OD1 ASP 131 E ASP 131 1_555 O CA CA . E CA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.631 ? metalc ? metalc35 E OD1 ASP 133 E ASP 133 1_555 O CA CA . E CA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc36 E O GLN 135 E GLN 135 1_555 O CA CA . E CA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.909 ? metalc ? metalc37 E OE1 GLU 140 E GLU 140 1_555 O CA CA . E CA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? metalc ? metalc38 E OE2 GLU 140 E GLU 140 1_555 O CA CA . E CA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.49 ? metalc ? metalc39 F OD1 ASP 93 F ASP 93 1_555 R CA CA . F CA 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? metalc ? metalc40 F OD1 ASP 95 F ASP 95 1_555 R CA CA . F CA 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? metalc ? metalc41 F OD1 ASN 97 F ASN 97 1_555 R CA CA . F CA 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? metalc ? metalc42 F O TYR 99 F TYR 99 1_555 R CA CA . F CA 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc43 F OE1 GLU 104 F GLU 104 1_555 R CA CA . F CA 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.404 ? metalc ? metalc44 F OE2 GLU 104 F GLU 104 1_555 R CA CA . F CA 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.777 ? metalc ? metalc45 F OD1 ASP 131 F ASP 131 1_555 Q CA CA . F CA 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? metalc ? metalc46 F OD1 ASP 133 F ASP 133 1_555 Q CA CA . F CA 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc47 F O GLN 135 F GLN 135 1_555 Q CA CA . F CA 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc48 F OE1 GLU 140 F GLU 140 1_555 Q CA CA . F CA 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? metalc ? metalc49 F OE2 GLU 140 F GLU 140 1_555 Q CA CA . F CA 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id APC _chem_comp.mon_nstd_flag . _chem_comp.name 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ALPHA,BETA-METHYLENEADENOSINE-5'-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 APC doub 13 n n PG O2G APC sing 14 n n PG O3G APC sing 15 n n PG O3B APC sing 16 n n O2G HOG2 APC sing 17 n n O3G HOG3 APC sing 18 n n PB O1B APC doub 19 n n PB O2B APC sing 20 n n PB O3B APC sing 21 n n PB C3A APC sing 22 n n O2B HOB2 APC sing 23 n n PA O1A APC doub 24 n n PA O2A APC sing 25 n n PA C3A APC sing 26 n n PA O5' APC sing 27 n n O2A HOA2 APC sing 28 n n C3A H3A1 APC sing 29 n n C3A H3A2 APC sing 30 n n O5' C5' APC sing 31 n n C5' C4' APC sing 32 n n C5' "H5'1" APC sing 33 n n C5' "H5'2" APC sing 34 n n C4' O4' APC sing 35 n n C4' C3' APC sing 36 n n C4' H4' APC sing 37 n n O4' C1' APC sing 38 n n C3' O3' APC sing 39 n n C3' C2' APC sing 40 n n C3' H3' APC sing 41 n n O3' HO3' APC sing 42 n n C2' O2' APC sing 43 n n C2' C1' APC sing 44 n n C2' H2' APC sing 45 n n O2' HO2' APC sing 46 n n C1' N9 APC sing 47 n n C1' H1' APC sing 48 n n N9 C8 APC sing 49 n y N9 C4 APC sing 50 n y C8 N7 APC doub 51 n y C8 H8 APC sing 52 n n N7 C5 APC sing 53 n y C5 C6 APC sing 54 n y C5 C4 APC doub 55 n y C6 N6 APC sing 56 n n C6 N1 APC doub 57 n y N6 HN61 APC sing 58 n n N6 HN62 APC sing 59 n n N1 C2 APC sing 60 n y C2 N3 APC doub 61 n y C2 H2 APC sing 62 n n N3 C4 APC sing 63 n y # _atom_sites.entry_id 1S26 _atom_sites.fract_transf_matrix[1][1] 0.008507 _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] 0.005966 _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] 0.002896 _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 3 YB A 1 901 901 YB YB . H 4 APC A 1 1139 1139 APC APC . I 3 YB B 1 902 902 YB YB . J 4 APC B 1 2139 2139 APC APC . K 3 YB C 1 903 903 YB YB . L 4 APC C 1 3139 3139 APC APC . M 5 CA D 1 800 800 CA CA . N 5 CA D 1 801 801 CA CA . O 5 CA E 1 802 802 CA CA . P 5 CA E 1 803 803 CA CA . Q 5 CA F 1 804 804 CA CA . R 5 CA F 1 805 805 CA CA . # 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 APC . . . L 4 2.924 56.313 61.416 1 65.08 ? PG APC 3139 C 1 HETATM 2 O O1G APC . . . L 4 2.27 57.399 62.187 1 66.51 ? O1G APC 3139 C 1 HETATM 3 O O2G APC . . . L 4 2.971 56.633 59.988 1 68.87 ? O2G APC 3139 C 1 HETATM 4 O O3G APC . . . L 4 2.088 54.982 61.571 1 70.97 ? O3G APC 3139 C 1 HETATM 5 P PB APC . . . L 4 5.034 54.876 62.762 1 86.75 ? PB APC 3139 C 1 HETATM 6 O O1B APC . . . L 4 6.458 55.192 63.142 1 87.95 ? O1B APC 3139 C 1 HETATM 7 O O2B APC . . . L 4 4.237 54.563 63.982 1 84.7 ? O2B APC 3139 C 1 HETATM 8 O O3B APC . . . L 4 4.395 56.126 61.959 1 76.19 ? O3B APC 3139 C 1 HETATM 9 P PA APC . . . L 4 6.267 52.18 61.572 1 96.85 ? PA APC 3139 C 1 HETATM 10 O O1A APC . . . L 4 5.62 50.848 61.804 1 96.7 ? O1A APC 3139 C 1 HETATM 11 O O2A APC . . . L 4 6.846 52.164 60.172 1 97.57 ? O2A APC 3139 C 1 HETATM 12 C C3A APC . . . L 4 5.006 53.474 61.618 1 90.98 ? C3A APC 3139 C 1 HETATM 13 O O5' APC . . . L 4 7.421 52.41 62.673 1 98.98 ? O5' APC 3139 C 1 HETATM 14 C C5' APC . . . L 4 8.777 52.31 62.201 1 105.51 ? C5' APC 3139 C 1 HETATM 15 C C4' APC . . . L 4 9.415 50.988 62.593 1 110.4 ? C4' APC 3139 C 1 HETATM 16 O O4' APC . . . L 4 9.53 50.2 61.36 1 112.98 ? O4' APC 3139 C 1 HETATM 17 C C3' APC . . . L 4 10.833 51.115 63.176 1 112.48 ? C3' APC 3139 C 1 HETATM 18 O O3' APC . . . L 4 10.918 50.63 64.547 1 112.88 ? O3' APC 3139 C 1 HETATM 19 C C2' APC . . . L 4 11.745 50.402 62.147 1 113.4 ? C2' APC 3139 C 1 HETATM 20 O O2' APC . . . L 4 12.518 49.342 62.729 1 112.45 ? O2' APC 3139 C 1 HETATM 21 C C1' APC . . . L 4 10.84 49.824 61.071 1 114.98 ? C1' APC 3139 C 1 HETATM 22 N N9 APC . . . L 4 11.122 50.242 59.657 1 117.14 ? N9 APC 3139 C 1 HETATM 23 C C8 APC . . . L 4 10.836 51.47 59.068 1 117.95 ? C8 APC 3139 C 1 HETATM 24 N N7 APC . . . L 4 11.194 51.566 57.795 1 118.98 ? N7 APC 3139 C 1 HETATM 25 C C5 APC . . . L 4 11.768 50.312 57.486 1 118.73 ? C5 APC 3139 C 1 HETATM 26 C C6 APC . . . L 4 12.347 49.781 56.263 1 118.38 ? C6 APC 3139 C 1 HETATM 27 N N6 APC . . . L 4 12.457 50.36 55.191 1 117.77 ? N6 APC 3139 C 1 HETATM 28 N N1 APC . . . L 4 12.779 48.498 56.447 1 117.79 ? N1 APC 3139 C 1 HETATM 29 C C2 APC . . . L 4 12.712 47.737 57.603 1 117.39 ? C2 APC 3139 C 1 HETATM 30 N N3 APC . . . L 4 12.199 48.192 58.705 1 117.36 ? N3 APC 3139 C 1 HETATM 31 C C4 APC . . . L 4 11.732 49.485 58.621 1 118.07 ? C4 APC 3139 C 1 # _model_server_stats.io_time_ms 32 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 56 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #