data_4Q7C # _model_server_result.job_id yehRnyZMiWhTMjhihtfVZQ _model_server_result.datetime_utc '2024-11-17 00:45:51' _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 4q7c # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":408}' # _entry.id 4Q7C # _exptl.entry_id 4Q7C _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 477.255 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "[CYTIDINE-5'-PHOSPHATE] GLYCERYLPHOSPHORIC ACID 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 92.21 _cell.angle_gamma 90 _cell.entry_id 4Q7C _cell.length_a 46.417 _cell.length_b 90.852 _cell.length_c 106.611 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4Q7C _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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,I,J,K,L,M,N,O,P,Q,R _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 ? 5 J N N ? 5 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 metalc ? metalc1 A O ASP 242 A ASP 214 1_555 C CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc2 A OD2 ASP 242 A ASP 214 1_555 C CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.483 ? metalc ? metalc3 A OD1 ASP 242 A ASP 214 1_555 D CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc4 A OD2 ASP 242 A ASP 214 1_555 D CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.099 ? metalc ? metalc5 A OD2 ASP 245 A ASP 217 1_555 C CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? metalc ? metalc6 A OD1 ASP 245 A ASP 217 1_555 C CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? metalc ? metalc7 A OD1 ASP 263 A ASP 235 1_555 C CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.401 ? metalc ? metalc8 A OD2 ASP 263 A ASP 235 1_555 C CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? metalc ? metalc9 A OD1 ASP 263 A ASP 235 1_555 D CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc10 A O ASP 263 A ASP 235 1_555 D CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? metalc ? metalc11 A OD1 ASP 267 A ASP 239 1_555 D CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc12 A OD2 ASP 267 A ASP 239 1_555 D CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc13 C CA CA . A CA 401 1_555 J O1B C2G . A C2G 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc14 C CA CA . A CA 401 1_555 J O2A C2G . A C2G 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.551 ? metalc ? metalc15 B O ASP 242 B ASP 214 1_555 K CA CA . B CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc16 B OD1 ASP 242 B ASP 214 1_555 K CA CA . B CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.587 ? metalc ? metalc17 B OD1 ASP 242 B ASP 214 1_555 L CA CA . B CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? metalc ? metalc18 B OD2 ASP 245 B ASP 217 1_555 K CA CA . B CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? metalc ? metalc19 B OD1 ASP 245 B ASP 217 1_555 K CA CA . B CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? metalc ? metalc20 B OD2 ASP 263 B ASP 235 1_555 K CA CA . B CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? metalc ? metalc21 B OD1 ASP 263 B ASP 235 1_555 K CA CA . B CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? metalc ? metalc22 B OD1 ASP 263 B ASP 235 1_555 L CA CA . B CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc23 B O ASP 263 B ASP 235 1_555 L CA CA . B CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.526 ? metalc ? metalc24 B OD1 ASP 267 B ASP 239 1_555 L CA CA . B CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? metalc ? metalc25 B OD2 ASP 267 B ASP 239 1_555 L CA CA . B CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.099 ? metalc ? metalc26 K CA CA . B CA 401 1_555 R O2A C2G . B C2G 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? metalc ? metalc27 K CA CA . B CA 401 1_555 R O1B C2G . B C2G 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.542 ? # _chem_comp.formula 'C12 H21 N3 O13 P2' _chem_comp.formula_weight 477.255 _chem_comp.id C2G _chem_comp.mon_nstd_flag . _chem_comp.name "[CYTIDINE-5'-PHOSPHATE] GLYCERYLPHOSPHORIC ACID ESTER" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "CYTIDINE 5'-DIPHOSPHOGLYCEROL" # 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 N1 C2 C2G sing 70 n y N1 C6 C2G sing 71 n y N1 C1' C2G sing 72 n n C2 N3 C2G sing 73 n y C2 O2 C2G doub 74 n n N3 C4 C2G doub 75 n y C4 C5 C2G sing 76 n y C4 N4 C2G sing 77 n n C5 C6 C2G doub 78 n y C5 HC5 C2G sing 79 n n C6 HC6 C2G sing 80 n n N4 HN41 C2G sing 81 n n N4 HN42 C2G sing 82 n n C1' C2' C2G sing 83 n n C1' O4' C2G sing 84 n n C1' HC1 C2G sing 85 n n C2' O2' C2G sing 86 n n C2' C3' C2G sing 87 n n C2' HC2 C2G sing 88 n n O2' HO2 C2G sing 89 n n C3' C4' C2G sing 90 n n C3' O3' C2G sing 91 n n C3' HC3 C2G sing 92 n n C4' O4' C2G sing 93 n n C4' C5' C2G sing 94 n n C4' HC4 C2G sing 95 n n O3' HO3 C2G sing 96 n n C5' O5' C2G sing 97 n n C5' HC51 C2G sing 98 n n C5' HC52 C2G sing 99 n n O5' PA C2G sing 100 n n PA O1A C2G doub 101 n n PA O2A C2G sing 102 n n PA O3A C2G sing 103 n n O2A H2A C2G sing 104 n n O3A PB C2G sing 105 n n PB O1B C2G doub 106 n n PB O2B C2G sing 107 n n PB O3B C2G sing 108 n n O2B H2B C2G sing 109 n n O3B C3G C2G sing 110 n n O1G C1G C2G sing 111 n n O1G H1G C2G sing 112 n n C1G C2G C2G sing 113 n n C1G H1G1 C2G sing 114 n n C1G H1G2 C2G sing 115 n n C2G O2G C2G sing 116 n n C2G C3G C2G sing 117 n n C2G H2G C2G sing 118 n n O2G HOG C2G sing 119 n n C3G H3G1 C2G sing 120 n n C3G H3G2 C2G sing 121 n n # _atom_sites.entry_id 4Q7C _atom_sites.fract_transf_matrix[1][1] 0.021544 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000831 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011007 _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] 0.009387 _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 C 2 CA A 1 401 2 CA CA . D 2 CA A 1 402 3 CA CA . E 3 MPG A 1 403 6 MPG MPG . F 3 MPG A 1 404 7 MPG MPG . G 3 MPG A 1 405 8 MPG MPG . H 3 MPG A 1 406 9 MPG MPG . I 4 TLA A 1 407 1 TLA TLA . J 5 C2G A 1 408 2 C2G C2G . K 2 CA B 1 401 1 CA CA . L 2 CA B 1 402 4 CA CA . M 3 MPG B 1 403 1 MPG MPG . N 3 MPG B 1 404 2 MPG MPG . O 3 MPG B 1 405 3 MPG MPG . P 3 MPG B 1 406 4 MPG MPG . Q 4 TLA B 1 407 2 TLA TLA . R 5 C2G B 1 408 1 C2G C2G . # 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 N N1 C2G . . . J 5 12.459 8.84 31.656 1 32.99 ? N1 C2G 408 A 1 HETATM 2 C C2 C2G . . . J 5 11.259 8.374 31.163 1 33.97 ? C2 C2G 408 A 1 HETATM 3 N N3 C2G . . . J 5 10.43 7.648 31.956 1 34.11 ? N3 C2G 408 A 1 HETATM 4 C C4 C2G . . . J 5 10.795 7.383 33.253 1 33.39 ? C4 C2G 408 A 1 HETATM 5 C C5 C2G . . . J 5 11.981 7.85 33.734 1 33.86 ? C5 C2G 408 A 1 HETATM 6 C C6 C2G . . . J 5 12.825 8.587 32.932 1 33.46 ? C6 C2G 408 A 1 HETATM 7 O O2 C2G . . . J 5 10.95 8.616 30.016 1 34.92 ? O2 C2G 408 A 1 HETATM 8 N N4 C2G . . . J 5 9.93 6.619 34.092 1 32.41 ? N4 C2G 408 A 1 HETATM 9 C C1' C2G . . . J 5 13.301 9.599 30.824 1 33.71 ? C1' C2G 408 A 1 HETATM 10 C C2' C2G . . . J 5 12.926 10.877 30.879 1 34.51 ? C2' C2G 408 A 1 HETATM 11 O O2' C2G . . . J 5 12.848 11.45 29.531 1 35.03 ? O2' C2G 408 A 1 HETATM 12 C C3' C2G . . . J 5 13.998 11.614 31.699 1 33.87 ? C3' C2G 408 A 1 HETATM 13 C C4' C2G . . . J 5 15.278 10.681 31.626 1 34.06 ? C4' C2G 408 A 1 HETATM 14 O O4' C2G . . . J 5 14.842 9.482 31.375 1 34.09 ? O4' C2G 408 A 1 HETATM 15 O O3' C2G . . . J 5 14.266 12.848 31.164 1 34.15 ? O3' C2G 408 A 1 HETATM 16 C C5' C2G . . . J 5 16.065 10.665 32.952 1 33.86 ? C5' C2G 408 A 1 HETATM 17 O O5' C2G . . . J 5 16.923 9.517 33.006 1 33.85 ? O5' C2G 408 A 1 HETATM 18 P PA C2G . . . J 5 17.606 9.158 34.364 1 33.24 ? PA C2G 408 A 1 HETATM 19 O O1A C2G . . . J 5 18.699 8.198 34.105 1 32.09 ? O1A C2G 408 A 1 HETATM 20 O O2A C2G . . . J 5 16.601 8.562 35.285 1 33.02 ? O2A C2G 408 A 1 HETATM 21 O O3A C2G . . . J 5 18.188 10.438 35.016 1 32.67 ? O3A C2G 408 A 1 HETATM 22 P PB C2G . . . J 5 17.958 10.882 36.517 1 33.11 ? PB C2G 408 A 1 HETATM 23 O O1B C2G . . . J 5 17.003 9.922 37.209 1 32.85 ? O1B C2G 408 A 1 HETATM 24 O O2B C2G . . . J 5 17.393 12.296 36.544 1 34.56 ? O2B C2G 408 A 1 HETATM 25 O O3B C2G . . . J 5 19.356 10.853 37.293 1 33.48 ? O3B C2G 408 A 1 HETATM 26 O O1G C2G . . . J 5 21.258 8.579 40.139 1 33.86 ? O1G C2G 408 A 1 HETATM 27 C C1G C2G . . . J 5 21.735 8.344 38.868 1 33.81 ? C1G C2G 408 A 1 HETATM 28 C C2G C2G . . . J 5 21.22 9.428 37.869 1 33.97 ? C2G C2G 408 A 1 HETATM 29 O O2G C2G . . . J 5 21.866 10.632 38.118 1 35.61 ? O2G C2G 408 A 1 HETATM 30 C C3G C2G . . . J 5 19.736 9.627 37.983 1 33.33 ? C3G C2G 408 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 344 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 30 #