data_4Q8F # _model_server_result.job_id nDsIgn9kJXHDs44m6OtKNg _model_server_result.datetime_utc '2024-11-14 17:36:58' _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 4q8f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":506}' # _entry.id 4Q8F # _exptl.entry_id 4Q8F _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 2 _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 4Q8F _cell.length_a 98.692 _cell.length_b 98.692 _cell.length_c 81.812 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4Q8F _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,K,L,M _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 F N N ? 5 I N 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' DC 3 T DC 4 1_555 B P P9G 4 T P9G 5 1_555 ? A ? ? A ? ? ? ? ? ? ? 1.614 ? covale ? covale2 B O3' DC 3 T DC 4 1_555 B P P9G 4 T P9G 5 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.609 ? covale ? covale3 B O3' P9G 4 T P9G 5 1_555 B P DT 5 T DT 6 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.603 ? metalc ? metalc1 A OD1 ASP 16 A ASP 13 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc2 A OD2 ASP 16 A ASP 13 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.867 ? metalc ? metalc3 A OD2 ASP 16 A ASP 13 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? metalc ? metalc4 A O MET 17 A MET 14 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? metalc ? metalc5 A OD2 ASP 118 A ASP 115 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc6 A OD1 ASP 118 A ASP 115 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc7 A OE2 GLU 119 A GLU 116 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc8 D MG MG . A MG 501 1_555 F O1B XG4 . A XG4 503 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.053 ? metalc ? metalc9 D MG MG . A MG 501 1_555 F O1B XG4 . A XG4 503 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.151 ? metalc ? metalc10 D MG MG . A MG 501 1_555 F O1A XG4 . A XG4 503 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.228 ? metalc ? metalc11 D MG MG . A MG 501 1_555 F O1G XG4 . A XG4 503 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.242 ? metalc ? metalc12 D MG MG . A MG 501 1_555 F O1G XG4 . A XG4 503 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.252 ? metalc ? metalc13 D MG MG . A MG 501 1_555 F O1A XG4 . A XG4 503 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.349 ? metalc ? metalc14 E MG MG . A MG 502 1_555 F O1A XG4 . A XG4 503 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.371 ? metalc ? metalc15 E MG MG . A MG 502 1_555 F O1A XG4 . A XG4 503 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.387 ? metalc ? metalc16 E MG MG . A MG 502 1_555 K O HOH . A HOH 615 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc17 E MG MG . A MG 502 1_555 C O3' DC 8 P DC 8 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.735 ? metalc ? metalc18 E MG MG . A MG 502 1_555 C O3' DC 8 P DC 8 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.775 ? hydrog WATSON-CRICK hydrog1 B N3 DT 5 T DT 6 1_555 C N1 DA 7 P DA 7 1_555 ? ? ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B O4 DT 5 T DT 6 1_555 C N6 DA 7 P DA 7 1_555 ? ? ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B N3 DC 6 T DC 7 1_555 C N1 DG 6 P DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N4 DC 6 T DC 7 1_555 C O6 DG 6 P DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O2 DC 6 T DC 7 1_555 C N2 DG 6 P DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N1 DA 7 T DA 8 1_555 C N3 DT 5 P DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N6 DA 7 T DA 8 1_555 C O4 DT 5 P DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N3 DC 8 T DC 9 1_555 C N1 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N4 DC 8 T DC 9 1_555 C O6 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B O2 DC 8 T DC 9 1_555 C N2 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N1 DA 9 T DA 10 1_555 C N3 DT 3 P DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N6 DA 9 T DA 10 1_555 C O4 DT 3 P DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N3 DC 10 T DC 11 1_555 C N1 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N4 DC 10 T DC 11 1_555 C O6 