data_6PL7 # _model_server_result.job_id WfA-B6YFlmoZCqsVx_GdHA _model_server_result.datetime_utc '2024-11-13 03:13:27' _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 6pl7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 6PL7 # _exptl.entry_id 6PL7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 481.184 _entity.id 4 _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 120 _cell.entry_id 6PL7 _cell.length_a 98.7 _cell.length_b 98.7 _cell.length_c 82.447 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6PL7 _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,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 4 _struct_asym.id D _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 metalc ? metalc1 A OD2 ASP 16 A ASP 13 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc2 A OD1 ASP 16 A ASP 13 1_555 F MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc3 A O MET 17 A MET 14 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? metalc ? metalc4 A OD2 ASP 118 A ASP 115 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? metalc ? metalc5 A OD1 ASP 118 A ASP 115 1_555 F MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.499 ? metalc ? metalc6 A OE1 GLU 119 A GLU 116 1_555 F MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? metalc ? metalc7 D O1A 1FZ . A 1FZ 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc8 D O2B 1FZ . A 1FZ 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.967 ? metalc ? metalc9 D O2G 1FZ . A 1FZ 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc10 D O1A 1FZ . A 1FZ 501 1_555 F MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? metalc ? metalc11 F MG MG . A MG 503 1_555 C O3' DT 8 P DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? hydrog WATSON-CRICK hydrog1 B N1 DA 5 T DA 5 1_555 C N3 DT 8 P DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N6 DA 5 T DA 5 1_555 C O4 DT 8 P DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B N3 DT 6 T DT 6 1_555 C N1 DA 7 P DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B O4 DT 6 T DT 6 1_555 C N6 DA 7 P DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N1 DG 7 T DG 7 1_555 C N3 DC 6 P DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N2 DG 7 T DG 7 1_555 C O2 DC 6 P DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B O6 DG 7 T DG 7 1_555 C N4 DC 6 P DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N1 DA 8 T DA 8 1_555 C N3 DT 5 P DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N6 DA 8 T DA 8 1_555 C O4 DT 5 P DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N3 DC 9 T DC 9 1_555 C N1 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N4 DC 9 T DC 9 1_555 C O6 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B O2 DC 9 T DC 9 1_555 C N2 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N1 DG 10 T DG 10 1_555 C N3 DC 3 P DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N2 DG 10 T DG 10 1_555 C O2 DC 3 P DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B O6 DG 10 T