data_7CPQ # _model_server_result.job_id dfF3DhqFQnKkxid6asccaw _model_server_result.datetime_utc '2025-01-10 11:02:00' _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 7cpq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":502}' # _entry.id 7CPQ # _exptl.entry_id 7CPQ _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 7CPQ _cell.length_a 104.877 _cell.length_b 156.616 _cell.length_c 182.624 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7CPQ _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 ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA _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 K N N ? 9 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 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.124 ? metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc8 G O2G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc9 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc10 B OE1 GLU 111 B GLU 113 1_555 M CA CA . B CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.853 ? metalc ? metalc11 B OE1 GLU 111 B GLU 113 1_555 S CA CA . C CA 505 4_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.706 ? metalc ? metalc12 B OE2 GLU 111 B GLU 113 1_555 S CA CA . C CA 505 4_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.982 ? metalc ? metalc13 K O2A GDP . B GDP 502 1_555 L MG MG . B MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.393 ? metalc ? metalc14 L MG MG . B MG 503 1_555 AA O HOH . B HOH 615 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.722 ? metalc ? metalc15 L MG MG . B MG 503 1_555 BA O HOH . C HOH 618 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc16 O O3G GTP . C GTP 501 1_555 R MG MG . C MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? metalc ? metalc17 O O1B GTP . C GTP 501 1_555 R MG MG . C MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? metalc ? metalc18 R MG MG . C MG 504 1_555 BA O HOH . C HOH 611 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc19 D OE1 GLN 11 D GLN 11 1_555 W MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc20 V O2A GDP . D GDP 501 1_555 W MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.71 ? metalc ? metalc21 F OE2 GLU 331 F GLU 331 1_555 Y MG MG . F MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.607 ? metalc ? metalc22 Y MG MG . F MG 401 1_555 EA O HOH . F HOH 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.8 ? # _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 127 n n PB O2B GDP sing 128 n n PB O3B GDP sing 129 n n PB O3A GDP sing 130 n n O2B HOB2 GDP sing 131 n n O3B HOB3 GDP sing 132 n n O3A PA GDP sing 133 n n PA O1A GDP doub 134 n n PA O2A GDP sing 135 n n PA O5' GDP sing 136 n n O2A HOA2 GDP sing 137 n n O5' C5' GDP sing 138 n n C5' C4' GDP sing 139 n n C5' H5' GDP sing 140 n n C5' "H5''" GDP sing 141 n n C4' O4' GDP sing 142 n n C4' C3' GDP sing 143 n n C4' H4' GDP sing 144 n n O4' C1' GDP sing 145 n n C3' O3' GDP sing 146 n n C3' C2' GDP sing 147 n n C3' H3' GDP sing 148 n n O3' HO3' GDP sing 149 n n C2' O2' GDP sing 150 n n C2' C1' GDP sing 151 n n C2' H2' GDP sing 152 n n O2' HO2' GDP sing 153 n n C1' N9 GDP sing 154 n n C1' H1' GDP sing 155 n n N9 C8 GDP sing 156 n y N9 C4 GDP sing 157 n y C8 N7 GDP doub 158 n y C8 H8 GDP sing 159 n n N7 C5 GDP sing 160 n y C5 C6 GDP sing 161 n n C5 C4 GDP doub 162 n y C6 O6 GDP doub 163 n n C6 N1 GDP sing 164 n n N1 C2 GDP sing 165 n n N1 HN1 GDP sing 166 n n C2 N2 GDP sing 167 n n C2 N3 GDP doub 168 n n N2 HN21 GDP sing 169 n n N2 HN22 GDP sing 170 n n N3 C4 GDP sing 171 n n # _atom_sites.entry_id 7CPQ _atom_sites.fract_transf_matrix[1][1] 0.009535 _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] 0.006385 _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] 0.005476 _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 1 GTP GTP . H 6 MG A 1 502 1 MG MG . I 7 CA A 1 503 1 CA CA . J 8 G9X B 1 501 1 G9X LIG . K 9 GDP B 1 502 1 GDP GDP . L 6 MG B 1 503 3 MG MG . M 7 CA B 1 504 2 CA CA . N 10 MES B 1 505 1 MES MES . O 5 GTP C 1 501 2 GTP GTP . P 11 GOL C 1 502 1 GOL GOL . Q 11 GOL C 1 503 2 GOL GOL . R 6 MG C 1 504 2 MG MG . S 7 CA C 1 505 3 CA CA . T 12 IMD C 1 506 1 IMD IMD . U 12 IMD C 1 507 3 IMD IMD . V 9 GDP D 1 501 2 GDP GDP . W 6 MG D 1 502 4 MG MG . X 12 IMD E 1 201 2 IMD IMD . Y 6 MG F 1 401 5 MG MG . Z 13 HOH A 1 601 17 HOH HOH . Z 13 HOH A 2 602 57 HOH HOH . Z 13 HOH A 3 603 5 HOH HOH . Z 13 HOH A 4 604 32 HOH HOH . Z 13 HOH A 5 605 31 HOH HOH . Z 13 HOH A 6 606 76 HOH HOH . Z 13 HOH A 7 607 46 HOH HOH . Z 13 HOH A 8 608 12 HOH HOH . Z 13 HOH A 9 609 70 HOH HOH . Z 13 HOH A 10 610 81 HOH HOH . Z 13 HOH A 11 611 80 HOH HOH . AA 13 HOH B 1 601 50 HOH HOH . AA 13 HOH B 2 602 86 HOH HOH . AA 13 HOH B 3 603 64 HOH HOH . AA 13 HOH B 4 604 28 HOH HOH . AA 13 HOH B 5 605 6 HOH HOH . AA 13 HOH B 6 606 8 HOH HOH . AA 13 HOH B 7 607 34 HOH HOH . AA 13 HOH B 8 608 45 HOH HOH . AA 13 HOH B 9 609 74 HOH HOH . AA 13 HOH B 10 610 23 HOH HOH . AA 13 HOH B 11 611 53 HOH HOH . AA 13 HOH B 12 612 13 HOH HOH . AA 13 HOH B 13 613 65 HOH HOH . AA 13 HOH B 14 614 69 HOH HOH . AA 13 HOH B 15 615 4 HOH HOH . BA 13 HOH C 1 601 39 HOH HOH . BA 13 HOH C 2 602 9 HOH HOH . BA 13 HOH C 3 603 33 HOH HOH . BA 13 HOH C 4 604 11 HOH HOH . BA 13 HOH C 5 605 71 HOH HOH . BA 13 HOH C 6 606 41 HOH HOH . BA 13 HOH C 7 607 82 HOH HOH . BA 13 HOH C 8 608 44 HOH HOH . BA 13 HOH C 9 609 48 HOH HOH . BA 13 HOH C 10 610 52 HOH HOH . BA 13 HOH C 11 611 60 HOH HOH . BA 13 HOH C 12 612 47 HOH HOH . BA 13 HOH C 13 613 30 HOH HOH . BA 13 HOH C 14 614 58 HOH HOH . BA 13 HOH C 15 615 63 HOH HOH . BA 13 HOH C 16 616 29 HOH HOH . BA 13 HOH C 17 617 15 HOH HOH . BA 13 HOH C 18 618 21 HOH HOH . BA 13 HOH C 19 619 3 HOH HOH . BA 13 HOH C 20 620 51 HOH HOH . BA 13 HOH C 21 621 16 HOH HOH . BA 13 HOH C 22 622 78 HOH HOH . BA 13 HOH C 23 623 61 HOH HOH . BA 13 HOH C 24 624 20 HOH HOH . BA 13 HOH C 25 625 56 HOH HOH . BA 13 HOH C 26 626 7 HOH HOH . BA 13 HOH C 27 627 54 HOH HOH . BA 13 HOH C 28 628 49 HOH HOH . BA 13 HOH C 29 629 55 HOH HOH . BA 13 HOH C 30 630 72 HOH HOH . BA 13 HOH C 31 631 10 HOH HOH . BA 13 HOH C 32 632 62 HOH HOH . BA 13 HOH C 33 633 25 HOH HOH . BA 13 HOH C 34 634 37 HOH HOH . BA 13 HOH C 35 635 26 HOH HOH . BA 13 HOH C 36 636 27 HOH HOH . BA 13 HOH C 37 637 2 HOH HOH . CA 13 HOH D 1 601 24 HOH HOH . CA 13 HOH D 2 602 68 HOH HOH . DA 13 HOH E 1 301 75 HOH HOH . EA 13 HOH F 1 501 42 HOH HOH . EA 13 HOH F 2 502 84 HOH HOH . EA 13 HOH F 3 503 35 HOH HOH . EA 13 HOH F 4 504 43 HOH HOH . EA 13 HOH F 5 505 36 HOH HOH . EA 13 HOH F 6 506 67 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 . . . K 9 -18.607 49.083 -15.963 1 25.47 ? PB GDP 502 B 1 HETATM 2 O O1B GDP . . . K 9 -19.143 49.867 -17.015 1 25.54 ? O1B GDP 502 B 1 HETATM 3 O O2B GDP . . . K 9 -19.395 47.989 -15.573 1 25.39 -1 O2B GDP 502 B 1 HETATM 4 O O3B GDP . . . K 9 -18.232 49.853 -14.857 1 25.88 -1 O3B GDP 502 B 1 HETATM 5 O O3A GDP . . . K 9 -17.335 48.358 -16.567 1 25.1 ? O3A GDP 502 B 1 HETATM 6 P PA GDP . . . K 9 -15.904 48.859 -16.992 1 25.13 ? PA GDP 502 B 1 HETATM 7 O O1A GDP . . . K 9 -15.962 49.965 -17.842 1 25.34 -1 O1A GDP 502 B 1 HETATM 8 O O2A GDP . . . K 9 -15.105 48.943 -15.842 1 25.41 ? O2A GDP 502 B 1 HETATM 9 O O5' GDP . . . K 9 -15.075 47.834 -17.741 1 24.84 ? O5' GDP 502 B 1 HETATM 10 C C5' GDP . . . K 9 -15.18 46.795 -18.669 1 24.55 ? C5' GDP 502 B 1 HETATM 11 C C4' GDP . . . K 9 -14.258 47.036 -19.864 1 24.49 ? C4' GDP 502 B 1 HETATM 12 O O4' GDP . . . K 9 -13.629 48.282 -19.787 1 24.76 ? O4' GDP 502 B 1 HETATM 13 C C3' GDP . . . K 9 -13.121 46.08 -20.06 1 24.48 ? C3' GDP 502 B 1 HETATM 14 O O3' GDP . . . K 9 -13.051 45.733 -21.415 1 24.38 ? O3' GDP 502 B 1 HETATM 15 C C2' GDP . . . K 9 -11.901 46.839 -19.628 1 24.81 ? C2' GDP 502 B 1 HETATM 16 O O2' GDP . . . K 9 -10.788 46.46 -20.341 1 24.88 ? O2' GDP 502 B 1 HETATM 17 C C1' GDP . . . K 9 -12.268 48.22 -19.993 1 24.92 ? C1' GDP 502 B 1 HETATM 18 N N9 GDP . . . K 9 -11.807 49.321 -19.202 1 25.3 ? N9 GDP 502 B 1 HETATM 19 C C8 GDP . . . K 9 -12.073 49.541 -17.956 1 25.52 ? C8 GDP 502 B 1 HETATM 20 N N7 GDP . . . K 9 -11.537 50.654 -17.553 1 25.95 ? N7 GDP 502 B 1 HETATM 21 C C5 GDP . . . K 9 -10.91 51.152 -18.585 1 25.97 ? C5 GDP 502 B 1 HETATM 22 C C6 GDP . . . K 9 -10.175 52.338 -18.853 1 26.42 ? C6 GDP 502 B 1 HETATM 23 O O6 GDP . . . K 9 -9.986 53.116 -17.971 1 26.86 ? O6 GDP 502 B 1 HETATM 24 N N1 GDP . . . K 9 -9.712 52.525 -20.04 1 26.37 ? N1 GDP 502 B 1 HETATM 25 C C2 GDP . . . K 9 -9.911 51.673 -21.001 1 25.92 ? C2 GDP 502 B 1 HETATM 26 N N2 GDP . . . K 9 -9.395 51.953 -22.178 1 25.93 ? N2 GDP 502 B 1 HETATM 27 N N3 GDP . . . K 9 -10.597 50.569 -20.845 1 25.53 ? N3 GDP 502 B 1 HETATM 28 C C4 GDP . . . K 9 -11.103 50.28 -19.673 1 25.56 ? C4 GDP 502 B 1 HETATM 29 H H5' GDP . . . K 9 -16.21 46.698 -18.984 1 29.46 ? H5' GDP 502 B 1 HETATM 30 H "H5''" GDP . . . K 9 -14.88 45.867 -18.198 1 29.46 ? "H5''" GDP 502 B 1 HETATM 31 H H4' GDP . . . K 9 -14.86 47.014 -20.772 1 29.39 ? H4' GDP 502 B 1 HETATM 32 H H3' GDP . . . K 9 -13.275 45.202 -19.432 1 29.38 ? H3' GDP 502 B 1 HETATM 33 H HO3' GDP . . . K 9 -12.249 45.238 -21.596 1 29.26 ? HO3' GDP 502 B 1 HETATM 34 H H2' GDP . . . K 9 -11.735 46.76 -18.551 1 29.78 ? H2' GDP 502 B 1 HETATM 35 H HO2' GDP . . . K 9 -10.088 46.261 -19.713 1 29.86 ? HO2' GDP 502 B 1 HETATM 36 H H1' GDP . . . K 9 -12.027 48.397 -21.041 1 29.91 ? H1' GDP 502 B 1 HETATM 37 H H8 GDP . . . K 9 -12.639 48.876 -17.332 1 30.62 ? H8 GDP 502 B 1 HETATM 38 H HN1 GDP . . . K 9 -9.146 53.372 -20.236 1 31.65 ? HN1 GDP 502 B 1 HETATM 39 H HN21 GDP . . . K 9 -8.867 52.797 -22.288 1 31.11 ? HN21 GDP 502 B 1 HETATM 40 H HN22 GDP . . . K 9 -9.528 51.327 -22.953 1 31.11 ? HN22 GDP 502 B 1 # _model_server_stats.io_time_ms 39 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 40 #