data_6Q52 # _model_server_result.job_id r9aerPEJMR5ZNNGYZWMRVg _model_server_result.datetime_utc '2025-01-10 12:20:42' _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 6q52 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 6Q52 # _exptl.entry_id 6Q52 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 481.184 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine" _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 90 _cell.entry_id 6Q52 _cell.length_a 71.45 _cell.length_b 71.45 _cell.length_c 293.61 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6Q52 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 # _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 # _chem_comp.formula 'C10 H18 N3 O13 P3' _chem_comp.formula_weight 481.184 _chem_comp.id 2TM _chem_comp.mon_nstd_flag . _chem_comp.name "5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms CMPcPP # 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 N4 C4 2TM sing 1 n n N3 C4 2TM doub 2 n n N3 C2 2TM sing 3 n n O2 C2 2TM doub 4 n n C4 C5 2TM sing 5 n n C2 N1 2TM sing 6 n n C5 C6 2TM doub 7 n n N1 C6 2TM sing 8 n n N1 C1' 2TM sing 9 n n O2' C2' 2TM sing 10 n n C2' C1' 2TM sing 11 n n C2' C3' 2TM sing 12 n n C1' O4' 2TM sing 13 n n C3' O3' 2TM sing 14 n n C3' C4' 2TM sing 15 n n O4' C4' 2TM sing 16 n n C4' C5' 2TM sing 17 n n C5' O5' 2TM sing 18 n n O5' PA 2TM sing 19 n n O1A PA 2TM doub 20 n n PA O2A 2TM sing 21 n n PA C1 2TM sing 22 n n O2B PB 2TM doub 23 n n C1 PB 2TM sing 24 n n PB O3B 2TM sing 25 n n PB O1B 2TM sing 26 n n O3B PG 2TM sing 27 n n PG O1G 2TM doub 28 n n PG O2G 2TM sing 29 n n PG O3G 2TM sing 30 n n C5' H1 2TM sing 31 n n C5' H2 2TM sing 32 n n C4' H3 2TM sing 33 n n C3' H4 2TM sing 34 n n O3' H5 2TM sing 35 n n C2' H6 2TM sing 36 n n O2' H7 2TM sing 37 n n C1' H8 2TM sing 38 n n C5 H9 2TM sing 39 n n C6 H10 2TM sing 40 n n O3G H11 2TM sing 41 n n O2G H12 2TM sing 42 n n O1B H13 2TM sing 43 n n O2A H14 2TM sing 44 n n N4 H15 2TM sing 45 n n N4 H16 2TM sing 46 n n C1 H17 2TM sing 47 n n C1 H18 2TM sing 48 n n # _atom_sites.entry_id 6Q52 _atom_sites.fract_transf_matrix[1][1] 0.013996 _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] 0.013996 _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] 0.003406 _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 2TM A 1 401 1 2TM 2TM . C 3 HOH A 1 501 9 HOH HOH . C 3 HOH A 2 502 2 HOH HOH . C 3 HOH A 3 503 6 HOH HOH . C 3 HOH A 4 504 4 HOH HOH . C 3 HOH A 5 505 18 HOH HOH . C 3 HOH A 6 506 7 HOH HOH . C 3 HOH A 7 507 3 HOH HOH . C 3 HOH A 8 508 8 HOH HOH . C 3 HOH A 9 509 10 HOH HOH . C 3 HOH A 10 510 14 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 O O5' 2TM . A . B 2 40.223 53.565 49.743 0.4 63.45 ? O5' 2TM 401 A 1 HETATM 2 O O5' 2TM . B . B 2 39.589 54.157 50.193 0.3 62.43 ? O5' 2TM 401 A 1 HETATM 3 C C5' 2TM . A . B 2 40.071 54.213 48.493 0.4 60.38 ? C5' 2TM 401 A 1 HETATM 4 C C5' 2TM . B . B 2 39.454 55.078 49.122 0.3 59.91 ? C5' 2TM 401 A 1 HETATM 5 C C4' 2TM . A . B 2 40.686 55.632 48.533 0.4 58.01 ? C4' 2TM 401 A 1 HETATM 6 C C4' 2TM . B . B 2 40.638 56.074 49.009 0.3 57.28 ? C4' 2TM 401 A 1 HETATM 7 O O4' 2TM . A . B 2 41.285 55.809 49.667 0.4 56.23 ? O4' 2TM 401 A 1 HETATM 8 O O4' 2TM . B . B 2 41.405 55.962 50.037 0.3 55.81 ? O4' 2TM 401 A 1 HETATM 9 C C3' 2TM . A . B 2 41.771 55.857 47.316 0.4 55.49 ? C3' 2TM 401 A 1 HETATM 10 C C3' 2TM . B . B 2 41.554 55.831 47.662 0.3 56.14 ? C3' 2TM 401 A 1 HETATM 11 O O3' 2TM . A . B 2 41.622 57.173 46.69 0.4 49.33 ? O3' 2TM 401 A 1 HETATM 12 O O3' 2TM . B . B 2 41.494 56.986 46.766 0.3 50 ? O3' 2TM 401 A 1 HETATM 13 C C2' 2TM . A . B 2 42.952 55.774 47.857 0.4 55.02 ? C2' 2TM 401 A 1 HETATM 14 C C2' 2TM . B . B 2 42.789 55.661 48.051 0.3 55.18 ? C2' 2TM 401 A 1 HETATM 15 O O2' 2TM . A . B 2 43.86 56.795 47.256 0.4 53.54 ? O2' 2TM 401 A 1 HETATM 16 O O2' 2TM . B . B 2 43.701 56.505 47.22 0.3 53.47 ? O2' 2TM 401 A 1 HETATM 17 C C1' 2TM . A . B 2 42.752 56.176 49.323 0.4 55.36 ? C1' 2TM 401 A 1 HETATM 18 C C1' 2TM . B . B 2 42.833 56.194 49.488 0.3 55.3 ? C1' 2TM 401 A 1 HETATM 19 C C5 2TM . A . B 2 44.231 53.667 51.738 0.4 55.19 ? C5 2TM 401 A 1 HETATM 20 C C5 2TM . B . B 2 44.343 53.621 51.808 0.3 55.41 ? C5 2TM 401 A 1 HETATM 21 C C6 2TM . A . B 2 43.24 54.331 50.849 0.4 55.05 ? C6 2TM 401 A 1 HETATM 22 C C6 2TM . B . B 2 43.346 54.318 50.951 0.3 55.11 ? C6 2TM 401 A 1 HETATM 23 N N1 2TM . A . B 2 43.62 55.54 50.125 0.4 54.91 ? N1 2TM 401 A 1 HETATM 24 N N1 2TM . B . B 2 43.723 55.542 50.25 0.3 54.89 ? N1 2TM 401 A 1 HETATM 25 C C2 2TM . A . B 2 44.994 56.11 50.272 0.4 52.49 ? C2 2TM 401 A 1 HETATM 26 C C2 2TM . B . B 2 45.101 56.1 50.396 0.3 52.52 ? C2 2TM 401 A 1 HETATM 27 N N3 2TM . A . B 2 45.999 55.439 51.172 0.4 54.02 ? N3 2TM 401 A 1 HETATM 28 N N3 2TM . B . B 2 46.11 55.395 51.262 0.3 53.95 ? N3 2TM 401 A 1 HETATM 29 C C4 2TM . A . B 2 45.622 54.242 51.891 0.4 54.34 ? C4 2TM 401 A 1 HETATM 30 C C4 2TM . B . B 2 45.738 54.183 51.954 0.3 54.24 ? C4 2TM 401 A 1 HETATM 31 O O3G 2TM . A . B 2 39.915 47.74 48.266 0.4 64.47 ? O3G 2TM 401 A 1 HETATM 32 O O3G 2TM . B . B 2 40.577 48.772 46.395 0.3 68.14 ? O3G 2TM 401 A 1 HETATM 33 P PG 2TM . A . B 2 39.85 48.24 46.833 0.4 73.32 ? PG 2TM 401 A 1 HETATM 34 P PG 2TM . B . B 2 40.682 50.112 47.089 0.3 69.82 ? PG 2TM 401 A 1 HETATM 35 O O1G 2TM . A . B 2 40.212 47.125 45.863 0.4 66.29 ? O1G 2TM 401 A 1 HETATM 36 O O1G 2TM . B . B 2 41.508 51.063 46.243 0.3 63.01 ? O1G 2TM 401 A 1 HETATM 37 O O2G 2TM . A . B 2 38.46 48.72 46.523 0.4 72.46 ? O2G 2TM 401 A 1 HETATM 38 O O2G 2TM . B . B 2 39.304 50.703 47.171 0.3 70.3 ? O2G 2TM 401 A 1 HETATM 39 O O3B 2TM . A . B 2 40.877 49.536 46.595 0.4 68.73 ? O3B 2TM 401 A 1 HETATM 40 O O3B 2TM . B . B 2 41.394 49.942 48.596 0.3 61.78 ? O3B 2TM 401 A 1 HETATM 41 P PB 2TM . A . B 2 40.691 51.024 47.338 0.4 68.88 ? PB 2TM 401 A 1 HETATM 42 P PB 2TM . B . B 2 40.629 49.681 50.064 0.3 69.34 ? PB 2TM 401 A 1 HETATM 43 O O1B 2TM . A . B 2 41.915 51.896 47.119 0.4 63.78 ? O1B 2TM 401 A 1 HETATM 44 O O1B 2TM . B . B 2 41.498 48.81 50.962 0.3 61.55 ? O1B 2TM 401 A 1 HETATM 45 O O2B 2TM . A . B 2 39.493 51.738 46.735 0.4 66.19 ? O2B 2TM 401 A 1 HETATM 46 O O2B 2TM . B . B 2 39.314 48.974 49.797 0.3 67.95 ? O2B 2TM 401 A 1 HETATM 47 P PA 2TM . A . B 2 39.522 52.057 50.042 0.4 68.26 ? PA 2TM 401 A 1 HETATM 48 P PA 2TM . B . B 2 39.746 52.567 49.685 0.3 67.56 ? PA 2TM 401 A 1 HETATM 49 O O1A 2TM . A . B 2 38.088 52.02 49.536 0.4 70.09 ? O1A 2TM 401 A 1 HETATM 50 O O1A 2TM . B . B 2 40.77 52.649 48.567 0.3 64.5 ? O1A 2TM 401 A 1 HETATM 51 O O2A 2TM . A . B 2 39.519 51.788 51.527 0.4 64.22 ? O2A 2TM 401 A 1 HETATM 52 O O2A 2TM . B . B 2 38.408 52.098 49.154 0.3 69.29 ? O2A 2TM 401 A 1 HETATM 53 N N4 2TM . A . B 2 46.563 53.583 52.759 0.4 54.22 ? N4 2TM 401 A 1 HETATM 54 N N4 2TM . B . B 2 46.695 53.502 52.786 0.3 54.22 ? N4 2TM 401 A 1 HETATM 55 O O2 2TM . A . B 2 45.269 57.088 49.67 0.4 51.23 ? O2 2TM 401 A 1 HETATM 56 O O2 2TM . B . B 2 45.385 57.092 49.822 0.3 51.37 ? O2 2TM 401 A 1 HETATM 57 C C1 2TM . A . B 2 40.483 50.699 49.179 0.4 65.32 ? C1 2TM 401 A 1 HETATM 58 C C1 2TM . B . B 2 40.352 51.326 50.952 0.3 64.28 ? C1 2TM 401 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 450 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 58 #