data_8FOG # _model_server_result.job_id 1v5zJwkgVWrJJ4tMc3gluA _model_server_result.datetime_utc '2024-11-22 21:07:09' _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 8fog # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 8FOG # _exptl.entry_id 8FOG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 492.166 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-deoxyinosine 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 120 _cell.entry_id 8FOG _cell.length_a 99.329 _cell.length_b 99.329 _cell.length_c 80.617 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8FOG _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall 'P 61' _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 _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 OD1 ASP 13 A ASP 13 1_555 E CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc2 A O MET 14 A MET 14 1_555 E CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? metalc ? metalc3 A OD1 ASP 115 A ASP 115 1_555 E CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.43 ? metalc ? metalc4 D OAJ Y43 . A Y43 501 1_555 E CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.531 ? metalc ? metalc5 D OAO Y43 . A Y43 501 1_555 E CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? metalc ? metalc6 D OAS Y43 . A Y43 501 1_555 E CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? hydrog WATSON-CRICK hydrog1 B N3 DC 5 T DC 5 1_555 C N1 DG 8 P DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N4 DC 5 T DC 5 1_555 C O6 DG 8 P DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O2 DC 5 T DC 5 1_555 C N2 DG 8 P DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N3 DT 6 T DT 6 1_555 C N1 DA 7 P DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O4 DT 6 T DT 6 1_555 C N6 DA 7 P DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N3 DC 7 T DC 7 1_555 C N1 DG 6 P DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N4 DC 7 T DC 7 1_555 C O6 DG 6 P DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B O2 DC 7 T DC 7 1_555 C N2 DG 6 P DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N1 DA 8 T DA 8 1_555 C N3 DT 5 P DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N6 DA 8 T DA 8 1_555 C O4 DT 5 P DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N3 DC 9 T DC 9 1_555 C N1 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N4 DC 9 T DC 9 1_555 C O6 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B O2 DC 9 T DC 9 1_555 C N2 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N1 DA 10 T DA 10 1_555 C N3 DT 3 P DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N6 DA 10 T DA 10 1_555 C O4 DT 3 P DT 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 H15 N4 O13 P3' _chem_comp.formula_weight 492.166 _chem_comp.id Y43 _chem_comp.mon_nstd_flag . _chem_comp.name "2'-deoxyinosine 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 OAE CAF Y43 sing 525 n n OAE CAD Y43 sing 526 n n CAG CAF Y43 sing 527 n n CAG OAH Y43 sing 528 n n CAF CAB Y43 sing 529 n n CAD N9 Y43 sing 530 n n CAD CAC Y43 sing 531 n n OAH PAI Y43 sing 532 n n OAK PAI Y43 doub 533 n n N3 C4 Y43 sing 534 n n N3 C2 Y43 sing 535 n n N9 C4 Y43 sing 536 n y N9 C8 Y43 sing 537 n y CAC CAB Y43 sing 538 n n CAB OAA Y43 sing 539 n n C4 C5 Y43 doub 540 n y C2 N1 Y43 doub 541 n n PAI OAJ Y43 sing 542 n n PAI OAL Y43 sing 543 n n OAN PAM Y43 doub 544 n n C8 N7 Y43 doub 545 n y C5 N7 Y43 sing 546 n y C5 C6 Y43 sing 547 n n N1 C6 Y43 sing 548 n n C6 O6 Y43 doub 549 n n OAR PAQ Y43 doub 550 n n OAL PAM Y43 sing 551 n n PAM OAO Y43 sing 552 n n PAM OAP Y43 sing 553 n n PAQ OAP Y43 sing 554 n n PAQ OAS Y43 sing 555 n n PAQ OAT Y43 sing 556 n n C8 H1 Y43 sing 557 n n N3 H2 Y43 sing 558 n n C2 H3 Y43 sing 559 n n CAB H4 Y43 sing 560 n n CAC H5 Y43 sing 561 n n CAC H6 Y43 sing 562 n n CAD H7 Y43 sing 563 n n CAF H8 Y43 sing 564 n n CAG H9 Y43 sing 565 n n CAG H10 Y43 sing 566 n n OAA H11 Y43 sing 567 n n OAJ H12 Y43 sing 568 n n OAO H13 Y43 sing 569 n n OAS H14 Y43 sing 570 n n OAT H15 Y43 sing 571 n n # _atom_sites.entry_id 8FOG _atom_sites.fract_transf_matrix[1][1] 0.010068 _atom_sites.fract_transf_matrix[1][2] 0.005813 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011625 _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] 0.012404 _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 Y43 A 1 501 502 Y43 DRG . E 5 CA A 1 502 1 CA CA . F 6 HOH A 1 601 21 HOH HOH . F 6 HOH A 2 602 11 HOH HOH . F 6 HOH A 3 603 36 HOH HOH . F 6 HOH A 4 604 29 HOH HOH . F 6 HOH A 5 605 33 HOH HOH . F 6 HOH A 6 606 27 HOH HOH . F 6 HOH A 7 607 26 HOH HOH . F 6 HOH A 8 608 7 HOH HOH . F 6 HOH A 9 609 28 HOH HOH . F 6 HOH A 10 610 18 HOH HOH . F 6 HOH A 11 611 10 HOH HOH . F 6 HOH A 12 612 12 HOH HOH . F 6 HOH A 13 613 2 HOH HOH . F 6 HOH A 14 614 1 HOH HOH . F 6 HOH A 15 615 5 HOH HOH . F 6 HOH A 16 616 41 HOH HOH . F 6 HOH A 17 617 9 HOH HOH . F 6 HOH A 18 618 4 HOH HOH . F 6 HOH A 19 619 43 HOH HOH . F 6 HOH A 20 620 42 HOH HOH . F 6 HOH A 21 621 38 HOH HOH . F 6 HOH A 22 622 6 HOH HOH . F 6 HOH A 23 623 25 HOH HOH . F 6 HOH A 24 624 15 HOH HOH . F 6 HOH A 25 625 31 HOH HOH . F 6 HOH A 26 626 34 HOH HOH . F 6 HOH A 27 627 23 HOH HOH . F 6 HOH A 28 628 3 HOH HOH . F 6 HOH A 29 629 13 HOH HOH . F 6 HOH A 30 630 20 HOH HOH . F 6 HOH A 31 631 8 HOH HOH . F 6 HOH A 32 632 17 HOH HOH . F 6 HOH A 33 633 40 HOH HOH . F 6 HOH A 34 634 22 HOH HOH . F 6 HOH A 35 635 24 HOH HOH . F 6 HOH A 36 636 37 HOH HOH . F 6 HOH A 37 637 14 HOH HOH . F 6 HOH A 38 638 39 HOH HOH . F 6 HOH A 39 639 32 HOH HOH . G 6 HOH T 1 101 30 HOH HOH . G 6 HOH T 2 102 19 HOH HOH . H 6 HOH P 1 101 35 HOH HOH . H 6 HOH P 2 102 16 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 C C4 Y43 . . . D 4 53.657 2.979 -4.948 1 60.98 ? C4 Y43 501 A 1 HETATM 2 C C5 Y43 . . . D 4 53.696 2.065 -5.94 1 60.01 ? C5 Y43 501 A 1 HETATM 3 C C6 Y43 . . . D 4 54.82 1.85 -6.633 1 63.46 ? C6 Y43 501 A 1 HETATM 4 C C8 Y43 . . . D 4 51.714 2.079 -5.112 1 62.77 ? C8 Y43 501 A 1 HETATM 5 N N1 Y43 . . . D 4 55.98 2.587 -6.318 1 63.83 ? N1 Y43 501 A 1 HETATM 6 N N3 Y43 . . . D 4 54.752 3.699 -4.633 1 62.39 ? N3 Y43 501 A 1 HETATM 7 C C2 Y43 . . . D 4 55.937 3.489 -5.344 1 62.65 ? C2 Y43 501 A 1 HETATM 8 C CAB Y43 . . . D 4 50.373 5.28 -4.301 1 55.66 ? CAB Y43 501 A 1 HETATM 9 C CAC Y43 . . . D 4 51.683 5.355 -3.544 1 58.63 ? CAC Y43 501 A 1 HETATM 10 C CAD Y43 . . . D 4 51.881 3.832 -3.292 1 63.27 ? CAD Y43 501 A 1 HETATM 11 C CAF Y43 . . . D 4 49.614 4.448 -3.298 1 61.3 ? CAF Y43 501 A 1 HETATM 12 C CAG Y43 . . . D 4 48.262 3.956 -3.863 1 62.2 ? CAG Y43 501 A 1 HETATM 13 N N7 Y43 . . . D 4 52.493 1.507 -6.036 1 61.74 ? N7 Y43 501 A 1 HETATM 14 N N9 Y43 . . . D 4 52.425 2.995 -4.439 1 59.95 ? N9 Y43 501 A 1 HETATM 15 O O6 Y43 . . . D 4 54.849 1.012 -7.538 1 62.37 ? O6 Y43 501 A 1 HETATM 16 O OAA Y43 . . . D 4 49.781 6.563 -4.432 1 57.98 ? OAA Y43 501 A 1 HETATM 17 O OAE Y43 . . . D 4 50.517 3.312 -3.106 1 62.54 ? OAE Y43 501 A 1 HETATM 18 O OAH Y43 . . . D 4 48.478 2.719 -4.595 1 63.29 ? OAH Y43 501 A 1 HETATM 19 O OAJ Y43 . . . D 4 46.174 1.309 -4.63 1 59.83 ? OAJ Y43 501 A 1 HETATM 20 O OAK Y43 . . . D 4 48.089 0.604 -6.186 1 65.03 ? OAK Y43 501 A 1 HETATM 21 O OAL Y43 . . . D 4 46.877 2.878 -6.647 1 62.72 ? OAL Y43 501 A 1 HETATM 22 O OAN Y43 . . . D 4 46.926 5.513 -6.841 1 58.89 ? OAN Y43 501 A 1 HETATM 23 O OAO Y43 . . . D 4 45.337 4.507 -5.106 1 45.08 ? OAO Y43 501 A 1 HETATM 24 O OAP Y43 . . . D 4 44.834 4.119 -7.707 1 52.96 ? OAP Y43 501 A 1 HETATM 25 O OAR Y43 . . . D 4 44.543 1.687 -8.769 1 56.61 ? OAR Y43 501 A 1 HETATM 26 O OAS Y43 . . . D 4 43.609 2.209 -6.425 1 43.52 ? OAS Y43 501 A 1 HETATM 27 O OAT Y43 . . . D 4 42.433 3.141 -8.466 1 49.24 ? OAT Y43 501 A 1 HETATM 28 P PAI Y43 . . . D 4 47.322 1.866 -5.433 1 75.26 ? PAI Y43 501 A 1 HETATM 29 P PAM Y43 . . . D 4 46.054 4.318 -6.554 1 54.56 ? PAM Y43 501 A 1 HETATM 30 P PAQ Y43 . . . D 4 43.904 2.738 -7.907 1 49.76 ? PAQ Y43 501 A 1 # _model_server_stats.io_time_ms 51 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 30 #