data_4CYU # _model_server_result.job_id Go3m6IXnc4rPzM9rIhChWQ _model_server_result.datetime_utc '2024-11-05 07:54:18' _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 4cyu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":1158}' # _entry.id 4CYU # _exptl.entry_id 4CYU _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 112.44 _cell.angle_gamma 90 _cell.entry_id 4CYU _cell.length_a 62.002 _cell.length_b 94.263 _cell.length_c 62.989 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4CYU _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 PISA monomeric 1 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,F,G,H,S 1 1 B,I,J,K,L,T 2 1 C,M,N,O,U 3 1 D,P,Q,R,V 4 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 G N N ? 4 K N N ? 4 O N N ? 4 R 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 disulf ? disulf1 B SG CYS 83 B CYS 80 1_555 D SG CYS 83 D CYS 80 2_746 ? ? ? ? ? ? ? ? ? ? ? ? 1.961 ? metalc ? metalc1 A OD1 ASP 98 A ASP 95 1_555 E MG MG . A MG 170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? metalc ? metalc2 A OD2 ASP 98 A ASP 95 1_555 F MG MG . A MG 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc3 A OD1 ASP 100 A ASP 97 1_555 E MG MG . A MG 170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc4 A OD2 ASP 100 A ASP 97 1_555 F MG MG . A MG 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc5 E MG MG . A MG 170 1_555 G O1A APC . A APC 1158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? metalc ? metalc6 E MG MG . A MG 170 1_555 G O1B APC . A APC 1158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc7 E MG MG . A MG 170 1_555 S O HOH . A HOH 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc8 F MG MG . A MG 171 1_555 G O1B APC . A APC 1158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? metalc ? metalc9 F MG MG . A MG 171 1_555 G O1G APC . A APC 1158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc10 B OE2 GLU 81 B GLU 78 1_555 I MG MG . B MG 170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.82 ? metalc ? metalc11 B OD1 ASP 98 B ASP 95 1_555 I MG MG . B MG 170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc12 B OD2 ASP 98 B ASP 95 1_555 J MG MG . B MG 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc13 B OD1 ASP 100 B ASP 97 1_555 I MG MG . B MG 170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? metalc ? metalc14 B OD2 ASP 100 B ASP 97 1_555 J MG MG . B MG 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc15 I MG MG . B MG 170 1_555 K O1A APC . B APC 1159 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.302 ? metalc ? metalc16 I MG MG . B MG 170 1_555 K O1A APC . B APC 1159 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.603 ? metalc ? metalc17 I MG MG . B MG 170 1_555 T O HOH . B HOH 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc18 J MG MG . B MG 171 1_555 K O1B APC . B APC 1159 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.813 ? metalc ? metalc19 J MG MG . B MG 171 1_555 K O2B APC . B APC 1159 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.641 ? metalc ? metalc20 J MG MG . B MG 171 1_555 K O1B APC . B APC 1159 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.47 ? metalc ? metalc21 J MG MG . B MG 171 1_555 K O1G APC . B APC 1159 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.858 ? metalc ? metalc22 C OD1 ASP 98 C ASP 95 1_555 M MG MG . C MG 170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc23 C OD2 ASP 98 C ASP 95 1_555 N MG MG . C MG 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc24 C OD1 ASP 100 C ASP 97 1_555 M MG MG . C MG 170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc25 C OD2 ASP 100 C ASP 97 1_555 N MG MG . C MG 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc26 M MG MG . C MG 170 1_555 O O1B APC . C APC 1158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? metalc ? metalc27 M MG MG . C MG 170 1_555 O O1A APC . C APC 1158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.93 ? metalc ? metalc28 M MG MG . C MG 170 1_555 U O HOH . C HOH 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc29 M MG MG . C MG 170 1_555 U O HOH . C HOH 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc30 N MG MG . C MG 171 1_555 O O1G APC . C APC 1158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? metalc ? metalc31 N MG MG . C MG 171 1_555 O O1B APC . C APC 1158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.535 ? metalc ? metalc32 D OD1 ASP 98 D ASP 95 1_555 P MG MG . D MG 170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? metalc ? metalc33 D OD2 ASP 98 D ASP 95 1_555 Q MG MG . D MG 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? metalc ? metalc34 D OD1 ASP 100 D ASP 97 1_555 P MG MG . D MG 170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? metalc ? metalc35 D OD2 ASP 100 D ASP 97 1_555 Q MG MG . D MG 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? metalc ? metalc36 P MG MG . D MG 170 1_555 R O1B APC . D APC 1158 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.207 ? metalc ? metalc37 P MG MG . D MG 170 1_555 R O1A APC . D APC 1158 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.074 ? metalc ? metalc38 P MG MG . D MG 170 1_555 R O2B APC . D APC 1158 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.438 ? metalc ? metalc39 P MG MG . D MG 170 1_555 R O1A APC . D APC 1158 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.877 ? metalc ? metalc40 P MG MG . D MG 170 1_555 V O HOH . D HOH 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc41 Q MG MG . D MG 171 1_555 R O1G APC . D APC 1158 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.841 ? metalc ? metalc42 Q MG MG . D MG 171 1_555 R O1B APC . D APC 1158 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.418 ? metalc ? metalc43 Q MG MG . D MG 171 1_555 R O2B APC . D APC 1158 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.393 ? metalc ? metalc44 Q MG MG . D MG 171 1_555 R O1B APC . D APC 1158 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.848 ? # _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 4CYU _atom_sites.fract_transf_matrix[1][1] 0.016129 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.006661 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010609 _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] 0.017176 _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 MG A 1 170 170 MG MG . F 3 MG A 1 171 171 MG MG . G 4 APC A 1 1158 1158 APC APC . H 5 TRS A 1 1159 1159 TRS TRS . I 3 MG B 1 170 170 MG MG . J 3 MG B 1 171 171 MG MG . K 4 APC B 1 1159 1159 APC APC . L 5 TRS B 1 1160 1160 TRS TRS . M 3 MG C 1 170 170 MG MG . N 3 MG C 1 171 171 MG MG . O 4 APC C 1 1158 1158 APC APC . P 3 MG D 1 170 170 MG MG . Q 3 MG D 1 171 171 MG MG . R 4 APC D 1 1158 1158 APC APC . S 6 HOH A 1 2001 2001 HOH HOH . S 6 HOH A 2 2002 2002 HOH HOH . S 6 HOH A 3 2003 2003 HOH HOH . S 6 HOH A 4 2004 2004 HOH HOH . S 6 HOH A 5 2005 2005 HOH HOH . T 6 HOH B 1 2001 2001 HOH HOH . T 6 HOH B 2 2002 2002 HOH HOH . T 6 HOH B 3 2003 2003 HOH HOH . U 6 HOH C 1 2001 2001 HOH HOH . U 6 HOH C 2 2002 2002 HOH HOH . U 6 HOH C 3 2003 2003 HOH HOH . V 6 HOH D 1 2001 2001 HOH HOH . V 6 HOH D 2 2002 2002 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 APC . . . O 4 81.128 -1.605 34.128 1 44.56 ? PG APC 1158 C 1 HETATM 2 O O1G APC . . . O 4 80.506 -2.015 32.808 1 48.6 ? O1G APC 1158 C 1 HETATM 3 O O2G APC . . . O 4 81.632 -2.718 34.974 1 41.61 ? O2G APC 1158 C 1 HETATM 4 O O3G APC . . . O 4 82.066 -0.417 34.086 1 42.05 ? O3G APC 1158 C 1 HETATM 5 P PB APC . . . O 4 78.907 0.131 34.415 1 43.16 ? PB APC 1158 C 1 HETATM 6 O O1B APC . . . O 4 78.803 0.113 32.919 1 40.13 ? O1B APC 1158 C 1 HETATM 7 O O2B APC . . . O 4 77.488 -0.017 35.121 1 42.88 ? O2B APC 1158 C 1 HETATM 8 O O3B APC . . . O 4 79.854 -1.065 34.935 1 45.29 ? O3B APC 1158 C 1 HETATM 9 P PA APC . . . O 4 78.125 2.835 34.712 1 40.21 ? PA APC 1158 C 1 HETATM 10 O O1A APC . . . O 4 77.431 2.45 33.472 1 35.54 ? O1A APC 1158 C 1 HETATM 11 O O2A APC . . . O 4 77.099 3.07 35.921 1 42.94 ? O2A APC 1158 C 1 HETATM 12 C C3A APC . . . O 4 79.445 1.675 35.115 1 39.97 ? C3A APC 1158 C 1 HETATM 13 O O5' APC . . . O 4 78.915 4.208 34.533 1 43.75 ? O5' APC 1158 C 1 HETATM 14 C C5' APC . . . O 4 79.408 4.906 35.676 1 43.78 ? C5' APC 1158 C 1 HETATM 15 C C4' APC . . . O 4 80.471 5.914 35.26 1 44.04 ? C4' APC 1158 C 1 HETATM 16 O O4' APC . . . O 4 81.685 5.245 34.88 1 46.54 ? O4' APC 1158 C 1 HETATM 17 C C3' APC . . . O 4 80.087 6.749 34.047 1 45 ? C3' APC 1158 C 1 HETATM 18 O O3' APC . . . O 4 79.443 7.954 34.438 1 45.78 ? O3' APC 1158 C 1 HETATM 19 C C2' APC . . . O 4 81.388 7.006 33.308 1 44.28 ? C2' APC 1158 C 1 HETATM 20 O O2' APC . . . O 4 81.79 8.365 33.412 1 40.86 ? O2' APC 1158 C 1 HETATM 21 C C1' APC . . . O 4 82.411 6.1 33.986 1 45.75 ? C1' APC 1158 C 1 HETATM 22 N N9 APC . . . O 4 83.254 5.346 33.025 1 48.38 ? N9 APC 1158 C 1 HETATM 23 C C8 APC . . . O 4 84.535 5.007 33.27 1 51.53 ? C8 APC 1158 C 1 HETATM 24 N N7 APC . . . O 4 85.085 4.338 32.231 1 50.91 ? N7 APC 1158 C 1 HETATM 25 C C5 APC . . . O 4 84.133 4.248 31.278 1 53.42 ? C5 APC 1158 C 1 HETATM 26 C C6 APC . . . O 4 84.028 3.667 29.912 1 52.06 ? C6 APC 1158 C 1 HETATM 27 N N6 APC . . . O 4 85.067 3.023 29.34 1 49.78 ? N6 APC 1158 C 1 HETATM 28 N N1 APC . . . O 4 82.852 3.776 29.26 1 53.06 ? N1 APC 1158 C 1 HETATM 29 C C2 APC . . . O 4 81.799 4.4 29.813 1 52.6 ? C2 APC 1158 C 1 HETATM 30 N N3 APC . . . O 4 81.828 4.94 31.037 1 50.06 ? N3 APC 1158 C 1 HETATM 31 C C4 APC . . . O 4 82.932 4.904 31.811 1 49.97 ? C4 APC 1158 C 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #