data_5LP6 # _model_server_result.job_id eBewomoKXnKnp2ymXYlKag _model_server_result.datetime_utc '2025-07-07 08:28:06' _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 5lp6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":600}' # _entry.id 5LP6 # _exptl.entry_id 5LP6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 8 _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 5LP6 _cell.length_a 103.619 _cell.length_b 155.285 _cell.length_c 180.445 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5LP6 _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,V,W,X,Y,Z,AA,BA _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 ? 8 M N N ? 8 V 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 J MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.664 ? metalc ? metalc2 A OG1 THR 41 A THR 41 1_555 J MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.387 ? metalc ? metalc3 A O GLY 44 A GLY 44 1_555 J MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc4 A OE2 GLU 55 A GLU 55 1_555 J MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.54 ? metalc ? metalc5 G O2G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? metalc ? metalc6 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? metalc ? metalc7 B OE2 GLU 111 B GLU 113 1_555 Q MG MG . B MG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.874 ? metalc ? metalc8 M O1A GDP . B GDP 501 1_555 N MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.635 ? metalc ? metalc9 R MG MG . B MG 506 1_555 X O HOH . B HOH 613 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc10 C OD1 ASP 39 C ASP 39 1_555 U CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.939 ? metalc ? metalc11 C OG1 THR 41 C THR 41 1_555 U CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc12 C O GLY 44 C GLY 44 1_555 U CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.021 ? metalc ? metalc13 C OD2 ASP 47 C ASP 47 1_555 U CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.07 ? metalc ? metalc14 C OE2 GLU 55 C GLU 55 1_555 U CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.681 ? metalc ? metalc15 S O1G GTP . C GTP 501 1_555 T MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? metalc ? metalc16 S O1B GTP . C GTP 501 1_555 T MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? # _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 139 n n PB O2B GDP sing 140 n n PB O3B GDP sing 141 n n PB O3A GDP sing 142 n n O2B HOB2 GDP sing 143 n n O3B HOB3 GDP sing 144 n n O3A PA GDP sing 145 n n PA O1A GDP doub 146 n n PA O2A GDP sing 147 n n PA O5' GDP sing 148 n n O2A HOA2 GDP sing 149 n n O5' C5' GDP sing 150 n n C5' C4' GDP sing 151 n n C5' H5' GDP sing 152 n n C5' "H5''" GDP sing 153 n n C4' O4' GDP sing 154 n n C4' C3' GDP sing 155 n n C4' H4' GDP sing 156 n n O4' C1' GDP sing 157 n n C3' O3' GDP sing 158 n n C3' C2' GDP sing 159 n n C3' H3' GDP sing 160 n n O3' HO3' GDP sing 161 n n C2' O2' GDP sing 162 n n C2' C1' GDP sing 163 n n C2' H2' GDP sing 164 n n O2' HO2' GDP sing 165 n n C1' N9 GDP sing 166 n n C1' H1' GDP sing 167 n n N9 C8 GDP sing 168 n y N9 C4 GDP sing 169 n y C8 N7 GDP doub 170 n y C8 H8 GDP sing 171 n n N7 C5 GDP sing 172 n y C5 C6 GDP sing 173 n n C5 C4 GDP doub 174 n y C6 O6 GDP doub 175 n n C6 N1 GDP sing 176 n n N1 C2 GDP sing 177 n n N1 HN1 GDP sing 178 n n C2 N2 GDP sing 179 n n C2 N3 GDP doub 180 n n N2 HN21 GDP sing 181 n n N2 HN22 GDP sing 182 n n N3 C4 GDP sing 183 n n # _atom_sites.entry_id 5LP6 _atom_sites.fract_transf_matrix[1][1] 0.009651 _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] 0.00644 _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] 0.005542 _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 CL A 1 503 504 CL CL . J 6 MG A 1 504 1 MG MG . K 6 MG A 1 505 2 MG MG . L 6 MG A 1 506 4 MG MG . M 8 GDP B 1 501 501 GDP GDP . N 6 MG B 1 502 502 MG MG . O 9 MES B 1 503 504 MES MES . P 10 71P B 1 504 385 71P DRG . Q 6 MG B 1 505 3 MG MG . R 6 MG B 1 506 5 MG MG . S 5 GTP C 1 501 501 GTP GTP . T 6 MG C 1 502 502 MG MG . U 11 CA C 1 503 503 CA CA . V 8 GDP D 1 600 600 GDP GDP . W 12 HOH A 1 601 107 HOH HOH . W 12 HOH A 2 602 102 HOH HOH . W 12 HOH A 3 603 110 HOH HOH . W 12 HOH A 4 604 31 HOH HOH . W 12 HOH A 5 605 105 HOH HOH . W 12 HOH A 6 606 10 HOH HOH . W 12 HOH A 7 607 106 HOH HOH . W 12 HOH A 8 608 113 HOH HOH . W 12 HOH A 9 609 111 HOH HOH . W 12 HOH A 10 610 101 HOH HOH . W 12 HOH A 11 611 108 HOH HOH . W 12 HOH A 12 612 14 HOH HOH . W 12 HOH A 13 613 103 HOH HOH . W 12 HOH A 14 614 104 HOH HOH . W 12 HOH A 15 615 16 HOH HOH . W 12 HOH A 16 616 112 HOH HOH . W 12 HOH A 17 617 114 HOH HOH . W 12 HOH A 18 618 8 HOH HOH . W 12 HOH A 19 619 109 HOH HOH . W 12 HOH A 20 620 56 HOH HOH . W 12 HOH A 21 621 19 HOH HOH . X 12 HOH B 1 601 95 HOH HOH . X 12 HOH B 2 602 120 HOH HOH . X 12 HOH B 3 603 98 HOH HOH . X 12 HOH B 4 604 115 HOH HOH . X 12 HOH B 5 605 121 HOH HOH . X 12 HOH B 6 606 21 HOH HOH . X 12 HOH B 7 607 99 HOH HOH . X 12 HOH B 8 608 119 HOH HOH . X 12 HOH B 9 609 122 HOH HOH . X 12 HOH B 10 610 117 HOH HOH . X 12 HOH B 11 611 100 HOH HOH . X 12 HOH B 12 612 82 HOH HOH . X 12 HOH B 13 613 96 HOH HOH . X 12 HOH B 14 614 118 HOH HOH . X 12 HOH B 15 615 15 HOH HOH . X 12 HOH B 16 616 58 HOH HOH . Y 12 HOH C 1 601 124 HOH HOH . Y 12 HOH C 2 602 127 HOH HOH . Y 12 HOH C 3 603 136 HOH HOH . Y 12 HOH C 4 604 123 HOH HOH . Y 12 HOH C 5 605 125 HOH HOH . Y 12 HOH C 6 606 134 HOH HOH . Y 12 HOH C 7 607 132 HOH HOH . Y 12 HOH C 8 608 139 HOH HOH . Y 12 HOH C 9 609 141 HOH HOH . Y 12 HOH C 10 610 71 HOH HOH . Y 12 HOH C 11 611 80 HOH HOH . Y 12 HOH C 12 612 135 HOH HOH . Y 12 HOH C 13 613 140 HOH HOH . Y 12 HOH C 14 614 91 HOH HOH . Y 12 HOH C 15 615 66 HOH HOH . Y 12 HOH C 16 616 133 HOH HOH . Y 12 HOH C 17 617 81 HOH HOH . Y 12 HOH C 18 618 131 HOH HOH . Y 12 HOH C 19 619 83 HOH HOH . Y 12 HOH C 20 620 74 HOH HOH . Y 12 HOH C 21 621 126 HOH HOH . Y 12 HOH C 22 622 78 HOH HOH . Y 12 HOH C 23 623 24 HOH HOH . Y 12 HOH C 24 624 129 HOH HOH . Y 12 HOH C 25 625 79 HOH HOH . Y 12 HOH C 26 626 76 HOH HOH . Y 12 HOH C 27 627 57 HOH HOH . Y 12 HOH C 28 628 137 HOH HOH . Y 12 HOH C 29 629 130 HOH HOH . Y 12 HOH C 30 630 138 HOH HOH . Y 12 HOH C 31 631 116 HOH HOH . Y 12 HOH C 32 632 128 HOH HOH . Y 12 HOH C 33 633 97 HOH HOH . Y 12 HOH C 34 634 46 HOH HOH . Y 12 HOH C 35 635 47 HOH HOH . Z 12 HOH D 1 701 145 HOH HOH . Z 12 HOH D 2 702 142 HOH HOH . Z 12 HOH D 3 703 42 HOH HOH . Z 12 HOH D 4 704 146 HOH HOH . Z 12 HOH D 5 705 27 HOH HOH . Z 12 HOH D 6 706 143 HOH HOH . Z 12 HOH D 7 707 38 HOH HOH . Z 12 HOH D 8 708 45 HOH HOH . Z 12 HOH D 9 709 43 HOH HOH . Z 12 HOH D 10 710 144 HOH HOH . Z 12 HOH D 11 711 28 HOH HOH . AA 12 HOH E 1 201 33 HOH HOH . BA 12 HOH F 1 401 148 HOH HOH . BA 12 HOH F 2 402 94 HOH HOH . BA 12 HOH F 3 403 85 HOH HOH . BA 12 HOH F 4 404 86 HOH HOH . BA 12 HOH F 5 405 147 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 . . . V 8 25.722 -10.495 -44.106 1 106.99 ? PB GDP 600 D 1 HETATM 2 O O1B GDP . . . V 8 25.06 -9.822 -45.282 1 106.84 ? O1B GDP 600 D 1 HETATM 3 O O2B GDP . . . V 8 25.824 -9.636 -42.87 1 107.45 ? O2B GDP 600 D 1 HETATM 4 O O3B GDP . . . V 8 26.993 -11.228 -44.452 1 107.26 ? O3B GDP 600 D 1 HETATM 5 O O3A GDP . . . V 8 24.714 -11.68 -43.695 1 108.12 ? O3A GDP 600 D 1 HETATM 6 P PA GDP . . . V 8 23.143 -11.456 -43.413 1 107.99 ? PA GDP 600 D 1 HETATM 7 O O1A GDP . . . V 8 22.386 -12.109 -44.545 1 109.07 ? O1A GDP 600 D 1 HETATM 8 O O2A GDP . . . V 8 22.892 -9.999 -43.111 1 107.46 ? O2A GDP 600 D 1 HETATM 9 O O5' GDP . . . V 8 22.929 -12.285 -42.044 1 106.31 ? O5' GDP 600 D 1 HETATM 10 C C5' GDP . . . V 8 22.228 -13.529 -41.952 1 104.26 ? C5' GDP 600 D 1 HETATM 11 C C4' GDP . . . V 8 21.191 -13.455 -40.837 1 103.29 ? C4' GDP 600 D 1 HETATM 12 O O4' GDP . . . V 8 20.473 -12.222 -40.922 1 102.78 ? O4' GDP 600 D 1 HETATM 13 C C3' GDP . . . V 8 20.158 -14.574 -40.918 1 102.51 ? C3' GDP 600 D 1 HETATM 14 O O3' GDP . . . V 8 19.985 -15.16 -39.623 1 101.43 ? O3' GDP 600 D 1 HETATM 15 C C2' GDP . . . V 8 18.881 -13.915 -41.398 1 102.43 ? C2' GDP 600 D 1 HETATM 16 O O2' GDP . . . V 8 17.706 -14.467 -40.793 1 103.11 ? O2' GDP 600 D 1 HETATM 17 C C1' GDP . . . V 8 19.068 -12.462 -41.003 1 102.31 ? C1' GDP 600 D 1 HETATM 18 N N9 GDP . . . V 8 18.445 -11.536 -41.977 1 101.7 ? N9 GDP 600 D 1 HETATM 19 C C8 GDP . . . V 8 18.863 -11.286 -43.233 1 101.9 ? C8 GDP 600 D 1 HETATM 20 N N7 GDP . . . V 8 18.055 -10.372 -43.832 1 101.98 ? N7 GDP 600 D 1 HETATM 21 C C5 GDP . . . V 8 17.102 -10.027 -42.946 1 101.72 ? C5 GDP 600 D 1 HETATM 22 C C6 GDP . . . V 8 15.931 -9.114 -42.915 1 102.21 ? C6 GDP 600 D 1 HETATM 23 O O6 GDP . . . V 8 15.628 -8.421 -43.91 1 101.87 ? O6 GDP 600 D 1 HETATM 24 N N1 GDP . . . V 8 15.201 -9.059 -41.785 1 102.38 ? N1 GDP 600 D 1 HETATM 25 C C2 GDP . . . V 8 15.493 -9.792 -40.688 1 101.91 ? C2 GDP 600 D 1 HETATM 26 N N2 GDP . . . V 8 14.706 -9.675 -39.59 1 101.77 ? N2 GDP 600 D 1 HETATM 27 N N3 GDP . . . V 8 16.552 -10.647 -40.647 1 101.7 ? N3 GDP 600 D 1 HETATM 28 C C4 GDP . . . V 8 17.367 -10.801 -41.723 1 101.44 ? C4 GDP 600 D 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 344 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #