data_4G5G # _model_server_result.job_id SlDJ-lzVKL3m1s0M2U_snw _model_server_result.datetime_utc '2024-12-22 06:22:07' _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 4g5g # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 4G5G # _exptl.entry_id 4G5G _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 4 _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 4G5G _cell.length_a 80.305 _cell.length_b 123.577 _cell.length_c 45.092 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4G5G _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 4 _struct_asym.id D _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 covale ? covale1 B C SER 1 I SER 900 1_555 B N BB9 2 I BB9 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale2 B C SER 1 I SER 900 1_555 B SG BB9 2 I BB9 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.754 ? covale ? covale3 B CA SER 1 I SER 900 1_555 B C BB9 10 I BB9 909 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.419 ? covale ? covale4 B CB SER 1 I SER 900 1_555 B CB MH6 11 I MH6 910 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale5 B C BB9 2 I BB9 901 1_555 B N ASN 3 I ASN 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.345 ? covale ? covale6 B C ASN 3 I ASN 902 1_555 B SG BB6 4 I BB6 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.77 ? covale ? covale7 B C H14 5 I H14 904 1_555 B N BB9 6 I BB9 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.349 ? covale ? covale8 B C H14 5 I H14 904 1_555 B SG BB9 6 I BB9 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.763 ? covale ? covale9 B C BB9 6 I BB9 905 1_555 B N TYR 7 I TYR 906 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale10 B C TYR 7 I TYR 906 1_555 B N 05N 8 I 05N 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale11 B C 05N 8 I 05N 907 1_555 B N BB9 9 I BB9 908 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.297 ? covale ? covale12 B C 05N 8 I 05N 907 1_555 B SG BB9 9 I BB9 908 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.764 ? covale ? covale13 B C BB9 9 I BB9 908 1_555 B N BB9 10 I BB9 909 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale14 B C BB9 9 I BB9 908 1_555 B SG BB9 10 I BB9 909 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.742 ? covale ? covale15 B C BB9 10 I BB9 909 1_555 B N MH6 11 I MH6 910 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.346 ? covale ? covale16 B C MH6 11 I MH6 910 1_555 B N BB9 12 I BB9 911 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? covale ? covale17 B C MH6 11 I MH6 910 1_555 B SG BB9 12 I BB9 911 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.77 ? covale ? covale18 B C BB9 12 I BB9 911 1_555 B N NH2 13 I NH2 912 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? metalc ? metalc1 A OG1 THR 26 A THR 25 1_555 C MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc2 C MG MG . A MG 501 1_555 D O2B GDP . A GDP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc3 C MG MG . A MG 501 1_555 G O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc4 C MG MG . A MG 501 1_555 G O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? metalc ? metalc5 C MG MG . A MG 501 1_555 G O HOH . A HOH 615 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc6 C MG MG . A MG 501 1_555 G O HOH . A HOH 616 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? metalc ? metalc7 E MG MG . A MG 503 1_555 G O HOH . A HOH 653 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc8 E MG MG . A MG 503 1_555 G O HOH . A HOH 654 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc9 E MG MG . A MG 503 1_555 G O HOH . A HOH 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.437 ? # _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 129 n n PB O2B GDP sing 130 n n PB O3B GDP sing 131 n n PB O3A GDP sing 132 n n O2B HOB2 GDP sing 133 n n O3B HOB3 GDP sing 134 n n O3A PA GDP sing 135 n n PA O1A GDP doub 136 n n PA O2A GDP sing 137 n n PA O5' GDP sing 138 n n O2A HOA2 GDP sing 139 n n O5' C5' GDP sing 140 n n C5' C4' GDP sing 141 n n C5' H5' GDP sing 142 n n C5' "H5''" GDP sing 143 n n C4' O4' GDP sing 144 n n C4' C3' GDP sing 145 n n C4' H4' GDP sing 146 n n O4' C1' GDP sing 147 n n C3' O3' GDP sing 148 n n C3' C2' GDP sing 149 n n C3' H3' GDP sing 150 n n O3' HO3' GDP sing 151 n n C2' O2' GDP sing 152 n n C2' C1' GDP sing 153 n n C2' H2' GDP sing 154 n n O2' HO2' GDP sing 155 n n C1' N9 GDP sing 156 n n C1' H1' GDP sing 157 n n N9 C8 GDP sing 158 n y N9 C4 GDP sing 159 n y C8 N7 GDP doub 160 n y C8 H8 GDP sing 161 n n N7 C5 GDP sing 162 n y C5 C6 GDP sing 163 n n C5 C4 GDP doub 164 n y C6 O6 GDP doub 165 n n C6 N1 GDP sing 166 n n N1 C2 GDP sing 167 n n N1 HN1 GDP sing 168 n n C2 N2 GDP sing 169 n n C2 N3 GDP doub 170 n n N2 HN21 GDP sing 171 n n N2 HN22 GDP sing 172 n n N3 C4 GDP sing 173 n n # _atom_sites.entry_id 4G5G _atom_sites.fract_transf_matrix[1][1] 0.012453 _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] 0.008092 _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] 0.022177 _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 3 MG A 1 501 501 MG MG . D 4 GDP A 1 502 999 GDP GDP . E 3 MG A 1 503 1 MG MG . F 5 SO4 A 1 504 1 SO4 SO4 . G 6 HOH A 1 601 1 HOH HOH . G 6 HOH A 2 602 2 HOH HOH . G 6 HOH A 3 603 3 HOH HOH . G 6 HOH A 4 604 4 HOH HOH . G 6 HOH A 5 605 5 HOH HOH . G 6 HOH A 6 606 6 HOH HOH . G 6 HOH A 7 607 7 HOH HOH . G 6 HOH A 8 608 8 HOH HOH . G 6 HOH A 9 609 9 HOH HOH . G 6 HOH A 10 610 10 HOH HOH . G 6 HOH A 11 611 11 HOH HOH . G 6 HOH A 12 612 12 HOH HOH . G 6 HOH A 13 613 13 HOH HOH . G 6 HOH A 14 614 14 HOH HOH . G 6 HOH A 15 615 15 HOH HOH . G 6 HOH A 16 616 16 HOH HOH . G 6 HOH A 17 617 18 HOH HOH . G 6 HOH A 18 618 19 HOH HOH . G 6 HOH A 19 619 20 HOH HOH . G 6 HOH A 20 620 21 HOH HOH . G 6 HOH A 21 621 22 HOH HOH . G 6 HOH A 22 622 23 HOH HOH . G 6 HOH A 23 623 24 HOH HOH . G 6 HOH A 24 624 25 HOH HOH . G 6 HOH A 25 625 26 HOH HOH . G 6 HOH A 26 626 27 HOH HOH . G 6 HOH A 27 627 28 HOH HOH . G 6 HOH A 28 628 29 HOH HOH . G 6 HOH A 29 629 30 HOH HOH . G 6 HOH A 30 630 31 HOH HOH . G 6 HOH A 31 631 32 HOH HOH . G 6 HOH A 32 632 33 HOH HOH . G 6 HOH A 33 633 34 HOH HOH . G 6 HOH A 34 634 35 HOH HOH . G 6 HOH A 35 635 36 HOH HOH . G 6 HOH A 36 636 37 HOH HOH . G 6 HOH A 37 637 38 HOH HOH . G 6 HOH A 38 638 39 HOH HOH . G 6 HOH A 39 639 40 HOH HOH . G 6 HOH A 40 640 41 HOH HOH . G 6 HOH A 41 641 42 HOH HOH . G 6 HOH A 42 642 43 HOH HOH . G 6 HOH A 43 643 44 HOH HOH . G 6 HOH A 44 644 45 HOH HOH . G 6 HOH A 45 645 46 HOH HOH . G 6 HOH A 46 646 47 HOH HOH . G 6 HOH A 47 647 48 HOH HOH . G 6 HOH A 48 648 49 HOH HOH . G 6 HOH A 49 649 50 HOH HOH . G 6 HOH A 50 650 51 HOH HOH . G 6 HOH A 51 651 52 HOH HOH . G 6 HOH A 52 652 53 HOH HOH . G 6 HOH A 53 653 54 HOH HOH . G 6 HOH A 54 654 55 HOH HOH . G 6 HOH A 55 655 56 HOH HOH . G 6 HOH A 56 656 57 HOH HOH . G 6 HOH A 57 657 58 HOH HOH . G 6 HOH A 58 658 59 HOH HOH . G 6 HOH A 59 659 60 HOH HOH . G 6 HOH A 60 660 61 HOH HOH . G 6 HOH A 61 661 62 HOH HOH . G 6 HOH A 62 662 63 HOH HOH . G 6 HOH A 63 663 64 HOH HOH . G 6 HOH A 64 664 65 HOH HOH . G 6 HOH A 65 665 66 HOH HOH . G 6 HOH A 66 666 67 HOH HOH . G 6 HOH A 67 667 68 HOH HOH . G 6 HOH A 68 668 69 HOH HOH . G 6 HOH A 69 669 70 HOH HOH . G 6 HOH A 70 670 71 HOH HOH . G 6 HOH A 71 671 72 HOH HOH . G 6 HOH A 72 672 73 HOH HOH . G 6 HOH A 73 673 74 HOH HOH . G 6 HOH A 74 674 75 HOH HOH . G 6 HOH A 75 675 76 HOH HOH . G 6 HOH A 76 676 77 HOH HOH . G 6 HOH A 77 677 78 HOH HOH . G 6 HOH A 78 678 79 HOH HOH . G 6 HOH A 79 679 80 HOH HOH . G 6 HOH A 80 680 81 HOH HOH . G 6 HOH A 81 681 82 HOH HOH . G 6 HOH A 82 682 83 HOH HOH . G 6 HOH A 83 683 84 HOH HOH . G 6 HOH A 84 684 85 HOH HOH . G 6 HOH A 85 685 86 HOH HOH . G 6 HOH A 86 686 87 HOH HOH . G 6 HOH A 87 687 88 HOH HOH . G 6 HOH A 88 688 89 HOH HOH . G 6 HOH A 89 689 90 HOH HOH . G 6 HOH A 90 690 91 HOH HOH . G 6 HOH A 91 691 92 HOH HOH . G 6 HOH A 92 692 93 HOH HOH . G 6 HOH A 93 693 94 HOH HOH . G 6 HOH A 94 694 95 HOH HOH . G 6 HOH A 95 695 96 HOH HOH . G 6 HOH A 96 696 97 HOH HOH . G 6 HOH A 97 697 98 HOH HOH . G 6 HOH A 98 698 99 HOH HOH . G 6 HOH A 99 699 100 HOH HOH . G 6 HOH A 100 700 101 HOH HOH . G 6 HOH A 101 701 102 HOH HOH . G 6 HOH A 102 702 104 HOH HOH . G 6 HOH A 103 703 105 HOH HOH . G 6 HOH A 104 704 106 HOH HOH . G 6 HOH A 105 705 107 HOH HOH . G 6 HOH A 106 706 108 HOH HOH . G 6 HOH A 107 707 109 HOH HOH . G 6 HOH A 108 708 110 HOH HOH . G 6 HOH A 109 709 111 HOH HOH . G 6 HOH A 110 710 112 HOH HOH . G 6 HOH A 111 711 113 HOH HOH . G 6 HOH A 112 712 114 HOH HOH . G 6 HOH A 113 713 115 HOH HOH . G 6 HOH A 114 714 116 HOH HOH . G 6 HOH A 115 715 117 HOH HOH . H 6 HOH I 1 1001 17 HOH HOH . H 6 HOH I 2 1002 103 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 4 -16.057 2.813 -19.848 1 32.74 ? PB GDP 502 A 1 HETATM 2 O O1B GDP . . . D 4 -15.453 4.182 -20.237 1 26.92 ? O1B GDP 502 A 1 HETATM 3 O O2B GDP . . . D 4 -17.579 2.956 -19.784 1 30.83 ? O2B GDP 502 A 1 HETATM 4 O O3B GDP . . . D 4 -15.477 2.33 -18.53 1 32.15 ? O3B GDP 502 A 1 HETATM 5 O O3A GDP . . . D 4 -15.73 1.901 -21.078 1 31.68 ? O3A GDP 502 A 1 HETATM 6 P PA GDP . . . D 4 -16.55 1.112 -22.152 1 34.07 ? PA GDP 502 A 1 HETATM 7 O O1A GDP . . . D 4 -17.521 0.111 -21.582 1 31.7 ? O1A GDP 502 A 1 HETATM 8 O O2A GDP . . . D 4 -17.229 2.219 -22.997 1 32.73 ? O2A GDP 502 A 1 HETATM 9 O O5' GDP . . . D 4 -15.611 0.428 -23.177 1 33.56 ? O5' GDP 502 A 1 HETATM 10 C C5' GDP . . . D 4 -14.237 0.846 -23.379 1 32.62 ? C5' GDP 502 A 1 HETATM 11 C C4' GDP . . . D 4 -13.603 0.025 -24.518 1 33.94 ? C4' GDP 502 A 1 HETATM 12 O O4' GDP . . . D 4 -13.079 -1.252 -24.093 1 33.64 ? O4' GDP 502 A 1 HETATM 13 C C3' GDP . . . D 4 -14.6 -0.255 -25.703 1 35.16 ? C3' GDP 502 A 1 HETATM 14 O O3' GDP . . . D 4 -13.953 -0.161 -26.99 1 37.45 ? O3' GDP 502 A 1 HETATM 15 C C2' GDP . . . D 4 -15.063 -1.65 -25.405 1 34.86 ? C2' GDP 502 A 1 HETATM 16 O O2' GDP . . . D 4 -15.487 -2.427 -26.505 1 38.15 ? O2' GDP 502 A 1 HETATM 17 C C1' GDP . . . D 4 -13.888 -2.286 -24.648 1 35.3 ? C1' GDP 502 A 1 HETATM 18 N N9 GDP . . . D 4 -14.591 -3.237 -23.792 1 37.8 ? N9 GDP 502 A 1 HETATM 19 C C8 GDP . . . D 4 -15.162 -3.237 -22.501 1 38 ? C8 GDP 502 A 1 HETATM 20 N N7 GDP . . . D 4 -15.071 -4.388 -21.802 1 38.35 ? N7 GDP 502 A 1 HETATM 21 C C5 GDP . . . D 4 -14.257 -5.249 -22.669 1 39.63 ? C5 GDP 502 A 1 HETATM 22 C C6 GDP . . . D 4 -13.749 -6.652 -22.511 1 39.61 ? C6 GDP 502 A 1 HETATM 23 O O6 GDP . . . D 4 -14.146 -7.338 -21.58 1 37.84 ? O6 GDP 502 A 1 HETATM 24 N N1 GDP . . . D 4 -12.842 -7.098 -23.449 1 39.8 ? N1 GDP 502 A 1 HETATM 25 C C2 GDP . . . D 4 -12.404 -6.373 -24.53 1 38.62 ? C2 GDP 502 A 1 HETATM 26 N N2 GDP . . . D 4 -11.508 -6.909 -25.365 1 36.79 ? N2 GDP 502 A 1 HETATM 27 N N3 GDP . . . D 4 -12.925 -5.101 -24.748 1 38.1 ? N3 GDP 502 A 1 HETATM 28 C C4 GDP . . . D 4 -13.92 -4.554 -23.774 1 38.72 ? C4 GDP 502 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 362 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #