data_8CLB # _model_server_result.job_id RlG1SXlz7dMsiZ1qxI0ctg _model_server_result.datetime_utc '2024-11-24 11:28:20' _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 8clb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":501}' # _entry.id 8CLB # _exptl.entry_id 8CLB _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 8CLB _cell.length_a 106.71 _cell.length_b 160.61 _cell.length_c 180.73 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8CLB _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 _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 J N N ? 8 P 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.539 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.729 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.543 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.776 ? metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? metalc ? metalc8 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.973 ? metalc ? metalc9 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc10 H MG MG . A MG 502 1_555 T O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? metalc ? metalc11 H MG MG . A MG 502 1_555 T O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? metalc ? metalc12 B OE1 GLN 11 B GLN 11 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.662 ? metalc ? metalc13 B OD2 ASP 177 B ASP 179 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.821 ? metalc ? metalc14 J O1A GDP . B GDP 501 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? metalc ? metalc15 K MG MG . B MG 502 1_555 U O HOH . B HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.463 ? metalc ? metalc16 C OD1 ASP 39 C ASP 39 1_555 O CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.544 ? metalc ? metalc17 C OD2 ASP 39 C ASP 39 1_555 O CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? metalc ? metalc18 C O THR 41 C THR 41 1_555 O CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.631 ? metalc ? metalc19 C OG1 THR 41 C THR 41 1_555 O CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.897 ? metalc ? metalc20 C O GLY 44 C GLY 44 1_555 O CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc21 C OE1 GLU 55 C GLU 55 1_555 O CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.685 ? metalc ? metalc22 C OE2 GLU 55 C GLU 55 1_555 O CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc23 M O1G GTP . C GTP 501 1_555 N MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? metalc ? metalc24 M O1B GTP . C GTP 501 1_555 N MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? metalc ? metalc25 N MG MG . C MG 502 1_555 V O HOH . C HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.821 ? metalc ? metalc26 D OE1 GLN 11 D GLN 11 1_555 Q MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.771 ? metalc ? metalc27 P O1A GDP . D GDP 501 1_555 Q MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.744 ? # _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 134 n n PB O2B GDP sing 135 n n PB O3B GDP sing 136 n n PB O3A GDP sing 137 n n O2B HOB2 GDP sing 138 n n O3B HOB3 GDP sing 139 n n O3A PA GDP sing 140 n n PA O1A GDP doub 141 n n PA O2A GDP sing 142 n n PA O5' GDP sing 143 n n O2A HOA2 GDP sing 144 n n O5' C5' GDP sing 145 n n C5' C4' GDP sing 146 n n C5' H5' GDP sing 147 n n C5' "H5''" GDP sing 148 n n C4' O4' GDP sing 149 n n C4' C3' GDP sing 150 n n C4' H4' GDP sing 151 n n O4' C1' GDP sing 152 n n C3' O3' GDP sing 153 n n C3' C2' GDP sing 154 n n C3' H3' GDP sing 155 n n O3' HO3' GDP sing 156 n n C2' O2' GDP sing 157 n n C2' C1' GDP sing 158 n n C2' H2' GDP sing 159 n n O2' HO2' GDP sing 160 n n C1' N9 GDP sing 161 n n C1' H1' GDP sing 162 n n N9 C8 GDP sing 163 n y N9 C4 GDP sing 164 n y C8 N7 GDP doub 165 n y C8 H8 GDP sing 166 n n N7 C5 GDP sing 167 n y C5 C6 GDP sing 168 n n C5 C4 GDP doub 169 n y C6 O6 GDP doub 170 n n C6 N1 GDP sing 171 n n N1 C2 GDP sing 172 n n N1 HN1 GDP sing 173 n n C2 N2 GDP sing 174 n n C2 N3 GDP doub 175 n n N2 HN21 GDP sing 176 n n N2 HN22 GDP sing 177 n n N3 C4 GDP sing 178 n n # _atom_sites.entry_id 8CLB _atom_sites.fract_transf_matrix[1][1] 0.009371 _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] 0.006226 _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] 0.005533 _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 GDP B 1 501 504 GDP GDP . K 6 MG B 1 502 505 MG MG . L 9 LOC B 1 503 506 LOC LOC . M 5 GTP C 1 501 507 GTP GTP . N 6 MG C 1 502 508 MG MG . O 7 CA C 1 503 513 CA CA . P 8 GDP D 1 501 509 GDP GDP . Q 6 MG D 1 502 510 MG MG . R 9 LOC D 1 503 511 LOC LOC . S 10 ACP F 1 401 512 ACP ACP . T 11 HOH A 1 601 40 HOH HOH . T 11 HOH A 2 602 34 HOH HOH . T 11 HOH A 3 603 19 HOH HOH . T 11 HOH A 4 604 22 HOH HOH . T 11 HOH A 5 605 27 HOH HOH . T 11 HOH A 6 606 41 HOH HOH . T 11 HOH A 7 607 10 HOH HOH . U 11 HOH B 1 601 35 HOH HOH . U 11 HOH B 2 602 2 HOH HOH . U 11 HOH B 3 603 4 HOH HOH . U 11 HOH B 4 604 18 HOH HOH . U 11 HOH B 5 605 42 HOH HOH . V 11 HOH C 1 601 14 HOH HOH . V 11 HOH C 2 602 3 HOH HOH . V 11 HOH C 3 603 16 HOH HOH . V 11 HOH C 4 604 8 HOH HOH . V 11 HOH C 5 605 21 HOH HOH . V 11 HOH C 6 606 6 HOH HOH . W 11 HOH D 1 601 9 HOH HOH . X 11 HOH E 1 201 1 HOH HOH . Y 11 HOH F 1 501 5 HOH HOH . Y 11 HOH F 2 502 37 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 . . . J 8 19.065 50.863 15.853 1 38.05 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . J 8 18.661 51.779 14.742 1 40.96 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . J 8 19.497 51.599 17.079 1 68.34 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . J 8 20.061 49.835 15.423 1 41.65 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . J 8 17.748 50.042 16.268 1 55.67 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . J 8 16.313 50.451 16.844 1 48.08 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . J 8 15.277 50.05 15.851 1 52.65 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . J 8 16.36 51.871 17.288 1 46.2 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . J 8 16.215 49.502 18.126 1 39.12 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . J 8 15.179 48.496 18.159 1 42.92 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . J 8 14.575 48.457 19.539 1 36.09 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . J 8 14.109 49.784 19.884 1 37.53 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . J 8 13.354 47.551 19.716 1 43.13 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . J 8 13.252 47.081 21.053 1 46.09 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . J 8 12.202 48.494 19.375 1 35.12 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . J 8 10.996 48.099 19.989 1 56.37 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . J 8 12.703 49.816 19.944 1 36.33 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . J 8 12.252 50.987 19.204 1 41.46 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . J 8 12.525 51.284 17.895 1 42.13 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . J 8 11.992 52.413 17.499 1 44.6 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . J 8 11.33 52.889 18.621 1 43.68 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . J 8 10.574 54.072 18.797 1 39.53 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . J 8 10.334 54.96 17.97 1 49.33 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . J 8 10.076 54.169 20.094 1 44.68 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . J 8 10.279 53.25 21.092 1 46.68 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . J 8 9.718 53.52 22.276 1 40.61 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . J 8 10.989 52.136 20.933 1 43.48 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . J 8 11.484 52.022 19.678 1 46.27 ? C4 GDP 501 B 1 HETATM 29 H H5' GDP . . . J 8 15.547 47.628 17.93 1 42.92 ? H5' GDP 501 B 1 HETATM 30 H "H5''" GDP . . . J 8 14.496 48.697 17.5 1 42.92 ? "H5''" GDP 501 B 1 HETATM 31 H H4' GDP . . . J 8 15.288 48.109 20.097 1 36.09 ? H4' GDP 501 B 1 HETATM 32 H H3' GDP . . . J 8 13.38 46.751 19.168 1 43.13 ? H3' GDP 501 B 1 HETATM 33 H HO3' GDP . . . J 8 13.41 46.256 21.073 1 46.09 ? HO3' GDP 501 B 1 HETATM 34 H H2' GDP . . . J 8 11.993 48.522 18.428 1 35.12 ? H2' GDP 501 B 1 HETATM 35 H HO2' GDP . . . J 8 10.35 48.479 19.609 1 56.37 ? HO2' GDP 501 B 1 HETATM 36 H H1' GDP . . . J 8 12.352 49.9 20.844 1 36.33 ? H1' GDP 501 B 1 HETATM 37 H H8 GDP . . . J 8 13.059 50.715 17.319 1 42.13 ? H8 GDP 501 B 1 HETATM 38 H HN1 GDP . . . J 8 9.603 54.861 20.285 1 44.68 ? HN1 GDP 501 B 1 HETATM 39 H HN21 GDP . . . J 8 9.259 54.239 22.38 1 40.61 ? HN21 GDP 501 B 1 HETATM 40 H HN22 GDP . . . J 8 9.817 52.974 22.933 1 40.61 ? HN22 GDP 501 B 1 # _model_server_stats.io_time_ms 202 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 36 _model_server_stats.query_time_ms 365 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 40 #