DG 10 1_555 C N4 DC 3 P DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N3 DC 11 T DC 11 1_555 C N1 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N4 DC 11 T DC 11 1_555 C O6 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O2 DC 11 T DC 11 1_555 C N2 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N3 DT 12 T DT 12 1_555 C N1 DA 1 P DA 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B O4 DT 12 T DT 12 1_555 C N6 DA 1 P DA 1 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 1 n n O1G PG 1FZ sing 2 n n O2G PG 1FZ sing 3 n n PG O3B 1FZ sing 4 n n O1A PA 1FZ doub 5 n n O3B PB 1FZ sing 6 n n O2B PB 1FZ doub 7 n n PB N3A 1FZ sing 8 n n PB O1B 1FZ sing 9 n n PA N3A 1FZ sing 10 n n PA O2A 1FZ sing 11 n n PA O5' 1FZ sing 12 n n C5' O5' 1FZ sing 13 n n C5' C4' 1FZ sing 14 n n O3' C3' 1FZ sing 15 n n C4' C3' 1FZ sing 16 n n C4' O4' 1FZ sing 17 n n C3' C2' 1FZ sing 18 n n O4' C1' 1FZ sing 19 n n C5M C5 1FZ sing 20 n n C2' C1' 1FZ sing 21 n n C6 C5 1FZ doub 22 n n C6 N1 1FZ sing 23 n n C1' N1 1FZ sing 24 n n C5 C4 1FZ sing 25 n n N1 C2 1FZ sing 26 n n C4 O4 1FZ doub 27 n n C4 N3 1FZ sing 28 n n C2 N3 1FZ sing 29 n n C2 O2 1FZ doub 30 n n C6 H1 1FZ sing 31 n n C5M H2 1FZ sing 32 n n C5M H3 1FZ sing 33 n n C5M H4 1FZ sing 34 n n N3 H5 1FZ sing 35 n n C1' H6 1FZ sing 36 n n C2' H7 1FZ sing 37 n n C2' H8 1FZ sing 38 n n C3' H9 1FZ sing 39 n n O3' H10 1FZ sing 40 n n C4' H11 1FZ sing 41 n n C5' H12 1FZ sing 42 n n C5' H13 1FZ sing 43 n n O2A H14 1FZ sing 44 n n N3A H15 1FZ sing 45 n n O1B H16 1FZ sing 46 n n O1G H17 1FZ sing 47 n n O2G H18 1FZ sing 48 n n # _atom_sites.entry_id 6PL7 _atom_sites.fract_transf_matrix[1][1] 0.010132 _atom_sites.fract_transf_matrix[1][2] 0.00585 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011699 _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] 0.012129 _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 1FZ A 1 501 501 1FZ 1FZ . E 5 MG A 1 502 502 MG MG . F 5 MG A 1 503 503 MG MG . G 6 GOL A 1 504 504 GOL GOL . H 7 HOH A 1 601 33 HOH HOH . H 7 HOH A 2 602 11 HOH HOH . H 7 HOH A 3 603 6 HOH HOH . H 7 HOH A 4 604 27 HOH HOH . H 7 HOH A 5 605 8 HOH HOH . H 7 HOH A 6 606 5 HOH HOH . H 7 HOH A 7 607 54 HOH HOH . H 7 HOH A 8 608 47 HOH HOH . H 7 HOH A 9 609 3 HOH HOH . H 7 HOH A 10 610 46 HOH HOH . H 7 HOH A 11 611 59 HOH HOH . H 7 HOH A 12 612 7 HOH HOH . H 7 HOH A 13 613 4 HOH HOH . H 7 HOH A 14 614 24 HOH HOH . H 7 HOH A 15 615 10 HOH HOH . H 7 HOH A 16 616 19 HOH HOH . H 7 HOH A 17 617 18 HOH HOH . H 7 HOH A 18 618 12 HOH HOH . H 7 HOH A 19 619 1 HOH HOH . H 7 HOH A 20 620 22 HOH HOH . H 7 HOH A 21 621 15 HOH HOH . H 7 HOH A 22 622 25 HOH HOH . H 7 HOH A 23 623 30 HOH HOH . H 7 HOH A 24 624 43 HOH HOH . H 7 HOH A 25 625 9 HOH HOH . H 7 HOH A 26 626 40 HOH HOH . H 7 HOH A 27 627 13 HOH HOH . H 7 HOH A 28 628 51 HOH HOH . H 7 HOH A 29 629 23 HOH HOH . H 7 HOH A 30 630 39 HOH HOH . H 7 HOH A 31 631 29 HOH HOH . H 7 HOH A 32 632 32 HOH HOH . H 7 HOH A 33 633 49 HOH HOH . H 7 HOH A 34 634 