data_5XI7 # _model_server_result.job_id KD1DmhIPb84hj4D4NxTH2w _model_server_result.datetime_utc '2024-11-01 03:29:15' _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 5xi7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":501}' # _entry.id 5XI7 # _exptl.entry_id 5XI7 _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 5XI7 _cell.length_a 105.251 _cell.length_b 157.375 _cell.length_c 182.467 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5XI7 _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 _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.714 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.832 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.676 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.661 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc6 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? metalc ? metalc7 G O2G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.801 ? metalc ? metalc8 G O3G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.531 ? metalc ? metalc9 G O2B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc10 H MG MG . A MG 502 1_555 W O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.25 ? metalc ? metalc11 H MG MG . A MG 502 1_555 W O HOH . A HOH 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc12 H MG MG . A MG 502 1_555 X O HOH . B HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc13 B OE1 GLN 11 B GLN 11 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc14 B OE1 GLU 111 B GLU 111 1_555 M CA CA . B CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.538 ? metalc ? metalc15 J O2A GDP . B GDP 501 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc16 K MG MG . B MG 502 1_555 X O HOH . B HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc17 K MG MG . B MG 502 1_555 X O HOH . B HOH 611 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? metalc ? metalc18 K MG MG . B MG 502 1_555 X O HOH . B HOH 612 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.993 ? metalc ? metalc19 K MG MG . B MG 502 1_555 Y O HOH . C HOH 627 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc20 C OD1 ASP 39 C ASP 39 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? metalc ? metalc21 C OD2 ASP 39 C ASP 39 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.738 ? metalc ? metalc22 C O THR 41 C THR 41 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.813 ? metalc ? metalc23 C OG1 THR 41 C THR 41 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? metalc ? metalc24 C O GLY 44 C GLY 44 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.505 ? metalc ? metalc25 C OE1 GLU 55 C GLU 55 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.966 ? metalc ? metalc26 C OE2 GLU 55 C GLU 55 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc27 P O3G GTP . C GTP 501 1_555 Q MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.868 ? metalc ? metalc28 P O2B GTP . C GTP 501 1_555 Q MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? metalc ? metalc29 Q MG MG . C MG 502 1_555 Y O HOH . C HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc30 Q MG MG . C MG 502 1_555 Y O HOH . C HOH 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? metalc ? metalc31 Q MG MG . C MG 502 1_555 Y O HOH . C HOH 614 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? metalc ? metalc32 Q MG MG . C MG 502 1_555 Y O HOH . C HOH 620 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc33 S O2G GTP . D GTP 501 1_555 T MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.676 ? metalc ? metalc34 S O2B GTP . D GTP 501 1_555 T MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.991 ? # _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 5XI7 _atom_sites.fract_transf_matrix[1][1] 0.009501 _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] 0.006354 _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] 0.00548 _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 MES B 1 503 505 MES MES . M 7 CA B 1 504 2 CA CA . N 9 MES B 1 505 505 MES MES . O 10 PO7 B 1 506 1 PO7 PO7 . P 5 GTP C 1 501 501 GTP GTP . Q 6 MG C 1 502 502 MG MG . R 7 CA C 1 503 1 CA CA . S 5 GTP D 1 501 501 GTP GTP . T 6 MG D 1 502 502 MG MG . U 10 PO7 D 1 503 2 PO7 PO7 . V 11 ACP F 1 401 401 ACP ACP . W 12 HOH A 1 601 47 HOH HOH . W 12 HOH A 2 602 25 HOH HOH . W 12 HOH A 3 603 48 HOH HOH . W 12 HOH A 4 604 64 HOH HOH . W 12 HOH A 5 605 62 HOH HOH . W 12 HOH A 6 606 49 HOH HOH . W 12 HOH A 7 607 74 HOH HOH . W 12 HOH A 8 608 59 HOH HOH . W 12 HOH A 9 609 22 HOH HOH . W 12 HOH A 10 610 66 HOH HOH . W 12 HOH A 11 611 67 HOH HOH . W 12 HOH A 12 612 99 HOH HOH . W 12 HOH A 13 613 96 HOH HOH . W 12 HOH A 14 614 58 HOH HOH . W 12 HOH A 15 615 68 HOH HOH . W 12 HOH A 16 616 65 HOH HOH . X 12 HOH B 1 601 28 HOH HOH . X 12 HOH B 2 602 50 HOH HOH . X 12 HOH B 3 603 52 HOH HOH . X 12 HOH B 4 604 53 HOH HOH . X 12 HOH B 5 605 54 HOH HOH . X 12 HOH B 6 606 24 HOH HOH . X 12 HOH B 7 607 46 HOH HOH . X 12 HOH B 8 608 45 HOH HOH . X 12 HOH B 9 609 17 HOH HOH . X 12 HOH B 10 610 95 HOH HOH . X 12 HOH B 11 611 27 HOH HOH . X 12 HOH B 12 612 26 HOH HOH . X 12 HOH B 13 613 75 HOH HOH . X 12 HOH B 14 614 56 HOH HOH . X 12 HOH B 15 615 16 HOH HOH . Y 12 HOH C 1 601 43 HOH HOH . Y 12 HOH C 2 602 39 HOH HOH . Y 12 HOH C 3 603 101 HOH HOH . Y 12 HOH C 4 604 90 HOH HOH . Y 12 HOH C 5 605 8 HOH HOH . Y 12 HOH C 6 606 35 HOH HOH . Y 12 HOH C 7 607 37 HOH HOH . Y 12 HOH C 8 608 102 HOH HOH . Y 12 HOH C 9 609 31 HOH HOH . Y 12 HOH C 10 610 13 HOH HOH . Y 12 HOH C 11 611 80 HOH HOH . Y 12 HOH C 12 612 36 HOH HOH . Y 12 HOH C 13 613 79 HOH HOH . Y 12 HOH C 14 614 104 HOH HOH . Y 12 HOH C 15 615 84 HOH HOH . Y 12 HOH C 16 616 15 HOH HOH . Y 12 HOH C 17 617 87 HOH HOH . Y 12 HOH C 18 618 38 HOH HOH . Y 12 HOH C 19 619 40 HOH HOH . Y 12 HOH C 20 620 103 HOH HOH . Y 12 HOH C 21 621 4 HOH HOH . Y 12 HOH C 22 622 30 HOH HOH . Y 12 HOH C 23 623 1 HOH HOH . Y 12 HOH C 24 624 81 HOH HOH . Y 12 HOH C 25 625 6 HOH HOH . Y 12 HOH C 26 626 14 HOH HOH . Y 12 HOH C 27 627 29 HOH HOH . Y 12 HOH C 28 628 93 HOH HOH . Y 12 HOH C 29 629 34 HOH HOH . Y 12 HOH C 30 630 12 HOH HOH . Y 12 HOH C 31 631 82 HOH HOH . Y 12 HOH C 32 632 11 HOH HOH . Y 12 HOH C 33 633 88 HOH HOH . Z 12 HOH E 1 201 3 HOH HOH . Z 12 HOH E 2 202 61 HOH HOH . AA 12 HOH F 1 501 72 HOH HOH . AA 12 HOH F 2 502 70 HOH HOH . AA 12 HOH F 3 503 71 HOH HOH . AA 12 HOH F 4 504 69 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 -18.637 49.899 -15.751 1 32.94 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . J 8 -19.081 50.578 -17.021 1 32.36 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . J 8 -17.946 50.789 -14.743 1 32.83 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . J 8 -19.701 49.009 -15.163 1 32.52 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . J 8 -17.484 48.881 -16.233 1 32.36 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . J 8 -16.071 49.351 -16.856 1 31.45 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . J 8 -16.203 50.718 -17.48 1 31.7 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . J 8 -15.034 49.144 -15.775 1 32.24 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . J 8 -15.884 48.29 -18.049 1 30.02 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . J 8 -14.828 47.338 -18.116 1 30.37 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . J 8 -14.262 47.373 -19.522 1 30.49 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . J 8 -13.803 48.691 -19.782 1 30.11 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . J 8 -13.065 46.462 -19.696 1 30.92 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . J 8 -13.061 45.923 -21.024 1 30.61 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . J 8 -11.864 47.352 -19.499 1 31.29 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . J 8 -10.785 46.951 -20.349 1 33.92 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . J 8 -12.378 48.706 -19.922 1 30.89 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . J 8 -11.87 49.866 -19.147 1 30.16 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . J 8 -12.121 50.157 -17.854 1 30.14 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . J 8 -11.532 51.332 -17.506 1 29.8 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . J 8 -10.909 51.812 -18.6 1 29.53 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . J 8 -10.092 53.004 -18.951 1 29.63 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . J 8 -9.832 53.899 -18.117 1 29.48 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . J 8 -9.63 53.103 -20.208 1 29.41 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . J 8 -9.881 52.186 -21.161 1 28.79 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . J 8 -9.366 52.4 -22.392 1 28.54 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . J 8 -10.622 51.074 -20.919 1 28.82 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . J 8 -11.139 50.841 -19.681 1 29.46 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 47 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #