data_6IPK # _model_server_result.job_id leZQt-FQWB-jkgSqVwPEGA _model_server_result.datetime_utc '2024-11-26 12:15:10' _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 6ipk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 6IPK # _exptl.entry_id 6IPK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.18 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE" _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 6IPK _cell.length_a 122.827 _cell.length_b 122.827 _cell.length_c 49.859 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6IPK _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 _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 3 _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 OD1 ASP 204 A ASP 330 1_555 B MN MN . A MN 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.936 ? metalc ? metalc2 A OD2 ASP 204 A ASP 330 1_555 C MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc3 A OD2 ASP 206 A ASP 332 1_555 B MN MN . A MN 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc4 A OD1 ASP 206 A ASP 332 1_555 C MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc5 A OD2 ASP 280 A ASP 418 1_555 C MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? metalc ? metalc6 B MN MN . A MN 500 1_555 D O1A 8DG . A 8DG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc7 B MN MN . A MN 500 1_555 D O3G 8DG . A 8DG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc8 B MN MN . A MN 500 1_555 D O1B 8DG . A 8DG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc9 B MN MN . A MN 500 1_555 L O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc10 C MN MN . A MN 501 1_555 D O1A 8DG . A 8DG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.447 ? metalc ? metalc11 C MN MN . A MN 501 1_555 L O HOH . A HOH 629 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc12 C MN MN . A MN 501 1_555 L O HOH . A HOH 633 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.559 ? # _chem_comp.formula 'C10 H16 N5 O14 P3' _chem_comp.formula_weight 523.18 _chem_comp.id 8DG _chem_comp.mon_nstd_flag . _chem_comp.name "8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE" _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 PG O1G 8DG doub 1 n n PG O2G 8DG sing 2 n n PG O3G 8DG sing 3 n n PG O3B 8DG sing 4 n n O2G HOG2 8DG sing 5 n n O3G H3G 8DG sing 6 n n O3B PB 8DG sing 7 n n PB O1B 8DG doub 8 n n PB O2B 8DG sing 9 n n PB O3A 8DG sing 10 n n O2B HOB2 8DG sing 11 n n O3A PA 8DG sing 12 n n PA O1A 8DG doub 13 n n PA O2A 8DG sing 14 n n PA O5' 8DG sing 15 n n O2A HOA2 8DG sing 16 n n O5' C5' 8DG sing 17 n n C5' C4' 8DG sing 18 n n C5' "H5'1" 8DG sing 19 n n C5' "H5'2" 8DG sing 20 n n C4' O4' 8DG sing 21 n n C4' C3' 8DG sing 22 n n C4' H4' 8DG sing 23 n n O4' C1' 8DG sing 24 n n C3' O3' 8DG sing 25 n n C3' C2' 8DG sing 26 n n C3' H3' 8DG sing 27 n n O3' H1 8DG sing 28 n n C2' C1' 8DG sing 29 n n C2' "H2'1" 8DG sing 30 n n C2' "H2'2" 8DG sing 31 n n C1' N9 8DG sing 32 n n C1' H1' 8DG sing 33 n n N9 C8 8DG sing 34 n n N9 C4 8DG sing 35 n n C8 N7 8DG sing 36 n n C8 O8 8DG doub 37 n n N7 C5 8DG sing 38 n n N7 HN7 8DG sing 39 n n C5 C6 8DG sing 40 n n C5 C4 8DG doub 41 n n C6 O6 8DG doub 42 n n C6 N1 8DG sing 43 n n N1 C2 8DG sing 44 n n N1 HN1 8DG sing 45 n n C2 N2 8DG sing 46 n n C2 N3 8DG doub 47 n n N2 HN21 8DG sing 48 n n N2 HN22 8DG sing 49 n n N3 C4 8DG sing 50 n n # _atom_sites.entry_id 6IPK _atom_sites.fract_transf_matrix[1][1] 0.008142 _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] 0.008142 _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] 0.020057 _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 B 2 MN A 1 500 500 MN MN . C 2 MN A 1 501 501 MN MN . D 3 8DG A 1 502 502 8DG 8DG . E 4 SO4 A 1 503 503 SO4 SO4 . F 4 SO4 A 1 504 504 SO4 SO4 . G 4 SO4 A 1 505 505 SO4 SO4 . H 4 SO4 A 1 506 506 SO4 SO4 . I 4 SO4 A 1 507 507 SO4 SO4 . J 4 SO4 A 1 508 508 SO4 SO4 . K 5 EPE A 1 509 509 EPE EPE . L 6 HOH A 1 601 666 HOH HOH . L 6 HOH A 2 602 639 HOH HOH . L 6 HOH A 3 603 602 HOH HOH . L 6 HOH A 4 604 640 HOH HOH . L 6 HOH A 5 605 663 HOH HOH . L 6 HOH A 6 606 670 HOH HOH . L 6 HOH A 7 607 634 HOH HOH . L 6 HOH A 8 608 654 HOH HOH . L 6 HOH A 9 609 668 HOH HOH . L 6 HOH A 10 610 655 HOH HOH . L 6 HOH A 11 611 603 HOH HOH . L 6 HOH A 12 612 609 HOH HOH . L 6 HOH A 13 613 648 HOH HOH . L 6 HOH A 14 614 636 HOH HOH . L 6 HOH A 15 615 635 HOH HOH . L 6 HOH A 16 616 662 HOH HOH . L 6 HOH A 17 617 650 HOH HOH . L 6 HOH A 18 618 673 HOH HOH . L 6 HOH A 19 619 667 HOH HOH . L 6 HOH A 20 620 604 HOH HOH . L 6 HOH A 21 621 641 HOH HOH . L 6 HOH A 22 622 645 HOH HOH . L 6 HOH A 23 623 646 HOH HOH . L 6 HOH A 24 624 613 HOH HOH . L 6 HOH A 25 625 601 HOH HOH . L 6 HOH A 26 626 637 HOH HOH . L 6 HOH A 27 627 606 HOH HOH . L 6 HOH A 28 628 605 HOH HOH . L 6 HOH A 29 629 659 HOH HOH . L 6 HOH A 30 630 677 HOH HOH . L 6 HOH A 31 631 651 HOH HOH . L 6 HOH A 32 632 610 HOH HOH . L 6 HOH A 33 633 614 HOH HOH . L 6 HOH A 34 634 616 HOH HOH . L 6 HOH A 35 635 661 HOH HOH . L 6 HOH A 36 636 631 HOH HOH . L 6 HOH A 37 637 660 HOH HOH . L 6 HOH A 38 638 665 HOH HOH . L 6 HOH A 39 639 657 HOH HOH . L 6 HOH A 40 640 681 HOH HOH . L 6 HOH A 41 641 647 HOH HOH . L 6 HOH A 42 642 612 HOH HOH . L 6 HOH A 43 643 630 HOH HOH . L 6 HOH A 44 644 619 HOH HOH . L 6 HOH A 45 645 622 HOH HOH . L 6 HOH A 46 646 632 HOH HOH . L 6 HOH A 47 647 674 HOH HOH . L 6 HOH A 48 648 607 HOH HOH . L 6 HOH A 49 649 642 HOH HOH . L 6 HOH A 50 650 683 HOH HOH . L 6 HOH A 51 651 617 HOH HOH . L 6 HOH A 52 652 627 HOH HOH . L 6 HOH A 53 653 669 HOH HOH . L 6 HOH A 54 654 620 HOH HOH . L 6 HOH A 55 655 652 HOH HOH . L 6 HOH A 56 656 682 HOH HOH . L 6 HOH A 57 657 625 HOH HOH . L 6 HOH A 58 658 618 HOH HOH . L 6 HOH A 59 659 624 HOH HOH . L 6 HOH A 60 660 691 HOH HOH . L 6 HOH A 61 661 644 HOH HOH . L 6 HOH A 62 662 658 HOH HOH . L 6 HOH A 63 663 615 HOH HOH . L 6 HOH A 64 664 679 HOH HOH . L 6 HOH A 65 665 649 HOH HOH . L 6 HOH A 66 666 633 HOH HOH . L 6 HOH A 67 667 621 HOH HOH . L 6 HOH A 68 668 623 HOH HOH . L 6 HOH A 69 669 626 HOH HOH . L 6 HOH A 70 670 680 HOH HOH . L 6 HOH A 71 671 638 HOH HOH . L 6 HOH A 72 672 687 HOH HOH . L 6 HOH A 73 673 653 HOH HOH . L 6 HOH A 74 674 693 HOH HOH . L 6 HOH A 75 675 678 HOH HOH . L 6 HOH A 76 676 608 HOH HOH . L 6 HOH A 77 677 690 HOH HOH . L 6 HOH A 78 678 684 HOH HOH . L 6 HOH A 79 679 611 HOH HOH . L 6 HOH A 80 680 656 HOH HOH . L 6 HOH A 81 681 675 HOH HOH . L 6 HOH A 82 682 692 HOH HOH . L 6 HOH A 83 683 676 HOH HOH . L 6 HOH A 84 684 688 HOH HOH . L 6 HOH A 85 685 694 HOH HOH . L 6 HOH A 86 686 628 HOH HOH . L 6 HOH A 87 687 685 HOH HOH . L 6 HOH A 88 688 689 HOH HOH . L 6 HOH A 89 689 664 HOH HOH . L 6 HOH A 90 690 671 HOH HOH . L 6 HOH A 91 691 686 HOH HOH . L 6 HOH A 92 692 643 HOH HOH . L 6 HOH A 93 693 672 HOH HOH . L 6 HOH A 94 694 629 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 P PG 8DG . . . D 3 3.057 -38.753 -2.714 1 50.11 ? PG 8DG 502 A 1 HETATM 2 O O1G 8DG . . . D 3 3.58 -39.303 -3.999 1 54.22 ? O1G 8DG 502 A 1 HETATM 3 O O2G 8DG . . . D 3 3.818 -39.205 -1.487 1 54.29 ? O2G 8DG 502 A 1 HETATM 4 O O3G 8DG . . . D 3 1.564 -38.889 -2.57 1 51.98 ? O3G 8DG 502 A 1 HETATM 5 O O3B 8DG . . . D 3 3.448 -37.203 -2.795 1 44.94 ? O3B 8DG 502 A 1 HETATM 6 P PB 8DG . . . D 3 2.476 -35.954 -2.596 1 47.54 ? PB 8DG 502 A 1 HETATM 7 O O1B 8DG . . . D 3 1.191 -36.155 -3.381 1 43.96 ? O1B 8DG 502 A 1 HETATM 8 O O2B 8DG . . . D 3 3.312 -34.727 -2.86 1 44.58 ? O2B 8DG 502 A 1 HETATM 9 O O3A 8DG . . . D 3 2.134 -35.949 -1.01 1 48.92 ? O3A 8DG 502 A 1 HETATM 10 P PA 8DG . . . D 3 0.644 -35.843 -0.382 1 45.15 ? PA 8DG 502 A 1 HETATM 11 O O1A 8DG . . . D 3 -0.349 -36.691 -1.146 1 39.71 ? O1A 8DG 502 A 1 HETATM 12 O O2A 8DG . . . D 3 0.745 -36.11 1.103 1 44.16 ? O2A 8DG 502 A 1 HETATM 13 O O5' 8DG . . . D 3 0.278 -34.286 -0.525 1 47.94 ? O5' 8DG 502 A 1 HETATM 14 C C5' 8DG . . . D 3 0.881 -33.37 -1.429 1 57.34 ? C5' 8DG 502 A 1 HETATM 15 C C4' 8DG . . . D 3 0.454 -31.945 -1.113 1 59.68 ? C4' 8DG 502 A 1 HETATM 16 O O4' 8DG . . . D 3 -0.849 -31.968 -0.521 1 59.23 ? O4' 8DG 502 A 1 HETATM 17 C C3' 8DG . . . D 3 1.397 -31.245 -0.137 1 59.74 ? C3' 8DG 502 A 1 HETATM 18 O O3' 8DG . . . D 3 1.667 -29.909 -0.541 1 56.33 ? O3' 8DG 502 A 1 HETATM 19 C C2' 8DG . . . D 3 0.635 -31.174 1.153 1 60.99 ? C2' 8DG 502 A 1 HETATM 20 C C1' 8DG . . . D 3 -0.797 -31.18 0.661 1 60.65 ? C1' 8DG 502 A 1 HETATM 21 N N9 8DG . . . D 3 -1.664 -31.676 1.748 1 63.06 ? N9 8DG 502 A 1 HETATM 22 C C8 8DG . . . D 3 -1.785 -32.887 2.318 1 60.88 ? C8 8DG 502 A 1 HETATM 23 N N7 8DG . . . D 3 -2.673 -32.972 3.315 1 63.54 ? N7 8DG 502 A 1 HETATM 24 C C5 8DG . . . D 3 -3.173 -31.73 3.419 1 64.96 ? C5 8DG 502 A 1 HETATM 25 C C6 8DG . . . D 3 -4.182 -31.049 4.262 1 66.6 ? C6 8DG 502 A 1 HETATM 26 O O6 8DG . . . D 3 -4.789 -31.695 5.144 1 70.17 ? O6 8DG 502 A 1 HETATM 27 N N1 8DG . . . D 3 -4.417 -29.735 4.047 1 67.16 ? N1 8DG 502 A 1 HETATM 28 C C2 8DG . . . D 3 -3.767 -29.027 3.084 1 67.78 ? C2 8DG 502 A 1 HETATM 29 N N2 8DG . . . D 3 -4.04 -27.715 2.911 1 67.67 ? N2 8DG 502 A 1 HETATM 30 N N3 8DG . . . D 3 -2.828 -29.578 2.271 1 64.13 ? N3 8DG 502 A 1 HETATM 31 C C4 8DG . . . D 3 -2.506 -30.888 2.397 1 63.72 ? C4 8DG 502 A 1 HETATM 32 O O8 8DG . . . D 3 -1.104 -33.908 1.955 1 57.54 ? O8 8DG 502 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 247 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 32 #