data_8E88 # _model_server_result.job_id j05rNeUNtmzsmkAjLEfDmA _model_server_result.datetime_utc '2024-10-31 07:14:38' _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 8e88 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":503}' # _entry.id 8E88 # _exptl.entry_id 8E88 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _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]guanosine" _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 8E88 _cell.length_a 98.347 _cell.length_b 98.347 _cell.length_c 81.171 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8E88 _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 _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 metalc ? metalc1 A OD2 ASP 16 A ASP 13 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.9 ? metalc ? metalc2 A OD1 ASP 16 A ASP 13 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.558 ? metalc ? metalc3 A O MET 17 A MET 14 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc4 A OD2 ASP 118 A ASP 115 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? metalc ? metalc5 A OD1 ASP 118 A ASP 115 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? metalc ? metalc6 A OE1 GLU 119 A GLU 116 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc7 D MG MG . A MG 501 1_555 F O1A XG4 . A XG4 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc8 D MG MG . A MG 501 1_555 F O1B XG4 . A XG4 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.899 ? metalc ? metalc9 D MG MG . A MG 501 1_555 F O3G XG4 . A XG4 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc10 E MG MG . A MG 502 1_555 F O1A XG4 . A XG4 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc11 E MG MG . A MG 502 1_555 G O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? metalc ? metalc12 E MG MG . A MG 502 1_555 C O3' U 8 P U 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? hydrog WATSON-CRICK hydrog1 B N1 DA 5 T DA 6 1_555 C N3 U 8 P U 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N6 DA 5 T DA 6 1_555 C O4 U 8 P U 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B N3 DT 6 T DT 7 1_555 C N1 DA 7 P DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B O4 DT 6 T DT 7 1_555 C N6 DA 7 P DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N1 DG 7 T DG 8 1_555 C N3 DC 6 P DC 7 1_555 ? A ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N1 DG 7 T DG 8 1_555 C N3 DC 6 P DC 7 1_555 ? B ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N2 DG 7 T DG 8 1_555 C O2 DC 6 P DC 7 1_555 ? A ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N2 DG 7 T DG 8 1_555 C O2 DC 6 P DC 7 1_555 ? B ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B O6 DG 7 T DG 8 1_555 C N4 DC 6 P DC 7 1_555 ? A ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B O6 DG 7 T DG 8 1_555 C N4 DC 6 P DC 7 1_555 ? B ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N1 DA 8 T DA 9 1_555 C N3 DT 5 P DT 6 1_555 ? A ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N1 DA 8 T DA 9 1_555 C N3 DT 5 P DT 6 1_555 ? B ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N6 DA 8 T DA 9 1_555 C O4 DT 5 P DT 6 1_555 ? A ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N6 DA 8 T DA 9 1_555 C O4 DT 5 P DT 6 1_555 ? B ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N3 DC 9 T DC 10 1_555 C N1 DG 4 P DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N4 DC 9 T DC 10 1_555 C O6 DG 4 P DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B O2 DC 9 T DC 10 1_555 C N2 DG 4 P DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N1 DG 10 T DG 11 1_555 C N3 DC 3 P DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N2 DG 10 T DG 11 1_555 C O2 DC 3 P DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B O6 DG 10 T DG 11 1_555 C N4 DC 3 P DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B N3 DC 11 T DC 12 1_555 C N1 DG 2 P DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N4 DC 11 T DC 12 1_555 C O6 DG 2 P DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B O2 DC 11 T DC 12 1_555 C N2 DG 2 P DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B N3 DT 12 T DT 13 1_555 C N1 DA 1 P DA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B O4 DT 12 T DT 13 1_555 C N6 DA 1 P DA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H17 N6 O12 P3' _chem_comp.formula_weight 506.196 _chem_comp.id XG4 _chem_comp.mon_nstd_flag . _chem_comp.name "2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine" _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 C2 N1 XG4 sing 560 n n N1 C6 XG4 sing 561 n n N1 HN1 XG4 sing 562 n n N3 C2 XG4 doub 563 n n N2 C2 XG4 sing 564 n n N2 HN2 XG4 sing 565 n n N2 HN2A XG4 sing 566 n n N3 C4 XG4 sing 567 n n N9 C4 XG4 sing 568 n y C4 C5 XG4 doub 569 n y C5 N7 XG4 sing 570 n y C5 C6 XG4 sing 571 n n C6 O6 XG4 doub 572 n n C8 N7 XG4 doub 573 n y N9 C8 XG4 sing 574 n y C8 H8 XG4 sing 575 n n C1' N9 XG4 sing 576 n n O5' PA XG4 sing 577 n n O1A PA XG4 doub 578 n n PA O2A XG4 sing 579 n n PA N3A XG4 sing 580 n n O1B PB XG4 doub 581 n n N3A PB XG4 sing 582 n n PB O2B XG4 sing 583 n n PB O3B XG4 sing 584 n n O1G PG XG4 doub 585 n n PG O3B XG4 sing 586 n n PG O2G XG4 sing 587 n n PG O3G XG4 sing 588 n n O4' C1' XG4 sing 589 n n C1' C2' XG4 sing 590 n n C1' H1' XG4 sing 591 n n C2' C3' XG4 sing 592 n n C2' H2' XG4 sing 593 n n C2' "H2'A" XG4 sing 594 n n O2A HO2A XG4 sing 595 n n O2B HO2B XG4 sing 596 n n O2G HO2G XG4 sing 597 n n C4' C3' XG4 sing 598 n n C3' O3' XG4 sing 599 n n C3' H3' XG4 sing 600 n n O3' HO3' XG4 sing 601 n n N3A HN3A XG4 sing 602 n n O3G HO3G XG4 sing 603 n n O4' C4' XG4 sing 604 n n C4' C5' XG4 sing 605 n n C4' H4' XG4 sing 606 n n C5' O5' XG4 sing 607 n n C5' H5' XG4 sing 608 n n C5' "H5'A" XG4 sing 609 n n # _atom_sites.entry_id 8E88 _atom_sites.fract_transf_matrix[1][1] 0.010168 _atom_sites.fract_transf_matrix[1][2] 0.005871 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011741 _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] 0.01232 _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 MG A 1 501 502 MG MG . E 4 MG A 1 502 503 MG MG . F 5 XG4 A 1 503 504 XG4 XG4 . G 6 HOH A 1 601 1 HOH HOH . G 6 HOH A 2 602 2 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 N N1 XG4 . . . F 5 -23.292 50.654 5.548 1 42.56 ? N1 XG4 503 A 1 HETATM 2 C C2 XG4 . . . F 5 -22.117 50.584 4.86 1 48.93 ? C2 XG4 503 A 1 HETATM 3 N N2 XG4 . . . F 5 -21.651 51.743 4.399 1 30.13 ? N2 XG4 503 A 1 HETATM 4 N N3 XG4 . . . F 5 -21.416 49.48 4.619 1 48.91 ? N3 XG4 503 A 1 HETATM 5 C C4 XG4 . . . F 5 -21.959 48.384 5.115 1 47.01 ? C4 XG4 503 A 1 HETATM 6 C C5 XG4 . . . F 5 -23.103 48.306 5.798 1 45.63 ? C5 XG4 503 A 1 HETATM 7 C C6 XG4 . . . F 5 -23.793 49.507 6.022 1 51.98 ? C6 XG4 503 A 1 HETATM 8 O O6 XG4 . . . F 5 -24.848 49.538 6.644 1 44.4 ? O6 XG4 503 A 1 HETATM 9 N N7 XG4 . . . F 5 -23.37 46.997 6.162 1 47.87 ? N7 XG4 503 A 1 HETATM 10 C C8 XG4 . . . F 5 -22.36 46.319 5.684 1 44.76 ? C8 XG4 503 A 1 HETATM 11 N N9 XG4 . . . F 5 -21.458 47.112 5.036 1 54.86 ? N9 XG4 503 A 1 HETATM 12 P PA XG4 . . . F 5 -21.521 41.73 5.467 1 45.97 ? PA XG4 503 A 1 HETATM 13 P PB XG4 . . . F 5 -19.006 41.285 6.836 1 50.58 ? PB XG4 503 A 1 HETATM 14 P PG XG4 . . . F 5 -19.342 38.633 7.897 1 42.34 ? PG XG4 503 A 1 HETATM 15 C C1' XG4 . . . F 5 -20.195 46.724 4.395 1 37.42 ? C1' XG4 503 A 1 HETATM 16 O O1A XG4 . . . F 5 -21.355 40.539 4.646 1 43.56 ? O1A XG4 503 A 1 HETATM 17 O O1B XG4 . . . F 5 -18.485 40.894 5.534 1 45.78 ? O1B XG4 503 A 1 HETATM 18 O O1G XG4 . . . F 5 -18.203 37.748 8.092 1 51.15 ? O1G XG4 503 A 1 HETATM 19 C C2' XG4 . . . F 5 -19.078 46.394 5.38 1 45 ? C2' XG4 503 A 1 HETATM 20 O O2A XG4 . . . F 5 -22.96 41.799 6.047 1 53.92 -1 O2A XG4 503 A 1 HETATM 21 O O2B XG4 . . . F 5 -18.285 42.554 7.373 1 43.68 -1 O2B XG4 503 A 1 HETATM 22 O O2G XG4 . . . F 5 -20.383 38.522 8.977 1 51.1 -1 O2G XG4 503 A 1 HETATM 23 C C3' XG4 . . . F 5 -19.022 44.874 5.379 1 40.14 ? C3' XG4 503 A 1 HETATM 24 O O3' XG4 . . . F 5 -17.687 44.408 5.562 1 27.46 ? O3' XG4 503 A 1 HETATM 25 N N3A XG4 . . . F 5 -20.561 41.701 6.758 1 52.68 ? N3A XG4 503 A 1 HETATM 26 O O3B XG4 . . . F 5 -18.893 40.158 7.932 1 40.02 ? O3B XG4 503 A 1 HETATM 27 O O3G XG4 . . . F 5 -20.006 38.472 6.556 1 47.43 -1 O3G XG4 503 A 1 HETATM 28 C C4' XG4 . . . F 5 -19.485 44.532 3.973 1 48.16 ? C4' XG4 503 A 1 HETATM 29 O O4' XG4 . . . F 5 -20.437 45.556 3.629 1 53.02 ? O4' XG4 503 A 1 HETATM 30 C C5' XG4 . . . F 5 -20.136 43.182 3.838 1 41.29 ? C5' XG4 503 A 1 HETATM 31 O O5' XG4 . . . F 5 -21.26 43.086 4.732 1 65.52 ? O5' XG4 503 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #