data_6D88 # _model_server_result.job_id u24FBBSGt2hyMJBBRGl5XA _model_server_result.datetime_utc '2025-07-07 21:36:55' _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 6d88 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":501}' # _entry.id 6D88 # _exptl.entry_id 6D88 _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 6D88 _cell.length_a 105.536 _cell.length_b 157.894 _cell.length_c 182.025 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6D88 _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 _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 R 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 H CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.852 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 H CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.8 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 H CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.762 ? metalc ? metalc4 A O GLY 44 A GLY 44 1_555 H CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? metalc ? metalc5 A OE1 GLU 55 A GLU 55 1_555 H CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.112 ? metalc ? metalc6 A OE2 GLU 55 A GLU 55 1_555 H CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc7 G O2G GTP . A GTP 501 1_555 I MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.741 ? metalc ? metalc8 G O2B GTP . A GTP 501 1_555 I MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.552 ? metalc ? metalc9 I MG MG . A MG 503 1_555 U O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.881 ? metalc ? metalc10 I MG MG . A MG 503 1_555 U O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? metalc ? metalc11 B OE1 GLN 11 B GLN 11 1_555 M MG MG . B MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.491 ? metalc ? metalc12 B OD2 ASP 177 B ASP 177 1_555 M MG MG . B MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.936 ? metalc ? metalc13 J O2A GDP . B GDP 501 1_555 M MG MG . B MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? metalc ? metalc14 M MG MG . B MG 504 1_555 V O HOH . B HOH 619 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? metalc ? metalc15 M MG MG . B MG 504 1_555 W O HOH . C HOH 619 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? metalc ? metalc16 C OD1 ASP 39 C ASP 39 1_555 P CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? metalc ? metalc17 C OD2 ASP 39 C ASP 39 1_555 P CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? metalc ? metalc18 C O THR 41 C THR 41 1_555 P CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.507 ? metalc ? metalc19 C OG1 THR 41 C THR 41 1_555 P CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc20 C O GLY 44 C GLY 44 1_555 P CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.576 ? metalc ? metalc21 C OE1 GLU 55 C GLU 55 1_555 P CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? metalc ? metalc22 C OE2 GLU 55 C GLU 55 1_555 P CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc23 O O3G GTP . C GTP 501 1_555 Q MG MG . C MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc24 O O2B GTP . C GTP 501 1_555 Q MG MG . C MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.638 ? metalc ? metalc25 Q MG MG . C MG 503 1_555 W O HOH . C HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.92 ? metalc ? metalc26 Q MG MG . C MG 503 1_555 W O HOH . C HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? # _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 181 n n PB O2B GDP sing 182 n n PB O3B GDP sing 183 n n PB O3A GDP sing 184 n n O2B HOB2 GDP sing 185 n n O3B HOB3 GDP sing 186 n n O3A PA GDP sing 187 n n PA O1A GDP doub 188 n n PA O2A GDP sing 189 n n PA O5' GDP sing 190 n n O2A HOA2 GDP sing 191 n n O5' C5' GDP sing 192 n n C5' C4' GDP sing 193 n n C5' H5' GDP sing 194 n n C5' "H5''" GDP sing 195 n n C4' O4' GDP sing 196 n n C4' C3' GDP sing 197 n n C4' H4' GDP sing 198 n n O4' C1' GDP sing 199 n n C3' O3' GDP sing 200 n n C3' C2' GDP sing 201 n n C3' H3' GDP sing 202 n n O3' HO3' GDP sing 203 n n C2' O2' GDP sing 204 n n C2' C1' GDP sing 205 n n C2' H2' GDP sing 206 n n O2' HO2' GDP sing 207 n n C1' N9 GDP sing 208 n n C1' H1' GDP sing 209 n n N9 C8 GDP sing 210 n y N9 C4 GDP sing 211 n y C8 N7 GDP doub 212 n y C8 H8 GDP sing 213 n n N7 C5 GDP sing 214 n y C5 C6 GDP sing 215 n n C5 C4 GDP doub 216 n y C6 O6 GDP doub 217 n n C6 N1 GDP sing 218 n n N1 C2 GDP sing 219 n n N1 HN1 GDP sing 220 n n C2 N2 GDP sing 221 n n C2 N3 GDP doub 222 n n N2 HN21 GDP sing 223 n n N2 HN22 GDP sing 224 n n N3 C4 GDP sing 225 n n # _atom_sites.entry_id 6D88 _atom_sites.fract_transf_matrix[1][1] 0.009475 _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] 0.006333 _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] 0.005494 _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 CA A 1 502 1 CA CA . I 7 MG A 1 503 1 MG MG . J 8 GDP B 1 501 501 GDP GDP . K 9 MES B 1 502 1 MES MES . L 9 MES B 1 503 2 MES MES . M 7 MG B 1 504 2 MG MG . N 10 G9K B 1 505 1 G9K G9K . O 5 GTP C 1 501 501 GTP GTP . P 6 CA C 1 502 2 CA CA . Q 7 MG C 1 503 3 MG MG . R 8 GDP D 1 501 1 GDP GDP . S 10 G9K D 1 502 2 G9K G9K . T 11 ACP F 1 401 1 ACP ACP . U 12 HOH A 1 601 98 HOH HOH . U 12 HOH A 2 602 27 HOH HOH . U 12 HOH A 3 603 119 HOH HOH . U 12 HOH A 4 604 99 HOH HOH . U 12 HOH A 5 605 95 HOH HOH . U 12 HOH A 6 606 115 HOH HOH . U 12 HOH A 7 607 25 HOH HOH . U 12 HOH A 8 608 13 HOH HOH . U 12 HOH A 9 609 63 HOH HOH . U 12 HOH A 10 610 56 HOH HOH . U 12 HOH A 11 611 60 HOH HOH . U 12 HOH A 12 612 33 HOH HOH . U 12 HOH A 13 613 50 HOH HOH . U 12 HOH A 14 614 8 HOH HOH . U 12 HOH A 15 615 30 HOH HOH . U 12 HOH A 16 616 75 HOH HOH . U 12 HOH A 17 617 22 HOH HOH . V 12 HOH B 1 601 53 HOH HOH . V 12 HOH B 2 602 44 HOH HOH . V 12 HOH B 3 603 112 HOH HOH . V 12 HOH B 4 604 89 HOH HOH . V 12 HOH B 5 605 24 HOH HOH . V 12 HOH B 6 606 107 HOH HOH . V 12 HOH B 7 607 18 HOH HOH . V 12 HOH B 8 608 116 HOH HOH . V 12 HOH B 9 609 125 HOH HOH . V 12 HOH B 10 610 85 HOH HOH . V 12 HOH B 11 611 108 HOH HOH . V 12 HOH B 12 612 109 HOH HOH . V 12 HOH B 13 613 126 HOH HOH . V 12 HOH B 14 614 92 HOH HOH . V 12 HOH B 15 615 96 HOH HOH . V 12 HOH B 16 616 70 HOH HOH . V 12 HOH B 17 617 124 HOH HOH . V 12 HOH B 18 618 21 HOH HOH . V 12 HOH B 19 619 101 HOH HOH . W 12 HOH C 1 601 103 HOH HOH . W 12 HOH C 2 602 102 HOH HOH . W 12 HOH C 3 603 121 HOH HOH . W 12 HOH C 4 604 114 HOH HOH . W 12 HOH C 5 605 104 HOH HOH . W 12 HOH C 6 606 97 HOH HOH . W 12 HOH C 7 607 123 HOH HOH . W 12 HOH C 8 608 19 HOH HOH . W 12 HOH C 9 609 72 HOH HOH . W 12 HOH C 10 610 1 HOH HOH . W 12 HOH C 11 611 20 HOH HOH . W 12 HOH C 12 612 106 HOH HOH . W 12 HOH C 13 613 111 HOH HOH . W 12 HOH C 14 614 105 HOH HOH . W 12 HOH C 15 615 23 HOH HOH . W 12 HOH C 16 616 6 HOH HOH . W 12 HOH C 17 617 83 HOH HOH . W 12 HOH C 18 618 65 HOH HOH . W 12 HOH C 19 619 100 HOH HOH . W 12 HOH C 20 620 87 HOH HOH . W 12 HOH C 21 621 122 HOH HOH . W 12 HOH C 22 622 42 HOH HOH . W 12 HOH C 23 623 29 HOH HOH . W 12 HOH C 24 624 71 HOH HOH . W 12 HOH C 25 625 110 HOH HOH . W 12 HOH C 26 626 7 HOH HOH . W 12 HOH C 27 627 41 HOH HOH . W 12 HOH C 28 628 86 HOH HOH . W 12 HOH C 29 629 88 HOH HOH . X 12 HOH D 1 601 118 HOH HOH . X 12 HOH D 2 602 74 HOH HOH . X 12 HOH D 3 603 54 HOH HOH . X 12 HOH D 4 604 90 HOH HOH . X 12 HOH D 5 605 12 HOH HOH . X 12 HOH D 6 606 5 HOH HOH . X 12 HOH D 7 607 32 HOH HOH . X 12 HOH D 8 608 80 HOH HOH . X 12 HOH D 9 609 57 HOH HOH . X 12 HOH D 10 610 76 HOH HOH . X 12 HOH D 11 611 77 HOH HOH . X 12 HOH D 12 612 82 HOH HOH . X 12 HOH D 13 613 69 HOH HOH . X 12 HOH D 14 614 94 HOH HOH . Y 12 HOH E 1 201 40 HOH HOH . Y 12 HOH E 2 202 93 HOH HOH . Y 12 HOH E 3 203 17 HOH HOH . Y 12 HOH E 4 204 67 HOH HOH . Y 12 HOH E 5 205 78 HOH HOH . Z 12 HOH F 1 501 59 HOH HOH . Z 12 HOH F 2 502 117 HOH HOH . Z 12 HOH F 3 503 79 HOH HOH . Z 12 HOH F 4 504 11 HOH HOH . Z 12 HOH F 5 505 81 HOH HOH . Z 12 HOH F 6 506 46 HOH HOH . Z 12 HOH F 7 507 38 HOH HOH . Z 12 HOH F 8 508 64 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 18.5 -49.774 -15.745 1 38.15 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . J 8 19.236 -50.435 -16.878 1 34.21 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . J 8 18.017 -50.801 -14.752 1 36.53 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . J 8 19.414 -48.782 -15.051 1 37.11 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . J 8 17.253 -48.912 -16.299 1 35.08 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . J 8 15.892 -49.519 -16.891 1 26.16 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . J 8 16.148 -50.884 -17.477 1 33.94 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . J 8 14.811 -49.583 -15.843 1 26.98 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . J 8 15.657 -48.431 -18.043 1 19.95 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . J 8 14.638 -47.453 -18.069 1 19.84 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . J 8 14.145 -47.498 -19.502 1 25.6 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . J 8 13.738 -48.847 -19.755 1 23.21 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . J 8 12.912 -46.643 -19.697 1 25.22 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . J 8 12.835 -46.198 -21.056 1 23.35 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . J 8 11.764 -47.585 -19.451 1 26.94 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . J 8 10.677 -47.188 -20.271 1 34.51 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . J 8 12.319 -48.898 -19.951 1 28.44 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . J 8 11.796 -50.091 -19.261 1 32.48 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . J 8 12.066 -50.441 -17.998 1 34.08 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . J 8 11.459 -51.617 -17.679 1 36.71 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . J 8 10.812 -52.042 -18.765 1 33.77 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . J 8 9.991 -53.216 -19.096 1 31.34 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . J 8 9.787 -54.074 -18.214 1 33.65 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . J 8 9.488 -53.316 -20.337 1 28.53 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . J 8 9.727 -52.366 -21.271 1 33.06 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . J 8 9.183 -52.517 -22.498 1 37.47 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . J 8 10.479 -51.251 -21.04 1 29.94 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . J 8 11.036 -51.04 -19.815 1 33.91 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 43 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #