data_8CLE # _model_server_result.job_id X1YIRYoIbo6AbIn8v0l_Eg _model_server_result.datetime_utc '2024-11-16 20:50:25' _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 8cle # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":501}' # _entry.id 8CLE # _exptl.entry_id 8CLE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 9 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _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 90 _cell.entry_id 8CLE _cell.length_a 106.39 _cell.length_b 159.74 _cell.length_c 182.24 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8CLE _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,N,O,P,Q,R,S,T,U _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 ? 9 N N N ? 9 O 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 metalc ? metalc1 A OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.658 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.091 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.571 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.671 ? metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.002 ? metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc8 G O2G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc9 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? metalc ? metalc10 B OD1 ASP 39 C ASP 39 1_555 M CA CA . C CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.711 ? metalc ? metalc11 B OD2 ASP 39 C ASP 39 1_555 M CA CA . C CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc12 B O THR 41 C THR 41 1_555 M CA CA . C CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc13 B OG1 THR 41 C THR 41 1_555 M CA CA . C CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? metalc ? metalc14 B OE1 GLU 55 C GLU 55 1_555 M CA CA . C CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.858 ? metalc ? metalc15 B OE2 GLU 55 C GLU 55 1_555 M CA CA . C CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.931 ? metalc ? metalc16 K O1G GTP . C GTP 502 1_555 L MG MG . C MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.847 ? metalc ? metalc17 K O1B GTP . C GTP 502 1_555 L MG MG . C MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.726 ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 PB O1B GDP doub 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 8CLE _atom_sites.fract_transf_matrix[1][1] 0.009399 _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] 0.00626 _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] 0.005487 _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 G 5 GTP A 1 501 501 GTP GTP . H 6 MG A 1 502 502 MG MG . I 7 CA A 1 503 503 CA CA . J 8 VLB C 1 501 505 VLB VLB . K 5 GTP C 1 502 506 GTP GTP . L 6 MG C 1 503 507 MG MG . M 7 CA C 1 504 509 CA CA . N 9 GDP D 1 501 508 GDP GDP . O 9 GDP B 1 501 504 GDP GDP . P 10 HOH A 1 601 21 HOH HOH . P 10 HOH A 2 602 8 HOH HOH . Q 10 HOH C 1 601 1 HOH HOH . Q 10 HOH C 2 602 36 HOH HOH . Q 10 HOH C 3 603 12 HOH HOH . Q 10 HOH C 4 604 39 HOH HOH . Q 10 HOH C 5 605 34 HOH HOH . Q 10 HOH C 6 606 38 HOH HOH . R 10 HOH D 1 601 27 HOH HOH . R 10 HOH D 2 602 29 HOH HOH . R 10 HOH D 3 603 26 HOH HOH . R 10 HOH D 4 604 25 HOH HOH . R 10 HOH D 5 605 28 HOH HOH . S 10 HOH E 1 201 22 HOH HOH . T 10 HOH F 1 401 2 HOH HOH . T 10 HOH F 2 402 11 HOH HOH . T 10 HOH F 3 403 33 HOH HOH . T 10 HOH F 4 404 42 HOH HOH . T 10 HOH F 5 405 43 HOH HOH . T 10 HOH F 6 406 17 HOH HOH . T 10 HOH F 7 407 44 HOH HOH . T 10 HOH F 8 408 13 HOH HOH . U 10 HOH B 1 601 16 HOH HOH . U 10 HOH B 2 602 10 HOH HOH . U 10 HOH B 3 603 45 HOH HOH . U 10 HOH B 4 604 18 HOH HOH . U 10 HOH B 5 605 7 HOH HOH . U 10 HOH B 6 606 19 HOH HOH . U 10 HOH B 7 607 14 HOH HOH . U 10 HOH B 8 608 46 HOH HOH . U 10 HOH B 9 609 37 HOH HOH . U 10 HOH B 10 610 35 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 PB GDP . . . N 9 25.243 -9.762 -42.833 1 88.41 ? PB GDP 501 D 1 HETATM 2 O O1B GDP . . . N 9 24.688 -8.747 -43.803 1 84.3 ? O1B GDP 501 D 1 HETATM 3 O O2B GDP . . . N 9 26.302 -9.104 -41.974 1 86.01 ? O2B GDP 501 D 1 HETATM 4 O O3B GDP . . . N 9 25.918 -10.878 -43.599 1 87.45 ? O3B GDP 501 D 1 HETATM 5 O O3A GDP . . . N 9 24.079 -10.314 -41.856 1 89.11 ? O3A GDP 501 D 1 HETATM 6 P PA GDP . . . N 9 22.607 -10.832 -42.278 1 89.62 ? PA GDP 501 D 1 HETATM 7 O O1A GDP . . . N 9 22.662 -11.882 -43.355 1 101.53 ? O1A GDP 501 D 1 HETATM 8 O O2A GDP . . . N 9 21.704 -9.699 -42.715 1 81.18 ? O2A GDP 501 D 1 HETATM 9 O O5' GDP . . . N 9 22.044 -11.461 -40.898 1 81.95 ? O5' GDP 501 D 1 HETATM 10 C C5' GDP . . . N 9 21.381 -12.729 -40.84 1 81.26 ? C5' GDP 501 D 1 HETATM 11 C C4' GDP . . . N 9 20.487 -12.748 -39.609 1 78.77 ? C4' GDP 501 D 1 HETATM 12 O O4' GDP . . . N 9 19.756 -11.527 -39.605 1 78.96 ? O4' GDP 501 D 1 HETATM 13 C C3' GDP . . . N 9 19.477 -13.881 -39.669 1 81.92 ? C3' GDP 501 D 1 HETATM 14 O O3' GDP . . . N 9 19.452 -14.545 -38.402 1 81.26 ? O3' GDP 501 D 1 HETATM 15 C C2' GDP . . . N 9 18.136 -13.235 -39.958 1 76.28 ? C2' GDP 501 D 1 HETATM 16 O O2' GDP . . . N 9 17.12 -13.742 -39.089 1 79.93 ? O2' GDP 501 D 1 HETATM 17 C C1' GDP . . . N 9 18.351 -11.762 -39.665 1 75 ? C1' GDP 501 D 1 HETATM 18 N N9 GDP . . . N 9 17.816 -10.897 -40.736 1 76.79 ? N9 GDP 501 D 1 HETATM 19 C C8 GDP . . . N 9 18.341 -10.731 -41.965 1 78.37 ? C8 GDP 501 D 1 HETATM 20 N N7 GDP . . . N 9 17.607 -9.847 -42.684 1 77.28 ? N7 GDP 501 D 1 HETATM 21 C C5 GDP . . . N 9 16.6 -9.432 -41.894 1 77.26 ? C5 GDP 501 D 1 HETATM 22 C C6 GDP . . . N 9 15.459 -8.502 -42.021 1 78.38 ? C6 GDP 501 D 1 HETATM 23 O O6 GDP . . . N 9 15.267 -7.875 -43.086 1 81.25 ? O6 GDP 501 D 1 HETATM 24 N N1 GDP . . . N 9 14.646 -8.358 -40.965 1 78.96 ? N1 GDP 501 D 1 HETATM 25 C C2 GDP . . . N 9 14.834 -9.023 -39.809 1 77.64 ? C2 GDP 501 D 1 HETATM 26 N N2 GDP . . . N 9 13.966 -8.818 -38.79 1 77.48 ? N2 GDP 501 D 1 HETATM 27 N N3 GDP . . . N 9 15.857 -9.891 -39.622 1 74.74 ? N3 GDP 501 D 1 HETATM 28 C C4 GDP . . . N 9 16.747 -10.124 -40.611 1 77.74 ? C4 GDP 501 D 1 # _model_server_stats.io_time_ms 44 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 35 _model_server_stats.query_time_ms 340 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 28 #