data_3VO8 # _model_server_result.job_id uqQKuJpTpxoD_rueThgNiA _model_server_result.datetime_utc '2024-12-26 12:03:22' _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 3vo8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 3VO8 # _exptl.entry_id 3VO8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _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 96.89 _cell.angle_beta 103.57 _cell.angle_gamma 108 _cell.entry_id 3VO8 _cell.length_a 44.039 _cell.length_b 44.079 _cell.length_c 85.993 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VO8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 2 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 ? 3 D N N ? 3 F 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 O LEU 202 A LEU 200 1_555 C CA CA . A CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc2 A O VAL 205 A VAL 203 1_555 C CA CA . A CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc3 A OD1 ASN 210 A ASN 208 1_555 C CA CA . A CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.404 ? metalc ? metalc4 A O LEU 211 A LEU 209 1_555 C CA CA . A CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? metalc ? metalc5 C CA CA . A CA 501 1_555 G O HOH . A HOH 641 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.462 ? metalc ? metalc6 C CA CA . A CA 501 1_555 G O HOH . A HOH 642 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.454 ? metalc ? metalc7 B O LEU 202 B LEU 200 1_555 E CA CA . B CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? metalc ? metalc8 B O VAL 205 B VAL 203 1_555 E CA CA . B CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc9 B OD1 ASN 210 B ASN 208 1_555 E CA CA . B CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? metalc ? metalc10 B O LEU 211 B LEU 209 1_555 E CA CA . B CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? metalc ? metalc11 E CA CA . B CA 501 1_555 H O HOH . B HOH 638 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.553 ? metalc ? metalc12 E CA CA . B CA 501 1_555 H O HOH . B HOH 639 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? # _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 70 n n PB O2B GDP sing 71 n n PB O3B GDP sing 72 n n PB O3A GDP sing 73 n n O2B HOB2 GDP sing 74 n n O3B HOB3 GDP sing 75 n n O3A PA GDP sing 76 n n PA O1A GDP doub 77 n n PA O2A GDP sing 78 n n PA O5' GDP sing 79 n n O2A HOA2 GDP sing 80 n n O5' C5' GDP sing 81 n n C5' C4' GDP sing 82 n n C5' H5' GDP sing 83 n n C5' "H5''" GDP sing 84 n n C4' O4' GDP sing 85 n n C4' C3' GDP sing 86 n n C4' H4' GDP sing 87 n n O4' C1' GDP sing 88 n n C3' O3' GDP sing 89 n n C3' C2' GDP sing 90 n n C3' H3' GDP sing 91 n n O3' HO3' GDP sing 92 n n C2' O2' GDP sing 93 n n C2' C1' GDP sing 94 n n C2' H2' GDP sing 95 n n O2' HO2' GDP sing 96 n n C1' N9 GDP sing 97 n n C1' H1' GDP sing 98 n n N9 C8 GDP sing 99 n y N9 C4 GDP sing 100 n y C8 N7 GDP doub 101 n y C8 H8 GDP sing 102 n n N7 C5 GDP sing 103 n y C5 C6 GDP sing 104 n n C5 C4 GDP doub 105 n y C6 O6 GDP doub 106 n n C6 N1 GDP sing 107 n n N1 C2 GDP sing 108 n n N1 HN1 GDP sing 109 n n C2 N2 GDP sing 110 n n C2 N3 GDP doub 111 n n N2 HN21 GDP sing 112 n n N2 HN22 GDP sing 113 n n N3 C4 GDP sing 114 n n # _atom_sites.entry_id 3VO8 _atom_sites.fract_transf_matrix[1][1] 0.022707 _atom_sites.fract_transf_matrix[1][2] 0.007378 _atom_sites.fract_transf_matrix[1][3] 0.007174 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.023854 _atom_sites.fract_transf_matrix[2][3] 0.005077 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.012231 _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 C 2 CA A 1 501 501 CA CA . D 3 GDP A 1 502 502 GDP GDP . E 2 CA B 1 501 501 CA CA . F 3 GDP B 1 502 502 GDP GDP . G 4 HOH A 1 601 1 HOH HOH . G 4 HOH A 2 602 2 HOH HOH . G 4 HOH A 3 603 5 HOH HOH . G 4 HOH A 4 604 7 HOH HOH . G 4 HOH A 5 605 10 HOH HOH . G 4 HOH A 6 606 11 HOH HOH . G 4 HOH A 7 607 12 HOH HOH . G 4 HOH A 8 608 14 HOH HOH . G 4 HOH A 9 609 17 HOH HOH . G 4 HOH A 10 610 19 HOH HOH . G 4 HOH A 11 611 22 HOH HOH . G 4 HOH A 12 612 31 HOH HOH . G 4 HOH A 13 613 33 HOH HOH . G 4 HOH A 14 614 35 HOH HOH . G 4 HOH A 15 615 38 HOH HOH . G 4 HOH A 16 616 39 HOH HOH . G 4 HOH A 17 617 43 HOH HOH . G 4 HOH A 18 618 44 HOH HOH . G 4 HOH A 19 619 47 HOH HOH . G 4 HOH A 20 620 51 HOH HOH . G 4 HOH A 21 621 57 HOH HOH . G 4 HOH A 22 622 58 HOH HOH . G 4 HOH A 23 623 59 HOH HOH . G 4 HOH A 24 624 60 HOH HOH . G 4 HOH A 25 625 61 HOH HOH . G 4 HOH A 26 626 63 HOH HOH . G 4 HOH A 27 627 65 HOH HOH . G 4 HOH A 28 628 69 HOH HOH . G 4 HOH A 29 629 75 HOH HOH . G 4 HOH A 30 630 79 HOH HOH . G 4 HOH A 31 631 84 HOH HOH . G 4 HOH A 32 632 85 HOH HOH . G 4 HOH A 33 633 87 HOH HOH . G 4 HOH A 34 634 96 HOH HOH . G 4 HOH A 35 635 102 HOH HOH . G 4 HOH A 36 636 106 HOH HOH . G 4 HOH A 37 637 107 HOH HOH . G 4 HOH A 38 638 112 HOH HOH . G 4 HOH A 39 639 118 HOH HOH . G 4 HOH A 40 640 184 HOH HOH . G 4 HOH A 41 641 188 HOH HOH . G 4 HOH A 42 642 189 HOH HOH . G 4 HOH A 43 643 197 HOH HOH . G 4 HOH A 44 644 198 HOH HOH . G 4 HOH A 45 645 202 HOH HOH . G 4 HOH A 46 646 203 HOH HOH . G 4 HOH A 47 647 204 HOH HOH . G 4 HOH A 48 648 205 HOH HOH . G 4 HOH A 49 649 206 HOH HOH . H 4 HOH B 1 601 3 HOH HOH . H 4 HOH B 2 602 4 HOH HOH . H 4 HOH B 3 603 8 HOH HOH . H 4 HOH B 4 604 13 HOH HOH . H 4 HOH B 5 605 15 HOH HOH . H 4 HOH B 6 606 16 HOH HOH . H 4 HOH B 7 607 18 HOH HOH . H 4 HOH B 8 608 21 HOH HOH . H 4 HOH B 9 609 25 HOH HOH . H 4 HOH B 10 610 26 HOH HOH . H 4 HOH B 11 611 28 HOH HOH . H 4 HOH B 12 612 29 HOH HOH . H 4 HOH B 13 613 32 HOH HOH . H 4 HOH B 14 614 34 HOH HOH . H 4 HOH B 15 615 36 HOH HOH . H 4 HOH B 16 616 37 HOH HOH . H 4 HOH B 17 617 42 HOH HOH . H 4 HOH B 18 618 45 HOH HOH . H 4 HOH B 19 619 48 HOH HOH . H 4 HOH B 20 620 49 HOH HOH . H 4 HOH B 21 621 52 HOH HOH . H 4 HOH B 22 622 54 HOH HOH . H 4 HOH B 23 623 56 HOH HOH . H 4 HOH B 24 624 62 HOH HOH . H 4 HOH B 25 625 66 HOH HOH . H 4 HOH B 26 626 71 HOH HOH . H 4 HOH B 27 627 72 HOH HOH . H 4 HOH B 28 628 76 HOH HOH . H 4 HOH B 29 629 81 HOH HOH . H 4 HOH B 30 630 82 HOH HOH . H 4 HOH B 31 631 83 HOH HOH . H 4 HOH B 32 632 90 HOH HOH . H 4 HOH B 33 633 99 HOH HOH . H 4 HOH B 34 634 101 HOH HOH . H 4 HOH B 35 635 110 HOH HOH . H 4 HOH B 36 636 113 HOH HOH . H 4 HOH B 37 637 151 HOH HOH . H 4 HOH B 38 638 185 HOH HOH . H 4 HOH B 39 639 186 HOH HOH . H 4 HOH B 40 640 187 HOH HOH . H 4 HOH B 41 641 190 HOH HOH . H 4 HOH B 42 642 191 HOH HOH . H 4 HOH B 43 643 192 HOH HOH . H 4 HOH B 44 644 194 HOH HOH . H 4 HOH B 45 645 195 HOH HOH . H 4 HOH B 46 646 196 HOH HOH . H 4 HOH B 47 647 207 HOH HOH . H 4 HOH B 48 648 208 HOH HOH . H 4 HOH B 49 649 209 HOH HOH . H 4 HOH B 50 650 211 HOH HOH . H 4 HOH B 51 651 212 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 . . . D 3 17.695 0.345 -4.182 1 22.39 ? PB GDP 502 A 1 HETATM 2 O O1B GDP . . . D 3 16.44 1.038 -4.656 1 28.85 ? O1B GDP 502 A 1 HETATM 3 O O2B GDP . . . D 3 17.509 -1.138 -4.303 1 21.36 ? O2B GDP 502 A 1 HETATM 4 O O3B GDP . . . D 3 18.901 0.839 -4.922 1 23.82 ? O3B GDP 502 A 1 HETATM 5 O O3A GDP . . . D 3 17.969 0.692 -2.639 1 22.91 ? O3A GDP 502 A 1 HETATM 6 P PA GDP . . . D 3 17.165 0.066 -1.393 1 20.9 ? PA GDP 502 A 1 HETATM 7 O O1A GDP . . . D 3 17.82 -1.197 -0.886 1 23.86 ? O1A GDP 502 A 1 HETATM 8 O O2A GDP . . . D 3 15.705 -0.146 -1.724 1 20.94 ? O2A GDP 502 A 1 HETATM 9 O O5' GDP . . . D 3 17.388 1.247 -0.32 1 22.3 ? O5' GDP 502 A 1 HETATM 10 C C5' GDP . . . D 3 16.705 2.495 -0.412 1 19.67 ? C5' GDP 502 A 1 HETATM 11 C C4' GDP . . . D 3 16.22 2.922 0.969 1 17 ? C4' GDP 502 A 1 HETATM 12 O O4' GDP . . . D 3 15.197 2.032 1.391 1 17.88 ? O4' GDP 502 A 1 HETATM 13 C C3' GDP . . . D 3 17.296 2.809 2.034 1 24.14 ? C3' GDP 502 A 1 HETATM 14 O O3' GDP . . . D 3 17.998 4.045 2.109 1 25.01 ? O3' GDP 502 A 1 HETATM 15 C C2' GDP . . . D 3 16.551 2.488 3.322 1 21.62 ? C2' GDP 502 A 1 HETATM 16 O O2' GDP . . . D 3 16.096 3.683 3.973 1 15.56 ? O2' GDP 502 A 1 HETATM 17 C C1' GDP . . . D 3 15.299 1.802 2.807 1 23.51 ? C1' GDP 502 A 1 HETATM 18 N N9 GDP . . . D 3 15.242 0.329 2.962 1 21.82 ? N9 GDP 502 A 1 HETATM 19 C C8 GDP . . . D 3 15.972 -0.596 2.322 1 15.43 ? C8 GDP 502 A 1 HETATM 20 N N7 GDP . . . D 3 15.582 -1.843 2.689 1 17.8 ? N7 GDP 502 A 1 HETATM 21 C C5 GDP . . . D 3 14.564 -1.72 3.57 1 20.83 ? C5 GDP 502 A 1 HETATM 22 C C6 GDP . . . D 3 13.665 -2.608 4.349 1 23.28 ? C6 GDP 502 A 1 HETATM 23 O O6 GDP . . . D 3 13.76 -3.846 4.277 1 21.68 ? O6 GDP 502 A 1 HETATM 24 N N1 GDP . . . D 3 12.748 -2.039 5.155 1 19.77 ? N1 GDP 502 A 1 HETATM 25 C C2 GDP . . . D 3 12.609 -0.704 5.251 1 21.75 ? C2 GDP 502 A 1 HETATM 26 N N2 GDP . . . D 3 11.654 -0.193 6.061 1 20.5 ? N2 GDP 502 A 1 HETATM 27 N N3 GDP . . . D 3 13.389 0.163 4.562 1 23.89 ? N3 GDP 502 A 1 HETATM 28 C C4 GDP . . . D 3 14.352 -0.279 3.733 1 21.48 ? C4 GDP 502 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #