data_6M7U # _model_server_result.job_id l8X9eOvgTg_ZKjVcSjNPaQ _model_server_result.datetime_utc '2024-11-22 19:24:38' _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 6m7u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":502}' # _entry.id 6M7U # _exptl.entry_id 6M7U _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 481.184 _entity.id 5 _entity.src_method syn _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 90 _cell.entry_id 6M7U _cell.length_a 63.31 _cell.length_b 80.47 _cell.length_c 142.07 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6M7U _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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,I,J _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 E _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 C O3' DT 2 T DT 3 1_555 C P 02I 3 T 02I 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.608 ? covale ? covale2 C O3' 02I 3 T 02I 4 1_555 C P DC 4 T DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.604 ? metalc ? metalc1 A OD1 ASP 16 A ASP 13 1_555 F MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc2 A OD2 ASP 16 A ASP 13 1_555 F MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.971 ? metalc ? metalc3 A O MET 17 A MET 14 1_555 F MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc4 A OD1 ASP 118 A ASP 115 1_555 F MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.547 ? metalc ? metalc5 A OD1 ASP 184 A ASP 181 1_555 D NI NI . A NI 501 2_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.56 ? metalc ? metalc6 A OD2 ASP 184 A ASP 181 1_555 D NI NI . A NI 501 2_554 ? ? ? ? ? ? ? ? ? ? ? ? 1.915 ? metalc ? metalc7 A NE2 HIS 292 A HIS 289 1_555 D NI NI . A NI 501 3_645 ? ? ? ? ? ? ? ? ? ? ? ? 2.702 ? metalc ? metalc8 A NE2 HIS 396 A HIS 393 1_555 D NI NI . A NI 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? metalc ? metalc9 A NE2 HIS 400 A HIS 397 1_555 D NI NI . A NI 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.842 ? metalc ? metalc10 E O1A 1FZ . A 1FZ 502 1_555 F MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? metalc ? metalc11 E O2B 1FZ . A 1FZ 502 1_555 F MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc12 E O1G 1FZ . A 1FZ 502 1_555 F MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? hydrog WATSON-CRICK hydrog1 B N1 DG 2 P DG 2 1_555 C N3 DC 10 T DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N2 DG 2 P DG 2 1_555 C O2 DC 10 T DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O6 DG 2 P DG 2 1_555 C N4 DC 10 T DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N3 DT 3 P DT 3 1_555 C N1 DA 9 T DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O4 DT 3 P DT 3 1_555 C N6 DA 9 T DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N1 DG 4 P DG 4 1_555 C N3 DC 8 T DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N2 DG 4 P DG 4 1_555 C O2 DC 8 T DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B O6 DG 4 P DG 4 1_555 C N4 DC 8 T DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N3 DT 5 P DT 5 1_555 C N1 DA 7 T DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B O4 DT 5 P DT 5 1_555 C N6 DA 7 T DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N1 DG 6 P DG 6 1_555 C N3 DC 6 T DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N2 DG 6 P DG 6 1_555 C O2 DC 6 T DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B O6 DG 6 P DG 6 1_555 C N4 DC 6 T DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N1 DA 7 P DA 7 1_555 C N3 DT 5 T DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N6 DA 7 P DA 7 1_555 C O4 DT 5 T DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N1 DG 8 P DG 8 1_555 C N3 DC 4 T DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N2 DG 8 P DG 8 1_555 C O2 DC 4 T DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O6 DG 8 P DG 8 1_555 C N4 DC 4 T DC 5 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 6M7U _atom_sites.fract_transf_matrix[1][1] 0.015795 _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] 0.012427 _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] 0.007039 _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 NI A 1 501 452 NI NI . E 5 1FZ A 1 502 501 1FZ 1FZ . F 6 MG A 1 503 2 MG MG . G 7 CL A 1 504 1 CL CL . H 8 HOH A 1 601 2 HOH HOH . H 8 HOH A 2 602 15 HOH HOH . H 8 HOH A 3 603 33 HOH HOH . H 8 HOH A 4 604 31 HOH HOH . H 8 HOH A 5 605 3 HOH HOH . H 8 HOH A 6 606 17 HOH HOH . H 8 HOH A 7 607 29 HOH HOH . H 8 HOH A 8 608 30 HOH HOH . H 8 HOH A 9 609 8 HOH HOH . H 8 HOH A 10 610 22 HOH HOH . H 8 HOH A 11 611 28 HOH HOH . H 8 HOH A 12 612 13 HOH HOH . H 8 HOH A 13 613 35 HOH HOH . H 8 HOH A 14 614 36 HOH HOH . H 8 HOH A 15 615 41 HOH HOH . H 8 HOH A 16 616 38 HOH HOH . H 8 HOH A 17 617 14 HOH HOH . H 8 HOH A 18 618 39 HOH HOH . H 8 HOH A 19 619 1 HOH HOH . I 8 HOH P 1 101 26 HOH HOH . J 8 HOH T 1 101 6 HOH HOH . J 8 HOH T 2 102 4 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 . . . E 5 35.006 4.811 23.052 1 131.83 ? O2 1FZ 502 A 1 HETATM 2 O O4 1FZ . . . E 5 36.097 0.959 21.202 1 128.16 ? O4 1FZ 502 A 1 HETATM 3 C C4 1FZ . . . E 5 35.35 1.894 21.338 1 129.22 ? C4 1FZ 502 A 1 HETATM 4 C C5 1FZ . . . E 5 34.094 1.862 20.492 1 132.91 ? C5 1FZ 502 A 1 HETATM 5 C C6 1FZ . . . E 5 33.216 2.926 20.617 1 130.49 ? C6 1FZ 502 A 1 HETATM 6 C C5M 1FZ . . . E 5 33.815 0.695 19.532 1 129.53 ? C5M 1FZ 502 A 1 HETATM 7 N N3 1FZ . . . E 5 35.662 2.862 22.206 1 127.65 ? N3 1FZ 502 A 1 HETATM 8 C C2 1FZ . . . E 5 34.741 3.931 22.291 1 129.61 ? C2 1FZ 502 A 1 HETATM 9 N N1 1FZ . . . E 5 33.486 4.002 21.514 1 128.98 ? N1 1FZ 502 A 1 HETATM 10 C C1' 1FZ . . . E 5 32.644 5.042 21.662 1 126.67 ? C1' 1FZ 502 A 1 HETATM 11 C C2' 1FZ . . . E 5 33.102 6.271 20.798 1 119.76 ? C2' 1FZ 502 A 1 HETATM 12 C C3' 1FZ . . . E 5 32.166 6.226 19.611 1 116.36 ? C3' 1FZ 502 A 1 HETATM 13 O O3' 1FZ . . . E 5 31.867 7.546 19.151 1 101.72 ? O3' 1FZ 502 A 1 HETATM 14 O O4' 1FZ . . . E 5 31.359 4.629 21.196 1 123.62 ? O4' 1FZ 502 A 1 HETATM 15 C C4' 1FZ . . . E 5 30.913 5.558 20.171 1 118.34 ? C4' 1FZ 502 A 1 HETATM 16 C C5' 1FZ . . . E 5 30.183 4.825 19.074 1 123.88 ? C5' 1FZ 502 A 1 HETATM 17 O O5' 1FZ . . . E 5 30.644 3.477 18.963 1 127.77 ? O5' 1FZ 502 A 1 HETATM 18 P PA 1FZ . . . E 5 30.796 2.802 17.547 1 119.99 ? PA 1FZ 502 A 1 HETATM 19 O O1A 1FZ . . . E 5 29.408 2.767 16.835 1 107.17 ? O1A 1FZ 502 A 1 HETATM 20 O O2A 1FZ . . . E 5 31.234 1.423 17.747 1 110.47 ? O2A 1FZ 502 A 1 HETATM 21 N N3A 1FZ . . . E 5 31.888 3.603 16.624 1 125.93 ? N3A 1FZ 502 A 1 HETATM 22 P PB 1FZ . . . E 5 31.634 5.072 15.946 1 121.34 ? PB 1FZ 502 A 1 HETATM 23 O O1B 1FZ . . . E 5 32.304 6.146 16.767 1 112.31 ? O1B 1FZ 502 A 1 HETATM 24 O O2B 1FZ . . . E 5 30.206 5.361 15.846 1 105.55 ? O2B 1FZ 502 A 1 HETATM 25 O O3B 1FZ . . . E 5 32.303 5.104 14.504 1 119.01 ? O3B 1FZ 502 A 1 HETATM 26 P PG 1FZ . . . E 5 31.91 4.449 13.099 1 123.21 ? PG 1FZ 502 A 1 HETATM 27 O O1G 1FZ . . . E 5 30.468 3.968 13.138 1 108.15 ? O1G 1FZ 502 A 1 HETATM 28 O O3G 1FZ . . . E 5 32.071 5.492 12.007 1 109.35 ? O3G 1FZ 502 A 1 HETATM 29 O O2G 1FZ . . . E 5 32.83 3.278 12.817 1 118.32 ? O2G 1FZ 502 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 244 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 29 #