58 HOH HOH . H 7 HOH A 35 635 45 HOH HOH . H 7 HOH A 36 636 53 HOH HOH . H 7 HOH A 37 637 38 HOH HOH . H 7 HOH A 38 638 52 HOH HOH . H 7 HOH A 39 639 42 HOH HOH . H 7 HOH A 40 640 2 HOH HOH . H 7 HOH A 41 641 28 HOH HOH . H 7 HOH A 42 642 48 HOH HOH . H 7 HOH A 43 643 36 HOH HOH . H 7 HOH A 44 644 35 HOH HOH . H 7 HOH A 45 645 21 HOH HOH . H 7 HOH A 46 646 50 HOH HOH . H 7 HOH A 47 647 44 HOH HOH . H 7 HOH A 48 648 20 HOH HOH . H 7 HOH A 49 649 56 HOH HOH . I 7 HOH T 1 101 41 HOH HOH . I 7 HOH T 2 102 26 HOH HOH . I 7 HOH T 3 103 57 HOH HOH . J 7 HOH P 1 101 16 HOH HOH . J 7 HOH P 2 102 17 HOH HOH . J 7 HOH P 3 103 14 HOH HOH . J 7 HOH P 4 104 37 HOH HOH . J 7 HOH P 5 105 34 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 . . . D 4 -53.428 -5.594 -4.136 1 20.96 ? O2 1FZ 501 A 1 HETATM 2 O O4 1FZ . . . D 4 -53.764 -1.567 -6.241 1 19.9 ? O4 1FZ 501 A 1 HETATM 3 C C4 1FZ . . . D 4 -53.056 -2.448 -5.754 1 20.52 ? C4 1FZ 501 A 1 HETATM 4 C C5 1FZ . . . D 4 -51.674 -2.35 -5.744 1 21.19 ? C5 1FZ 501 A 1 HETATM 5 C C6 1FZ . . . D 4 -50.942 -3.393 -5.208 1 21.32 ? C6 1FZ 501 A 1 HETATM 6 C C5M 1FZ . . . D 4 -51.03 -1.247 -6.307 1 21.24 ? C5M 1FZ 501 A 1 HETATM 7 N N3 1FZ . . . D 4 -53.647 -3.572 -5.203 1 21.08 ? N3 1FZ 501 A 1 HETATM 8 C C2 1FZ . . . D 4 -52.892 -4.603 -4.638 1 21.73 ? C2 1FZ 501 A 1 HETATM 9 N N1 1FZ . . . D 4 -51.573 -4.5 -4.577 1 21.41 ? N1 1FZ 501 A 1 HETATM 10 C C1' 1FZ . . . D 4 -50.865 -5.706 -4.002 1 22.19 ? C1' 1FZ 501 A 1 HETATM 11 C C2' 1FZ . . . D 4 -49.758 -6.697 -4.497 1 21.26 ? C2' 1FZ 501 A 1 HETATM 12 C C3' 1FZ . . . D 4 -48.667 -5.727 -4.71 1 22.04 ? C3' 1FZ 501 A 1 HETATM 13 O O3' 1FZ . . . D 4 -47.479 -6.45 -4.954 1 22.12 ? O3' 1FZ 501 A 1 HETATM 14 O O4' 1FZ . . . D 4 -49.836 -4.647 -3.772 1 22.38 ? O4' 1FZ 501 A 1 HETATM 15 C C4' 1FZ . . . D 4 -48.703 -5.269 -3.217 1 22.44 ? C4' 1FZ 501 A 1 HETATM 16 C C5' 1FZ . . . D 4 -47.647 -4.181 -2.998 1 22.63 ? C5' 1FZ 501 A 1 HETATM 17 O O5' 1FZ . . . D 4 -47.947 -3.045 -3.864 1 23.76 ? O5' 1FZ 501 A 1 HETATM 18 P PA 1FZ . . . D 4 -46.852 -2.139 -4.745 1 24.75 ? PA 1FZ 501 A 1 HETATM 19 O O1A 1FZ . . . D 4 -45.536 -1.905 -4.097 1 24.59 ? O1A 1FZ 501 A 1 HETATM 20 O O2A 1FZ . . . D 4 -47.57 -0.759 -5.257 1 26.72 ? O2A 1FZ 501 A 1 HETATM 21 N N3A 1FZ . . . D 4 -46.736 -3.057 -6.105 1 24.2 ? N3A 1FZ 501 A 1 HETATM 22 P PB 1FZ . . . D 4 -45.459 -4.192 -6.101 1 23.45 ? PB 1FZ 501 A 1 HETATM 23 O O1B 1FZ . . . D 4 -46.135 -5.528 -6.728 1 22.6 ? O1B 1FZ 501 A 1 HETATM 24 O O2B 1FZ . . . D 4 -44.777 -4.422 -4.801 1 23.78 ? O2B 1FZ 501 A 1 HETATM 25 O O3B 1FZ . . . D 4 -44.443 -3.668 -7.263 1 26.01 ? O3B 1FZ 501 A 1 HETATM 26 P PG 1FZ . . . D 4 -43.185 -2.668 -7.218 1 27.75 ? PG 1FZ 501 A 1 HETATM 27 O O1G 1FZ . . . D 4 -41.835 -3.5 -7.246 1 29.26 ? O1G 1FZ 501 A 1 HETATM 28 O O3G 1FZ . . . D 4 -43.262 -1.72 -8.363 1 30.73 ? O3G 1FZ 501 A 1 HETATM 29 O O2G 1FZ . . . D 4 -43.152 -1.908 -5.813 1 25.51 ? O2G 1FZ 501 A 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 29 #