data_4Q7C # _model_server_result.job_id 9KyDXs01LjOe1mAgRVkeTw _model_server_result.datetime_utc '2025-02-28 23:21:15' _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":"R","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 . . . R 5 10.227 38.747 32.693 1 31.54 ? N1 C2G 408 B 1 HETATM 2 C C2 C2G . . . R 5 11.326 39.402 32.179 1 31.46 ? C2 C2G 408 B 1 HETATM 3 N N3 C2G . . . R 5 12.197 40.036 33.004 1 32.15 ? N3 C2G 408 B 1 HETATM 4 C C4 C2G . . . R 5 11.977 40.023 34.363 1 31.55 ? C4 C2G 408 B 1 HETATM 5 C C5 C2G . . . R 5 10.891 39.377 34.869 1 31.59 ? C5 C2G 408 B 1 HETATM 6 C C6 C2G . . . R 5 10.007 38.735 34.029 1 32.39 ? C6 C2G 408 B 1 HETATM 7 O O2 C2G . . . R 5 11.509 39.407 30.985 1 32.15 ? O2 C2G 408 B 1 HETATM 8 N N4 C2G . . . R 5 12.885 40.686 35.242 1 30.3 ? N4 C2G 408 B 1 HETATM 9 C C1' C2G . . . R 5 9.327 38.088 31.826 1 32.43 ? C1' C2G 408 B 1 HETATM 10 C C2' C2G . . . R 5 9.642 36.795 31.697 1 33.1 ? C2' C2G 408 B 1 HETATM 11 O O2' C2G . . . R 5 9.446 36.363 30.307 1 32.39 ? O2' C2G 408 B 1 HETATM 12 C C3' C2G . . . R 5 8.659 36.046 32.612 1 32.09 ? C3' C2G 408 B 1 HETATM 13 C C4' C2G . . . R 5 7.363 36.944 32.507 1 32.26 ? C4' C2G 408 B 1 HETATM 14 O O4' C2G . . . R 5 7.811 38.162 32.454 1 32.8 ? O4' C2G 408 B 1 HETATM 15 O O3' C2G . . . R 5 8.416 34.771 32.173 1 31.67 ? O3' C2G 408 B 1 HETATM 16 C C5' C2G . . . R 5 6.435 36.804 33.723 1 32.32 ? C5' C2G 408 B 1 HETATM 17 O O5' C2G . . . R 5 5.546 37.927 33.772 1 33.7 ? O5' C2G 408 B 1 HETATM 18 P PA C2G . . . R 5 4.777 38.234 35.097 1 33.97 ? PA C2G 408 B 1 HETATM 19 O O1A C2G . . . R 5 3.618 39.094 34.786 1 33.69 ? O1A C2G 408 B 1 HETATM 20 O O2A C2G . . . R 5 5.684 38.93 36.049 1 33.17 ? O2A C2G 408 B 1 HETATM 21 O O3A C2G . . . R 5 4.289 36.892 35.709 1 34.88 ? O3A C2G 408 B 1 HETATM 22 P PB C2G . . . R 5 4.11 36.568 37.248 1 35.7 ? PB C2G 408 B 1 HETATM 23 O O1B C2G . . . R 5 5.424 36.774 37.994 1 33.44 ? O1B C2G 408 B 1 HETATM 24 O O2B C2G . . . R 5 3.614 35.133 37.39 1 36.44 ? O2B C2G 408 B 1 HETATM 25 O O3B C2G . . . R 5 3.005 37.556 37.856 1 37.21 ? O3B C2G 408 B 1 HETATM 26 O O1G C2G . . . R 5 0.538 36.945 41.6 1 35.54 ? O1G C2G 408 B 1 HETATM 27 C C1G C2G . . . R 5 1.654 37.563 41.069 1 36.22 ? C1G C2G 408 B 1 HETATM 28 C C2G C2G . . . R 5 1.43 38.056 39.602 1 35.89 ? C2G C2G 408 B 1 HETATM 29 O O2G C2G . . . R 5 0.095 38.373 39.379 1 34.59 ? O2G C2G 408 B 1 HETATM 30 C C3G C2G . . . R 5 1.886 37.015 38.617 1 36.14 ? C3G C2G 408 B 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 1196 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 30 #