data_6M7O # _model_server_result.job_id XoguYyJAsXb5Cl090cb2gA _model_server_result.datetime_utc '2024-11-22 14:28:01' _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 6m7o # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":503}' # _entry.id 6M7O # _exptl.entry_id 6M7O _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 481.184 _entity.id 5 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description "5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine" _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 6M7O _cell.length_a 98.9 _cell.length_b 98.9 _cell.length_c 81.06 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6M7O _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # _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,E,F,G,H _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 5 _struct_asym.id F _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 B O3' DT 2 T DT 3 1_555 B P 02I 3 T 02I 4 1_555 ? A ? ? A ? ? ? ? ? ? ? 1.608 ? covale ? covale2 B O3' DT 2 T DT 3 1_555 B P 02I 3 T 02I 4 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.62 ? covale ? covale3 B O3' 02I 3 T 02I 4 1_555 B P DC 4 T DC 5 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.61 ? covale ? covale4 B O3' 02I 3 T 02I 4 1_555 B P DC 4 T DC 5 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.601 ? metalc ? metalc1 A OD1 ASP 16 A ASP 13 1_555 D MN MN . A MN 501 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.163 ? metalc ? metalc2 A OD2 ASP 16 A ASP 13 1_555 E MN MN . A MN 502 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.175 ? metalc ? metalc3 A O MET 17 A MET 14 1_555 D MN MN . A MN 501 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.139 ? metalc ? metalc4 A OD1 ASP 118 A ASP 115 1_555 D MN MN . A MN 501 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.127 ? metalc ? metalc5 A OD2 ASP 118 A ASP 115 1_555 E MN MN . A MN 502 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.262 ? metalc ? metalc6 A OE2 GLU 119 A GLU 116 1_555 E MN MN . A MN 502 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.18 ? metalc ? metalc7 D MN MN . A MN 501 1_555 F O1A 1FZ . A 1FZ 503 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.135 ? metalc ? metalc8 D MN MN . A MN 501 1_555 F O2B 1FZ . A 1FZ 503 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc9 D MN MN . A MN 501 1_555 F O3G 1FZ . A 1FZ 503 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.942 ? metalc ? metalc10 E MN MN . A MN 502 1_555 F O1A 1FZ . A 1FZ 503 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc11 E MN MN . A MN 502 1_555 C O3' DG 8 P DG 9 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.946 ? hydrog WATSON-CRICK hydrog1 B N3 DC 4 T DC 5 1_555 C N1 DG 8 P DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N4 DC 4 T DC 5 1_555 C O6 DG 8 P DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O2 DC 4 T DC 5 1_555 C N2 DG 8 P DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N3 DT 5 T DT 6 1_555 C N1 DA 7 P DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O4 DT 5 T DT 6 1_555 C N6 DA 7 P DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N3 DC 6 T DC 7 1_555 C N1 DG 6 P DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N4 DC 6 T DC 7 1_555 C O6 DG 6 P DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B O2 DC 6 T DC 7 1_555 C N2 DG 6 P DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N1 DA 7 T DA 8 1_555 C N3 DT 5 P DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N6 DA 7 T DA 8 1_555 C O4 DT 5 P DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N3 DC 8 T DC 9 1_555 C N1 DG 4 P DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N4 DC 8 T DC 9 1_555 C O6 DG 4 P DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B O2 DC 8 T DC 9 1_555 C N2 DG 4 P DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N1 DA 9 T DA 10 1_555 C N3 DT 3 P DT 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N6 DA 9 T DA 10 1_555 C O4 DT 3 P DT 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N3 DC 10 T DC 11 1_555 C N1 DG 2 P DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N4 DC 10 T DC 11 1_555 C O6 DG 2 P DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O2 DC 10 T DC 11 1_555 C N2 DG 2 P DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N3 DT 11 T DT 12 1_555 C N1 DA 1 P DA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B O4 DT 11 T DT 12 1_555 C N6 DA 1 P DA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H18 N3 O13 P3' _chem_comp.formula_weight 481.184 _chem_comp.id 1FZ _chem_comp.mon_nstd_flag . _chem_comp.name "5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine" _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 O3G PG 1FZ doub 38 n n O1G PG 1FZ sing 39 n n O2G PG 1FZ sing 40 n n PG O3B 1FZ sing 41 n n O1A PA 1FZ doub 42 n n O3B PB 1FZ sing 43 n n O2B PB 1FZ doub 44 n n PB N3A 1FZ sing 45 n n PB O1B 1FZ sing 46 n n PA N3A 1FZ sing 47 n n PA O2A 1FZ sing 48 n n PA O5' 1FZ sing 49 n n C5' O5' 1FZ sing 50 n n C5' C4' 1FZ sing 51 n n O3' C3' 1FZ sing 52 n n C4' C3' 1FZ sing 53 n n C4' O4' 1FZ sing 54 n n C3' C2' 1FZ sing 55 n n O4' C1' 1FZ sing 56 n n C5M C5 1FZ sing 57 n n C2' C1' 1FZ sing 58 n n C6 C5 1FZ doub 59 n n C6 N1 1FZ sing 60 n n C1' N1 1FZ sing 61 n n C5 C4 1FZ sing 62 n n N1 C2 1FZ sing 63 n n C4 O4 1FZ doub 64 n n C4 N3 1FZ sing 65 n n C2 N3 1FZ sing 66 n n C2 O2 1FZ doub 67 n n C6 H1 1FZ sing 68 n n C5M H2 1FZ sing 69 n n C5M H3 1FZ sing 70 n n C5M H4 1FZ sing 71 n n N3 H5 1FZ sing 72 n n C1' H6 1FZ sing 73 n n C2' H7 1FZ sing 74 n n C2' H8 1FZ sing 75 n n C3' H9 1FZ sing 76 n n O3' H10 1FZ sing 77 n n C4' H11 1FZ sing 78 n n C5' H12 1FZ sing 79 n n C5' H13 1FZ sing 80 n n O2A H14 1FZ sing 81 n n N3A H15 1FZ sing 82 n n O1B H16 1FZ sing 83 n n O1G H17 1FZ sing 84 n n O2G H18 1FZ sing 85 n n # _atom_sites.entry_id 6M7O _atom_sites.fract_transf_matrix[1][1] 0.010111 _atom_sites.fract_transf_matrix[1][2] 0.005838 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011675 _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] 0.012337 _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 D 4 MN A 1 501 501 MN MN . E 4 MN A 1 502 502 MN MN . F 5 1FZ A 1 503 503 1FZ 1FZ . G 6 HOH A 1 601 31 HOH HOH . G 6 HOH A 2 602 9 HOH HOH . G 6 HOH A 3 603 6 HOH HOH . G 6 HOH A 4 604 29 HOH HOH . G 6 HOH A 5 605 11 HOH HOH . G 6 HOH A 6 606 8 HOH HOH . G 6 HOH A 7 607 3 HOH HOH . G 6 HOH A 8 608 5 HOH HOH . G 6 HOH A 9 609 2 HOH HOH . G 6 HOH A 10 610 25 HOH HOH . G 6 HOH A 11 611 33 HOH HOH . G 6 HOH A 12 612 24 HOH HOH . G 6 HOH A 13 613 21 HOH HOH . G 6 HOH A 14 614 32 HOH HOH . G 6 HOH A 15 615 12 HOH HOH . G 6 HOH A 16 616 26 HOH HOH . G 6 HOH A 17 617 36 HOH HOH . G 6 HOH A 18 618 1 HOH HOH . G 6 HOH A 19 619 18 HOH HOH . H 6 HOH P 1 101 4 HOH HOH . H 6 HOH P 2 102 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 O2 1FZ . . . F 5 45.514 5.594 3.586 1 100.68 ? O2 1FZ 503 A 1 HETATM 2 O O4 1FZ . . . F 5 44.27 1.951 5.738 1 89.11 ? O4 1FZ 503 A 1 HETATM 3 C C4 1FZ . . . F 5 45.131 2.619 5.225 1 86.89 ? C4 1FZ 503 A 1 HETATM 4 C C5 1FZ . . . F 5 46.519 2.078 5.233 1 80.34 ? C5 1FZ 503 A 1 HETATM 5 C C6 1FZ . . . F 5 47.506 2.829 4.627 1 83.21 ? C6 1FZ 503 A 1 HETATM 6 C C5M 1FZ . . . F 5 46.83 0.723 5.883 1 83.7 ? C5M 1FZ 503 A 1 HETATM 7 N N3 1FZ . . . F 5 44.777 3.788 4.647 1 89.04 ? N3 1FZ 503 A 1 HETATM 8 C C2 1FZ . . . F 5 45.805 4.546 4.078 1 88.26 ? C2 1FZ 503 A 1 HETATM 9 N N1 1FZ . . . F 5 47.212 4.093 4.042 1 88.01 ? N1 1FZ 503 A 1 HETATM 10 C C1' 1FZ . . . F 5 48.163 4.842 3.464 1 80.18 ? C1' 1FZ 503 A 1 HETATM 11 C C2' 1FZ . . . F 5 49.089 5.485 4.557 1 65.81 ? C2' 1FZ 503 A 1 HETATM 12 C C3' 1FZ . . . F 5 50.498 5.284 4.027 1 70.17 ? C3' 1FZ 503 A 1 HETATM 13 O O3' 1FZ . . . F 5 51.138 6.549 3.844 1 63.3 ? O3' 1FZ 503 A 1 HETATM 14 O O4' 1FZ . . . F 5 48.997 3.973 2.71 1 86.59 ? O4' 1FZ 503 A 1 HETATM 15 C C4' 1FZ . . . F 5 50.312 4.589 2.678 1 72.53 ? C4' 1FZ 503 A 1 HETATM 16 C C5' 1FZ . . . F 5 51.378 3.541 2.49 1 66.68 ? C5' 1FZ 503 A 1 HETATM 17 O O5' 1FZ . . . F 5 51.024 2.355 3.2 1 63.4 ? O5' 1FZ 503 A 1 HETATM 18 P PA 1FZ . . . F 5 52.088 1.702 4.153 1 64.49 ? PA 1FZ 503 A 1 HETATM 19 O O1A 1FZ . . . F 5 53.435 1.542 3.382 1 58.99 ? O1A 1FZ 503 A 1 HETATM 20 O O2A 1FZ . . . F 5 51.613 0.384 4.562 1 91.32 ? O2A 1FZ 503 A 1 HETATM 21 N N3A 1FZ . . . F 5 52.32 2.674 5.441 1 52.3 ? N3A 1FZ 503 A 1 HETATM 22 P PB 1FZ . . . F 5 53.315 3.96 5.325 1 73.97 ? PB 1FZ 503 A 1 HETATM 23 O O1B 1FZ . . . F 5 52.628 5.151 5.816 1 66.83 ? O1B 1FZ 503 A 1 HETATM 24 O O2B 1FZ . . . F 5 53.709 4.166 3.882 1 69.28 ? O2B 1FZ 503 A 1 HETATM 25 O O3B 1FZ . . . F 5 54.618 3.705 6.2 1 70.27 ? O3B 1FZ 503 A 1 HETATM 26 P PG 1FZ . . . F 5 55.699 2.526 6.21 1 58.67 ? PG 1FZ 503 A 1 HETATM 27 O O1G 1FZ . . . F 5 57.018 3.053 6.738 1 43.15 ? O1G 1FZ 503 A 1 HETATM 28 O O3G 1FZ . . . F 5 55.891 2.002 4.798 1 71.97 ? O3G 1FZ 503 A 1 HETATM 29 O O2G 1FZ . . . F 5 55.212 1.4 7.106 1 65.71 ? O2G 1FZ 503 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 29 #