data_6JCJ # _model_server_result.job_id LYVtnuxb7G-FQDoZAWXZSg _model_server_result.datetime_utc '2024-11-23 16:15:02' _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 6jcj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":501}' # _entry.id 6JCJ # _exptl.entry_id 6JCJ _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 1 _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 6JCJ _cell.length_a 105.544 _cell.length_b 157.329 _cell.length_c 184.031 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6JCJ _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 _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 # _struct_asym.details ? _struct_asym.entity_id 8 _struct_asym.id J _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.593 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.454 ? metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.013 ? metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc8 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc9 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc10 H MG MG . A MG 502 1_555 S O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc11 H MG MG . A MG 502 1_555 S O HOH . A HOH 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.963 ? metalc ? metalc12 H MG MG . A MG 502 1_555 S O HOH . A HOH 610 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc13 H MG MG . A MG 502 1_555 S O HOH . A HOH 611 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc14 B OE1 GLN 11 B GLN 11 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc15 B OD2 ASP 177 B ASP 177 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? metalc ? metalc16 J O1A GDP . B GDP 501 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.707 ? metalc ? metalc17 C OD1 ASP 39 C ASP 39 1_555 O CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? metalc ? metalc18 C OD2 ASP 39 C ASP 39 1_555 O CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? metalc ? metalc19 C O THR 41 C THR 41 1_555 O CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc20 C OG1 THR 41 C THR 41 1_555 O CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.928 ? metalc ? metalc21 C O GLY 44 C GLY 44 1_555 O CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.503 ? metalc ? metalc22 C OE1 GLU 55 C GLU 55 1_555 O CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc23 C OE2 GLU 55 C GLU 55 1_555 O CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? metalc ? metalc24 M O1G GTP . C GTP 501 1_555 N MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.922 ? metalc ? metalc25 M O1B GTP . C GTP 501 1_555 N MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? metalc ? metalc26 N MG MG . C MG 502 1_555 U O HOH . C HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc27 N MG MG . C MG 502 1_555 U O HOH . C HOH 617 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? metalc ? metalc28 N MG MG . C MG 502 1_555 U O HOH . C HOH 625 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? metalc ? metalc29 N MG MG . C MG 502 1_555 U O HOH . C HOH 633 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? # _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 179 n n PB O2B GDP sing 180 n n PB O3B GDP sing 181 n n PB O3A GDP sing 182 n n O2B HOB2 GDP sing 183 n n O3B HOB3 GDP sing 184 n n O3A PA GDP sing 185 n n PA O1A GDP doub 186 n n PA O2A GDP sing 187 n n PA O5' GDP sing 188 n n O2A HOA2 GDP sing 189 n n O5' C5' GDP sing 190 n n C5' C4' GDP sing 191 n n C5' H5' GDP sing 192 n n C5' "H5''" GDP sing 193 n n C4' O4' GDP sing 194 n n C4' C3' GDP sing 195 n n C4' H4' GDP sing 196 n n O4' C1' GDP sing 197 n n C3' O3' GDP sing 198 n n C3' C2' GDP sing 199 n n C3' H3' GDP sing 200 n n O3' HO3' GDP sing 201 n n C2' O2' GDP sing 202 n n C2' C1' GDP sing 203 n n C2' H2' GDP sing 204 n n O2' HO2' GDP sing 205 n n C1' N9 GDP sing 206 n n C1' H1' GDP sing 207 n n N9 C8 GDP sing 208 n y N9 C4 GDP sing 209 n y C8 N7 GDP doub 210 n y C8 H8 GDP sing 211 n n N7 C5 GDP sing 212 n y C5 C6 GDP sing 213 n n C5 C4 GDP doub 214 n y C6 O6 GDP doub 215 n n C6 N1 GDP sing 216 n n N1 C2 GDP sing 217 n n N1 HN1 GDP sing 218 n n C2 N2 GDP sing 219 n n C2 N3 GDP doub 220 n n N2 HN21 GDP sing 221 n n N2 HN22 GDP sing 222 n n N3 C4 GDP sing 223 n n # _atom_sites.entry_id 6JCJ _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] 0.006356 _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] 0.005434 _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 1 501 501 GDP GDP . K 6 MG B 1 502 502 MG MG . L 9 BG0 B 1 503 1 BG0 CRO . M 5 GTP C 1 501 501 GTP GTP . N 6 MG C 1 502 502 MG MG . O 7 CA C 1 503 1 CA CA . P 5 GTP D 1 501 501 GTP GTP . Q 9 BG0 D 1 502 2 BG0 CRO . R 10 ACP F 1 401 401 ACP ACP . S 11 HOH A 1 601 24 HOH HOH . S 11 HOH A 2 602 70 HOH HOH . S 11 HOH A 3 603 74 HOH HOH . S 11 HOH A 4 604 39 HOH HOH . S 11 HOH A 5 605 32 HOH HOH . S 11 HOH A 6 606 52 HOH HOH . S 11 HOH A 7 607 73 HOH HOH . S 11 HOH A 8 608 46 HOH HOH . S 11 HOH A 9 609 33 HOH HOH . S 11 HOH A 10 610 72 HOH HOH . S 11 HOH A 11 611 71 HOH HOH . S 11 HOH A 12 612 23 HOH HOH . S 11 HOH A 13 613 29 HOH HOH . S 11 HOH A 14 614 57 HOH HOH . S 11 HOH A 15 615 45 HOH HOH . S 11 HOH A 16 616 63 HOH HOH . T 11 HOH B 1 601 85 HOH HOH . T 11 HOH B 2 602 58 HOH HOH . T 11 HOH B 3 603 67 HOH HOH . T 11 HOH B 4 604 41 HOH HOH . T 11 HOH B 5 605 55 HOH HOH . T 11 HOH B 6 606 26 HOH HOH . T 11 HOH B 7 607 60 HOH HOH . T 11 HOH B 8 608 16 HOH HOH . T 11 HOH B 9 609 1 HOH HOH . T 11 HOH B 10 610 36 HOH HOH . T 11 HOH B 11 611 2 HOH HOH . T 11 HOH B 12 612 25 HOH HOH . T 11 HOH B 13 613 86 HOH HOH . T 11 HOH B 14 614 80 HOH HOH . T 11 HOH B 15 615 10 HOH HOH . T 11 HOH B 16 616 78 HOH HOH . U 11 HOH C 1 601 37 HOH HOH . U 11 HOH C 2 602 15 HOH HOH . U 11 HOH C 3 603 48 HOH HOH . U 11 HOH C 4 604 40 HOH HOH . U 11 HOH C 5 605 22 HOH HOH . U 11 HOH C 6 606 44 HOH HOH . U 11 HOH C 7 607 49 HOH HOH . U 11 HOH C 8 608 35 HOH HOH . U 11 HOH C 9 609 30 HOH HOH . U 11 HOH C 10 610 50 HOH HOH . U 11 HOH C 11 611 9 HOH HOH . U 11 HOH C 12 612 59 HOH HOH . U 11 HOH C 13 613 4 HOH HOH . U 11 HOH C 14 614 11 HOH HOH . U 11 HOH C 15 615 6 HOH HOH . U 11 HOH C 16 616 77 HOH HOH . U 11 HOH C 17 617 76 HOH HOH . U 11 HOH C 18 618 34 HOH HOH . U 11 HOH C 19 619 17 HOH HOH . U 11 HOH C 20 620 12 HOH HOH . U 11 HOH C 21 621 47 HOH HOH . U 11 HOH C 22 622 84 HOH HOH . U 11 HOH C 23 623 28 HOH HOH . U 11 HOH C 24 624 5 HOH HOH . U 11 HOH C 25 625 75 HOH HOH . U 11 HOH C 26 626 8 HOH HOH . U 11 HOH C 27 627 38 HOH HOH . U 11 HOH C 28 628 20 HOH HOH . U 11 HOH C 29 629 65 HOH HOH . U 11 HOH C 30 630 21 HOH HOH . U 11 HOH C 31 631 19 HOH HOH . U 11 HOH C 32 632 31 HOH HOH . U 11 HOH C 33 633 54 HOH HOH . U 11 HOH C 34 634 56 HOH HOH . U 11 HOH C 35 635 14 HOH HOH . U 11 HOH C 36 636 43 HOH HOH . U 11 HOH C 37 637 42 HOH HOH . U 11 HOH C 38 638 66 HOH HOH . U 11 HOH C 39 639 53 HOH HOH . U 11 HOH C 40 640 27 HOH HOH . U 11 HOH C 41 641 51 HOH HOH . U 11 HOH C 42 642 13 HOH HOH . U 11 HOH C 43 643 7 HOH HOH . U 11 HOH C 44 644 18 HOH HOH . U 11 HOH C 45 645 69 HOH HOH . U 11 HOH C 46 646 68 HOH HOH . V 11 HOH D 1 601 81 HOH HOH . V 11 HOH D 2 602 62 HOH HOH . V 11 HOH D 3 603 79 HOH HOH . V 11 HOH D 4 604 82 HOH HOH . W 11 HOH E 1 201 61 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 -18.461 -50.059 15.46 1 14.18 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . J 8 -19.23 -49.009 14.53 1 16.36 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . J 8 -19.222 -50.718 16.575 1 13.27 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . J 8 -17.816 -51.143 14.654 1 12.78 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . J 8 -17.235 -49.243 16.133 1 13.68 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . J 8 -15.784 -49.829 16.63 1 13.72 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . J 8 -14.73 -49.815 15.571 1 15.47 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . J 8 -15.953 -51.198 17.224 1 15.64 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . J 8 -15.546 -48.765 17.787 1 13.69 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . J 8 -14.583 -47.773 17.897 1 14.47 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . J 8 -14.045 -47.932 19.32 1 15.82 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . J 8 -13.541 -49.263 19.508 1 15.6 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . J 8 -12.868 -47.004 19.554 1 16.37 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . J 8 -12.766 -46.64 20.937 1 16.11 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . J 8 -11.704 -47.842 19.073 1 16.51 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . J 8 -10.442 -47.444 19.621 1 20.1 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . J 8 -12.109 -49.19 19.576 1 16.13 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . J 8 -11.652 -50.364 18.834 1 16 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . J 8 -11.939 -50.685 17.57 1 16.58 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . J 8 -11.431 -51.904 17.232 1 16.65 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . J 8 -10.803 -52.358 18.324 1 16.62 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . J 8 -10.051 -53.552 18.68 1 16.82 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . J 8 -9.899 -54.442 17.84 1 17.94 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . J 8 -9.585 -53.672 19.922 1 16.76 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . J 8 -9.761 -52.739 20.853 1 15.87 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . J 8 -9.239 -52.958 22.073 1 15.5 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . J 8 -10.444 -51.613 20.607 1 15.97 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . J 8 -10.974 -51.371 19.386 1 16.4 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 353 _model_server_stats.encode_time_ms 21 _model_server_stats.element_count 28 #