data_8E8J # _model_server_result.job_id sH6vmCREQjxyR7_OItvyzA _model_server_result.datetime_utc '2024-10-31 07:16:02' _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 8e8j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":503}' # _entry.id 8E8J # _exptl.entry_id 8E8J _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 8E8J _cell.length_a 98.019 _cell.length_b 98.019 _cell.length_c 81.849 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8E8J _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 OD1 ASP 16 A ASP 13 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? metalc ? metalc2 A OD2 ASP 16 A ASP 13 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? metalc ? metalc3 A O MET 17 A MET 14 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc4 A OD2 ASP 118 A ASP 115 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? metalc ? metalc5 A OD1 ASP 118 A ASP 115 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? metalc ? metalc6 A OE1 GLU 119 A GLU 116 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.974 ? metalc ? metalc7 D MG MG . A MG 501 1_555 F O1A XG4 . A XG4 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? metalc ? metalc8 D MG MG . A MG 501 1_555 F O1B XG4 . A XG4 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? metalc ? metalc9 D MG MG . A MG 501 1_555 F O2G XG4 . A XG4 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc10 E MG MG . A MG 502 1_555 F O1A XG4 . A XG4 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.425 ? metalc ? metalc11 E MG MG . A MG 502 1_555 G O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? metalc ? metalc12 E MG MG . A MG 502 1_555 G O HOH . A HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? hydrog WATSON-CRICK hydrog1 B N3 DC 5 T DC 6 1_555 C N1 G 8 P G 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N4 DC 5 T DC 6 1_555 C O6 G 8 P G 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O2 DC 5 T DC 6 1_555 C N2 G 8 P G 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N3 DT 6 T DT 7 1_555 C N1 DA 7 P DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O4 DT 6 T DT 7 1_555 C N6 DA 7 P DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N1 DG 7 T DG 8 1_555 C N3 DC 6 P DC 7 1_555 ? A ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N1 DG 7 T DG 8 1_555 C N3 DC 6 P DC 7 1_555 ? B ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N2 DG 7 T DG 8 1_555 C O2 DC 6 P DC 7 1_555 ? A ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N2 DG 7 T DG 8 1_555 C O2 DC 6 P DC 7 1_555 ? B ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B O6 DG 7 T DG 8 1_555 C N4 DC 6 P DC 7 1_555 ? A ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B O6 DG 7 T DG 8 1_555 C N4 DC 6 P DC 7 1_555 ? B ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N1 DA 8 T DA 9 1_555 C N3 DT 5 P DT 6 1_555 ? A ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N1 DA 8 T DA 9 1_555 C N3 DT 5 P DT 6 1_555 ? B ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N6 DA 8 T DA 9 1_555 C O4 DT 5 P DT 6 1_555 ? A ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N6 DA 8 T DA 9 1_555 C O4 DT 5 P DT 6 1_555 ? B ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N3 DC 9 T DC 10 1_555 C N1 DG 4 P DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N4 DC 9 T DC 10 1_555 C O6 DG 4 P DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O2 DC 9 T DC 10 1_555 C N2 DG 4 P DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N1 DG 10 T DG 11 1_555 C N3 DC 3 P DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N2 DG 10 T DG 11 1_555 C O2 DC 3 P DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B O6 DG 10 T DG 11 1_555 C N4 DC 3 P DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N3 DC 11 T DC 12 1_555 C N1 DG 2 P DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B N4 DC 11 T DC 12 1_555 C O6 DG 2 P DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B O2 DC 11 T DC 12 1_555 C N2 DG 2 P DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B N3 DT 12 T DT 13 1_555 C N1 DA 1 P DA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 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 565 n n N1 C6 XG4 sing 566 n n N1 HN1 XG4 sing 567 n n N3 C2 XG4 doub 568 n n N2 C2 XG4 sing 569 n n N2 HN2 XG4 sing 570 n n N2 HN2A XG4 sing 571 n n N3 C4 XG4 sing 572 n n N9 C4 XG4 sing 573 n y C4 C5 XG4 doub 574 n y C5 N7 XG4 sing 575 n y C5 C6 XG4 sing 576 n n C6 O6 XG4 doub 577 n n C8 N7 XG4 doub 578 n y N9 C8 XG4 sing 579 n y C8 H8 XG4 sing 580 n n C1' N9 XG4 sing 581 n n O5' PA XG4 sing 582 n n O1A PA XG4 doub 583 n n PA O2A XG4 sing 584 n n PA N3A XG4 sing 585 n n O1B PB XG4 doub 586 n n N3A PB XG4 sing 587 n n PB O2B XG4 sing 588 n n PB O3B XG4 sing 589 n n O1G PG XG4 doub 590 n n PG O3B XG4 sing 591 n n PG O2G XG4 sing 592 n n PG O3G XG4 sing 593 n n O4' C1' XG4 sing 594 n n C1' C2' XG4 sing 595 n n C1' H1' XG4 sing 596 n n C2' C3' XG4 sing 597 n n C2' H2' XG4 sing 598 n n C2' "H2'A" XG4 sing 599 n n O2A HO2A XG4 sing 600 n n O2B HO2B XG4 sing 601 n n O2G HO2G XG4 sing 602 n n C4' C3' XG4 sing 603 n n C3' O3' XG4 sing 604 n n C3' H3' XG4 sing 605 n n O3' HO3' XG4 sing 606 n n N3A HN3A XG4 sing 607 n n O3G HO3G XG4 sing 608 n n O4' C4' XG4 sing 609 n n C4' C5' XG4 sing 610 n n C4' H4' XG4 sing 611 n n C5' O5' XG4 sing 612 n n C5' H5' XG4 sing 613 n n C5' "H5'A" XG4 sing 614 n n # _atom_sites.entry_id 8E8J _atom_sites.fract_transf_matrix[1][1] 0.010202 _atom_sites.fract_transf_matrix[1][2] 0.00589 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01178 _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] 0.012218 _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 1 503 505 XG4 XG4 . G 6 HOH A 1 601 3 HOH HOH . G 6 HOH A 2 602 8 HOH HOH . G 6 HOH A 3 603 1 HOH HOH . G 6 HOH A 4 604 10 HOH HOH . G 6 HOH A 5 605 4 HOH HOH . G 6 HOH A 6 606 6 HOH HOH . G 6 HOH A 7 607 2 HOH HOH . G 6 HOH A 8 608 5 HOH HOH . G 6 HOH A 9 609 9 HOH HOH . G 6 HOH A 10 610 7 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 -23.234 50.702 5.584 1 28.46 ? N1 XG4 503 A 1 HETATM 2 C C2 XG4 . . . F 5 -22.089 50.632 4.852 1 23.87 ? C2 XG4 503 A 1 HETATM 3 N N2 XG4 . . . F 5 -21.725 51.757 4.246 1 19.75 ? N2 XG4 503 A 1 HETATM 4 N N3 XG4 . . . F 5 -21.327 49.556 4.694 1 20.59 ? N3 XG4 503 A 1 HETATM 5 C C4 XG4 . . . F 5 -21.778 48.489 5.324 1 22.58 ? C4 XG4 503 A 1 HETATM 6 C C5 XG4 . . . F 5 -22.884 48.414 6.06 1 27.87 ? C5 XG4 503 A 1 HETATM 7 C C6 XG4 . . . F 5 -23.637 49.583 6.196 1 26.87 ? C6 XG4 503 A 1 HETATM 8 O O6 XG4 . . . F 5 -24.656 49.62 6.871 1 26.49 ? O6 XG4 503 A 1 HETATM 9 N N7 XG4 . . . F 5 -23.055 47.135 6.561 1 22.23 ? N7 XG4 503 A 1 HETATM 10 C C8 XG4 . . . F 5 -22.025 46.475 6.111 1 26.55 ? C8 XG4 503 A 1 HETATM 11 N N9 XG4 . . . F 5 -21.2 47.25 5.349 1 32.95 ? N9 XG4 503 A 1 HETATM 12 P PA XG4 . . . F 5 -21.255 41.535 5.608 1 23.53 ? PA XG4 503 A 1 HETATM 13 P PB XG4 . . . F 5 -18.753 41.308 7.06 1 20.84 ? PB XG4 503 A 1 HETATM 14 P PG XG4 . . . F 5 -19.245 38.692 8.056 1 24.69 ? PG XG4 503 A 1 HETATM 15 C C1' XG4 . . . F 5 -19.931 46.902 4.69 1 25.79 ? C1' XG4 503 A 1 HETATM 16 O O1A XG4 . . . F 5 -21.465 40.142 5.262 1 39.58 ? O1A XG4 503 A 1 HETATM 17 O O1B XG4 . . . F 5 -18.146 40.943 5.791 1 20.11 ? O1B XG4 503 A 1 HETATM 18 O O1G XG4 . . . F 5 -20.273 38.477 9.022 1 25.71 ? O1G XG4 503 A 1 HETATM 19 C C2' XG4 . . . F 5 -18.875 46.322 5.611 1 18.34 ? C2' XG4 503 A 1 HETATM 20 O O2A XG4 . . . F 5 -22.593 42.2 5.977 1 22.56 -1 O2A XG4 503 A 1 HETATM 21 O O2B XG4 . . . F 5 -18.089 42.543 7.674 1 24.73 -1 O2B XG4 503 A 1 HETATM 22 O O2G XG4 . . . F 5 -19.706 38.545 6.629 1 17.69 -1 O2G XG4 503 A 1 HETATM 23 C C3' XG4 . . . F 5 -19.064 44.816 5.505 1 27.4 ? C3' XG4 503 A 1 HETATM 24 O O3' XG4 . . . F 5 -17.788 44.182 5.479 1 17.08 ? O3' XG4 503 A 1 HETATM 25 N N3A XG4 . . . F 5 -20.311 41.696 6.902 1 25.37 ? N3A XG4 503 A 1 HETATM 26 O O3B XG4 . . . F 5 -18.704 40.181 8.139 1 19.73 ? O3B XG4 503 A 1 HETATM 27 O O3G XG4 . . . F 5 -18.038 37.843 8.261 1 25.14 -1 O3G XG4 503 A 1 HETATM 28 C C4' XG4 . . . F 5 -19.777 44.62 4.164 1 26.41 ? C4' XG4 503 A 1 HETATM 29 O O4' XG4 . . . F 5 -20.196 45.922 3.711 1 24.63 ? O4' XG4 503 A 1 HETATM 30 C C5' XG4 . . . F 5 -20.99 43.731 4.222 1 29.17 ? C5' XG4 503 A 1 HETATM 31 O O5' XG4 . . . F 5 -20.579 42.384 4.488 1 36.35 ? O5' XG4 503 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 18 _model_server_stats.element_count 31 #