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B O2 DC 10 T DC 11 1_555 C N2 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N3 DT 11 T DT 12 1_555 C N1 DA 1 P DA 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B O4 DT 11 T DT 12 1_555 C N6 DA 1 P DA 1 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 610 n n N1 C6 XG4 sing 611 n n N1 HN1 XG4 sing 612 n n N3 C2 XG4 doub 613 n n N2 C2 XG4 sing 614 n n N2 HN2 XG4 sing 615 n n N2 HN2A XG4 sing 616 n n N3 C4 XG4 sing 617 n n N9 C4 XG4 sing 618 n y C4 C5 XG4 doub 619 n y C5 N7 XG4 sing 620 n y C5 C6 XG4 sing 621 n n C6 O6 XG4 doub 622 n n C8 N7 XG4 doub 623 n y N9 C8 XG4 sing 624 n y C8 H8 XG4 sing 625 n n C1' N9 XG4 sing 626 n n O5' PA XG4 sing 627 n n O1A PA XG4 doub 628 n n PA O2A XG4 sing 629 n n PA N3A XG4 sing 630 n n O1B PB XG4 doub 631 n n N3A PB XG4 sing 632 n n PB O2B XG4 sing 633 n n PB O3B XG4 sing 634 n n O1G PG XG4 doub 635 n n PG O3B XG4 sing 636 n n PG O2G XG4 sing 637 n n PG O3G XG4 sing 638 n n O4' C1' XG4 sing 639 n n C1' C2' XG4 sing 640 n n C1' H1' XG4 sing 641 n n C2' C3' XG4 sing 642 n n C2' H2' XG4 sing 643 n n C2' "H2'A" XG4 sing 644 n n O2A HO2A XG4 sing 645 n n O2B HO2B XG4 sing 646 n n O2G HO2G XG4 sing 647 n n C4' C3' XG4 sing 648 n n C3' O3' XG4 sing 649 n n C3' H3' XG4 sing 650 n n O3' HO3' XG4 sing 651 n n N3A HN3A XG4 sing 652 n n O3G HO3G XG4 sing 653 n n O4' C4' XG4 sing 654 n n C4' C5' XG4 sing 655 n n C4' H4' XG4 sing 656 n n C5' O5' XG4 sing 657 n n C5' H5' XG4 sing 658 n n C5' "H5'A" XG4 sing 659 n n # _atom_sites.entry_id 4Q8F _atom_sites.fract_transf_matrix[1][1] 0.010133 _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] 0.0117 _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] 0.012223 _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 1 501 433 MG MG . E 4 MG A 1 502 434 MG MG . F 5 XG4 A 1 503 435 XG4 XG4 . G 6 GOL A 1 504 503 GOL GOL . H 6 GOL A 1 505 504 GOL GOL . I 5 XG4 A 1 506 505 XG4 XG4 . J 6 GOL A 1 507 549 GOL GOL . K 7 HOH A 1 601 506 HOH HOH . K 7 HOH A 2 602 507 HOH HOH . K 7 HOH A 3 603 508 HOH HOH . K 7 HOH A 4 604 509 HOH HOH . K 7 HOH A 5 605 510 HOH HOH . K 7 HOH A 6 606 511 HOH HOH . K 7 HOH A 7 607 514 HOH HOH . K 7 HOH A 8 608 515 HOH HOH . K 7 HOH A 9 609 516 HOH HOH . K 7 HOH A 10 610 517 HOH HOH . K 7 HOH A 11 611 518 HOH HOH . K 7 HOH A 12 612 519 HOH HOH . K 7 HOH A 13 613 520 HOH HOH . K 7 HOH A 14 614 521 HOH HOH . K 7 HOH A 15 615 522 HOH HOH . K 7 HOH A 16 616 523 HOH HOH . K 7 HOH A 17 617 524 HOH HOH . K 7 HOH A 18 618 525 HOH HOH . K 7 HOH A 19 619 526 HOH HOH . K 7 HOH A 20 620 527 HOH HOH . K 7 HOH A 21 621 529 HOH HOH . K 7 HOH A 22 622 530 HOH HOH . K 7 HOH A 23 623 531 HOH HOH . K 7 HOH A 24 624 532 HOH HOH . K 7 HOH A 25 625 533 HOH HOH . K 7 HOH A 26 626 534 HOH HOH . K 7 HOH A 27 627 535 HOH HOH . K 7 HOH A 28 628 536 HOH HOH . K 7 HOH A 29 629 540 HOH HOH . K 7 HOH A 30 630 541 HOH HOH . K 7 HOH A 31 631 542 HOH HOH . K 7 HOH A 32 632 544 HOH HOH . K 7 HOH A 33 633 548 HOH HOH . L 7 HOH T 1 101 538 HOH HOH . L 7 HOH T 2 102 539 HOH HOH . L 7 HOH T 3 103 546 HOH HOH . L 7 HOH T 4 104 547 HOH HOH . M 7 HOH P 1 101 512 HOH HOH . M 7 HOH P 2 102 545 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 . . . I 5 46.881 -16.98 -1.277 0.67 29.17 ? N1 XG4 506 A 1 HETATM 2 C C2 XG4 . . . I 5 47.373 -16.034 -2.099 0.67 34.44 ? C2 XG4 506 A 1 HETATM 3 N N2 XG4 . . . I 5 47.566 -14.785 -1.617 0.67 36.25 ? N2 XG4 506 A 1 HETATM 4 N N3 XG4 . . . I 5 47.687 -16.273 -3.397 0.67 34.1 ? N3 XG4 506 A 1 HETATM 5 C C4 XG4 . . . I 5 47.518 -17.5 -3.94 0.67 35.12 ? C4 XG4 506 A 1 HETATM 6 C C5 XG4 . . . I 5 46.984 -18.576 -3.094 0.67 32.59 ? C5 XG4 506 A 1 HETATM 7 C C6 XG4 . . . I 5 46.664 -18.236 -1.686 0.67 32.27 ? C6 XG4 506 A 1 HETATM 8 O O6 XG4 . . . I 5 46.209 -19.093 -0.901 0.67 37 ? O6 XG4 506 A 1 HETATM 9 N N7 XG4 . . . I 5 46.917 -19.673 -3.872 0.67 33.26 ? N7 XG4 506 A 1 HETATM 10 C C8 XG4 . . . I 5 47.37 -19.328 -5.105 0.67 31.87 ? C8 XG4 506 A 1 HETATM 11 N N9 XG4 . . . I 5 47.727 -18.032 -5.146 0.67 32.83 ? N9 XG4 506 A 1 HETATM 12 C C1' XG4 . . . I 5 48.264 -17.311 -6.329 0.67 26.3 ? C1' XG4 506 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 12 #