data_4CM0 # _model_server_result.job_id sROflh5lKzbvi8IaeQsO2w _model_server_result.datetime_utc '2024-11-24 14:05:18' _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 4cm0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1468}' # _entry.id 4CM0 # _exptl.entry_id 4CM0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' _entity.pdbx_number_of_molecules 1 _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 4CM0 _cell.length_a 102.19 _cell.length_b 102.19 _cell.length_c 95.26 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4CM0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 3_565 -x+y,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -51.095 88.499136 0 3 'crystal symmetry operation' 2_665 -y+1,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 51.095 88.499136 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 covale ? covale1 A C ALA 252 A ALA 252 1_555 A N CME 253 A CME 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale2 A C CME 253 A CME 253 1_555 A N THR 254 A THR 254 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? metalc ? metalc1 A OD1 ASP 47 A ASP 47 1_555 C CA CA . A CA 1469 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.852 ? metalc ? metalc2 A OD1 ASP 99 A ASP 99 1_555 C CA CA . A CA 1469 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.778 ? metalc ? metalc3 B O1B APC . A APC 1468 1_555 C CA CA . A CA 1469 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.618 ? metalc ? metalc4 B O2G APC . A APC 1468 1_555 C CA CA . A CA 1469 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.447 ? # _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 4CM0 _atom_sites.fract_transf_matrix[1][1] 0.009786 _atom_sites.fract_transf_matrix[1][2] 0.00565 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.0113 _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] 0.010498 _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 B 2 APC A 1 1468 1468 APC APC . C 3 CA A 1 1469 1469 CA CA . D 4 CL A 1 1470 1470 CL CL . # 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 . . . B 2 24.053 37.082 1.19 1 70.46 ? PG APC 1468 A 1 HETATM 2 O O1G APC . . . B 2 24.687 36.662 2.492 1 66.89 ? O1G APC 1468 A 1 HETATM 3 O O2G APC . . . B 2 22.663 36.531 0.986 1 67.53 ? O2G APC 1468 A 1 HETATM 4 O O3G APC . . . B 2 24.193 38.55 0.867 1 69.9 ? O3G APC 1468 A 1 HETATM 5 P PB APC . . . B 2 24.757 34.785 -0.282 1 75.06 ? PB APC 1468 A 1 HETATM 6 O O1B APC . . . B 2 23.529 34.636 -1.097 1 73.65 ? O1B APC 1468 A 1 HETATM 7 O O2B APC . . . B 2 26.026 34.259 -1.123 1 75.63 ? O2B APC 1468 A 1 HETATM 8 O O3B APC . . . B 2 24.962 36.342 0.083 1 73.26 ? O3B APC 1468 A 1 HETATM 9 P PA APC . . . B 2 24.338 32.062 0.887 1 87.57 ? PA APC 1468 A 1 HETATM 10 O O1A APC . . . B 2 24.198 31.848 -0.57 1 78.68 ? O1A APC 1468 A 1 HETATM 11 O O2A APC . . . B 2 25.597 31.21 1.414 1 98.33 ? O2A APC 1468 A 1 HETATM 12 C C3A APC . . . B 2 24.605 33.819 1.246 1 81.16 ? C3A APC 1468 A 1 HETATM 13 O O5' APC . . . B 2 22.996 31.558 1.621 1 88.83 ? O5' APC 1468 A 1 HETATM 14 C C5' APC . . . B 2 22.761 31.77 3.014 1 84.12 ? C5' APC 1468 A 1 HETATM 15 C C4' APC . . . B 2 21.644 30.861 3.532 1 83.45 ? C4' APC 1468 A 1 HETATM 16 O O4' APC . . . B 2 20.756 31.605 4.376 1 77.69 ? O4' APC 1468 A 1 HETATM 17 C C3' APC . . . B 2 20.789 30.233 2.432 1 82.09 ? C3' APC 1468 A 1 HETATM 18 O O3' APC . . . B 2 20.779 28.807 2.563 1 86.58 ? O3' APC 1468 A 1 HETATM 19 C C2' APC . . . B 2 19.399 30.811 2.611 1 81.63 ? C2' APC 1468 A 1 HETATM 20 O O2' APC . . . B 2 18.381 29.821 2.427 1 84.77 ? O2' APC 1468 A 1 HETATM 21 C C1' APC . . . B 2 19.387 31.361 4.029 1 76.5 ? C1' APC 1468 A 1 HETATM 22 N N9 APC . . . B 2 18.563 32.596 4.139 1 79.48 ? N9 APC 1468 A 1 HETATM 23 C C8 APC . . . B 2 18.951 33.758 4.698 1 77.23 ? C8 APC 1468 A 1 HETATM 24 N N7 APC . . . B 2 17.958 34.683 4.637 1 74.9 ? N7 APC 1468 A 1 HETATM 25 C C5 APC . . . B 2 16.903 34.11 4.035 1 72.44 ? C5 APC 1468 A 1 HETATM 26 C C6 APC . . . B 2 15.529 34.524 3.653 1 70.5 ? C6 APC 1468 A 1 HETATM 27 N N6 APC . . . B 2 15.073 35.773 3.914 1 65.09 ? N6 APC 1468 A 1 HETATM 28 N N1 APC . . . B 2 14.746 33.61 3.034 1 70.45 ? N1 APC 1468 A 1 HETATM 29 C C2 APC . . . B 2 15.18 32.361 2.766 1 72.9 ? C2 APC 1468 A 1 HETATM 30 N N3 APC . . . B 2 16.414 31.925 3.086 1 74.5 ? N3 APC 1468 A 1 HETATM 31 C C4 APC . . . B 2 17.306 32.733 3.71 1 75.94 ? C4 APC 1468 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #