data_6YOM # _model_server_result.job_id Q0vyi4wvGG26OJmU4eQ5PA _model_server_result.datetime_utc '2025-06-21 01:01:46' _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 6yom # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":706}' # _entry.id 6YOM # _exptl.entry_id 6YOM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 466.172 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine" _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 90 _cell.angle_gamma 90 _cell.entry_id 6YOM _cell.length_a 105.298 _cell.length_b 105.298 _cell.length_c 195.629 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YOM _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 G N N ? 5 O 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 NE2 HIS 61 A HIS 167 1_555 C FE FE . A FE 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc2 A NE2 HIS 100 A HIS 206 1_555 C FE FE . A FE 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? metalc ? metalc3 A OD2 ASP 101 A ASP 207 1_555 C FE FE . A FE 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc4 A OD1 ASP 101 A ASP 207 1_555 D MN MN . A MN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? metalc ? metalc5 A NE2 HIS 127 A HIS 233 1_555 D MN MN . A MN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc6 A OD1 ASP 205 A ASP 311 1_555 C FE FE . A FE 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? metalc ? metalc7 C FE FE . A FE 701 1_555 G O2A 0KX . A 0KX 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? metalc ? metalc8 D MN MN . A MN 702 1_555 G O1A 0KX . A 0KX 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc9 E MG MG . A MG 703 1_555 G O3G 0KX . A 0KX 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc10 E MG MG . A MG 703 1_555 G O1B 0KX . A 0KX 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.489 ? metalc ? metalc11 F MG MG . A MG 704 1_555 H O9 CZF . A CZF 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc12 F MG MG . A MG 704 1_555 H O12 CZF . A CZF 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? metalc ? metalc13 F MG MG . A MG 704 1_555 H O14 CZF . A CZF 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? metalc ? metalc14 F MG MG . A MG 704 1_555 J O2B DTP . B DTP 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? metalc ? metalc15 F MG MG . A MG 704 1_555 J O1G DTP . B DTP 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? metalc ? metalc16 I O3G DTP . A DTP 707 1_555 N MG MG . B MG 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? metalc ? metalc17 I O1B DTP . A DTP 707 1_555 N MG MG . B MG 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? metalc ? metalc18 B NE2 HIS 61 B HIS 167 1_555 K FE FE . B FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc19 B NE2 HIS 100 B HIS 206 1_555 K FE FE . B FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc20 B OD2 ASP 101 B ASP 207 1_555 K FE FE . B FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc21 B OD1 ASP 101 B ASP 207 1_555 L MN MN . B MN 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? metalc ? metalc22 B NE2 HIS 127 B HIS 233 1_555 L MN MN . B MN 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc23 B OD1 ASP 205 B ASP 311 1_555 K FE FE . B FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc24 K FE FE . B FE 702 1_555 O O2A 0KX . B 0KX 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc25 L MN MN . B MN 703 1_555 O O1A 0KX . B 0KX 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? metalc ? metalc26 M MG MG . B MG 704 1_555 O O1B 0KX . B 0KX 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? metalc ? metalc27 M MG MG . B MG 704 1_555 O O3G 0KX . B 0KX 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc28 N MG MG . B MG 705 1_555 P O9 CZF . B CZF 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? metalc ? metalc29 N MG MG . B MG 705 1_555 P O14 CZF . B CZF 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc30 N MG MG . B MG 705 1_555 P O12 CZF . B CZF 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? # _chem_comp.formula 'C9 H17 N4 O12 P3' _chem_comp.formula_weight 466.172 _chem_comp.id 0KX _chem_comp.mon_nstd_flag . _chem_comp.name "2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 O4' C4' 0KX sing 1 n n O4' C1' 0KX sing 2 n n C4' C5' 0KX sing 3 n n C4' C3' 0KX sing 4 n n C5' O5' 0KX sing 5 n n C1' N1 0KX sing 6 n n C1' C2' 0KX sing 7 n n O5' PA 0KX sing 8 n n O1A PA 0KX doub 9 n n O2 C2 0KX doub 10 n n N1 C2 0KX sing 11 n n N1 C6 0KX sing 12 n n C3' C2' 0KX sing 13 n n C3' O3' 0KX sing 14 n n C2 N3 0KX sing 15 n n C6 C5 0KX doub 16 n n O2B PB 0KX doub 17 n n PA O2A 0KX sing 18 n n PA N3A 0KX sing 19 n n N3 C4 0KX doub 20 n n C5 C4 0KX sing 21 n n C4 N4 0KX sing 22 n n O2G PG 0KX doub 23 n n PB N3A 0KX sing 24 n n PB O1B 0KX sing 25 n n PB O3B 0KX sing 26 n n PG O3B 0KX sing 27 n n PG O3G 0KX sing 28 n n PG O1G 0KX sing 29 n n O1G H1 0KX sing 30 n n O3G H2 0KX sing 31 n n O1B H3 0KX sing 32 n n O2A H4 0KX sing 33 n n N3A H5 0KX sing 34 n n C5' H6 0KX sing 35 n n C5' H7 0KX sing 36 n n C4' H8 0KX sing 37 n n C3' H9 0KX sing 38 n n O3' H10 0KX sing 39 n n C2' H11 0KX sing 40 n n C2' H12 0KX sing 41 n n C1' H13 0KX sing 42 n n C5 H14 0KX sing 43 n n C6 H15 0KX sing 44 n n N4 H16 0KX sing 45 n n N4 H17 0KX sing 46 n n # _atom_sites.entry_id 6YOM _atom_sites.fract_transf_matrix[1][1] 0.009497 _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] 0.009497 _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] 0.005112 _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 FE A 1 701 701 FE FE . D 3 MN A 1 702 702 MN MN . E 4 MG A 1 703 703 MG MG . F 4 MG A 1 704 704 MG MG . G 5 0KX A 1 705 801 0KX dCN . H 6 CZF A 1 706 802 CZF XTP . I 7 DTP A 1 707 803 DTP DTP . J 7 DTP B 1 701 803 DTP DTP . K 2 FE B 1 702 701 FE FE . L 3 MN B 1 703 702 MN MN . M 4 MG B 1 704 703 MG MG . N 4 MG B 1 705 704 MG MG . O 5 0KX B 1 706 801 0KX dCN . P 6 CZF B 1 707 802 CZF XTP . # 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 0KX . . . O 5 -11.854 -3.269 -22.712 1 66.92 ? PG 0KX 706 B 1 HETATM 2 O O1G 0KX . . . O 5 -11.993 -2.627 -21.365 1 60.75 -1 O1G 0KX 706 B 1 HETATM 3 O O2G 0KX . . . O 5 -11.325 -2.277 -23.732 1 69.28 -1 O2G 0KX 706 B 1 HETATM 4 O O3G 0KX . . . O 5 -13.076 -4.063 -23.205 1 68.83 ? O3G 0KX 706 B 1 HETATM 5 P PB 0KX . . . O 5 -10.477 -5.657 -23.481 1 70.33 ? PB 0KX 706 B 1 HETATM 6 O O1B 0KX . . . O 5 -11.82 -6.291 -23.789 1 71.71 -1 O1B 0KX 706 B 1 HETATM 7 O O2B 0KX . . . O 5 -9.619 -5.092 -24.581 1 69.41 ? O2B 0KX 706 B 1 HETATM 8 O O3B 0KX . . . O 5 -10.759 -4.412 -22.521 1 65.81 ? O3B 0KX 706 B 1 HETATM 9 P PA 0KX . . . O 5 -8.014 -7.06 -22.721 1 66.61 ? PA 0KX 706 B 1 HETATM 10 O O1A 0KX . . . O 5 -7.771 -7.887 -23.962 1 68.81 ? O1A 0KX 706 B 1 HETATM 11 O O2A 0KX . . . O 5 -7.723 -7.68 -21.379 1 64.04 -1 O2A 0KX 706 B 1 HETATM 12 N N3A 0KX . . . O 5 -9.508 -6.486 -22.497 1 69.42 ? N3A 0KX 706 B 1 HETATM 13 O O5' 0KX . . . O 5 -7.252 -5.663 -22.925 1 61.46 ? O5' 0KX 706 B 1 HETATM 14 C C5' 0KX . . . O 5 -7.156 -4.731 -21.837 1 60.39 ? C5' 0KX 706 B 1 HETATM 15 C C4' 0KX . . . O 5 -5.722 -4.69 -21.383 1 60.58 ? C4' 0KX 706 B 1 HETATM 16 O O4' 0KX . . . O 5 -4.906 -4.248 -22.488 1 65.41 ? O4' 0KX 706 B 1 HETATM 17 C C3' 0KX . . . O 5 -5.387 -3.764 -20.218 1 59.58 ? C3' 0KX 706 B 1 HETATM 18 O O3' 0KX . . . O 5 -4.346 -4.35 -19.436 1 57.13 ? O3' 0KX 706 B 1 HETATM 19 C C2' 0KX . . . O 5 -4.926 -2.491 -20.915 1 61.91 ? C2' 0KX 706 B 1 HETATM 20 C C1' 0KX . . . O 5 -4.246 -3.041 -22.158 1 66.75 ? C1' 0KX 706 B 1 HETATM 21 N N1 0KX . . . O 5 -4.336 -2.169 -23.338 1 71.72 ? N1 0KX 706 B 1 HETATM 22 C C2 0KX . . . O 5 -3.162 -1.714 -23.969 1 76.72 ? C2 0KX 706 B 1 HETATM 23 N N3 0KX . . . O 5 -3.287 -0.911 -25.056 1 78.69 ? N3 0KX 706 B 1 HETATM 24 C C4 0KX . . . O 5 -4.496 -0.594 -25.532 1 74.51 ? C4 0KX 706 B 1 HETATM 25 C C5 0KX . . . O 5 -5.691 -1.068 -24.917 1 74.36 ? C5 0KX 706 B 1 HETATM 26 C C6 0KX . . . O 5 -5.564 -1.841 -23.832 1 72.29 ? C6 0KX 706 B 1 HETATM 27 O O2 0KX . . . O 5 -2.039 -2.029 -23.535 1 74.48 ? O2 0KX 706 B 1 HETATM 28 N N4 0KX . . . O 5 -4.536 0.194 -26.59 1 75.44 ? N4 0KX 706 B 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 34 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 822 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 28 #