data_7TTD # _model_server_result.job_id mzN8-5p0JiQKrCEusrZ0PA _model_server_result.datetime_utc '2024-11-09 01:57:36' _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 7ttd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":501}' # _entry.id 7TTD # _exptl.entry_id 7TTD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 6 _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 7TTD _cell.length_a 65.795 _cell.length_b 127.211 _cell.length_c 250.461 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7TTD _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _pdbx_struct_assembly.details author_and_software_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 _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 6 _struct_asym.id H _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 K O3G GTP . C GTP 501 1_555 L MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc2 K O2B GTP . C GTP 501 1_555 L MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc3 L MG MG . C MG 502 1_555 S O HOH . C HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? metalc ? metalc4 L MG MG . C MG 502 1_555 S O HOH . C HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.896 ? metalc ? metalc5 L MG MG . C MG 502 1_555 S O HOH . C HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc6 L MG MG . C MG 502 1_555 S O HOH . C HOH 617 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? # _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 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 7TTD _atom_sites.fract_transf_matrix[1][1] 0.015199 _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] 0.007861 _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] 0.003993 _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 F 4 GTP A 1 501 501 GTP GTP . G 5 SO4 A 1 502 2 SO4 SO4 . H 6 GDP B 1 501 501 GDP GDP . I 7 JUL B 1 502 502 JUL X23 . J 5 SO4 B 1 503 3 SO4 SO4 . K 4 GTP C 1 501 501 GTP GTP . L 8 MG C 1 502 502 MG MG . M 4 GTP D 1 501 501 GTP GTP . N 7 JUL D 1 502 502 JUL X23 . O 5 SO4 D 1 503 1 SO4 SO4 . P 5 SO4 D 1 504 4 SO4 SO4 . Q 9 HOH A 1 601 33 HOH HOH . Q 9 HOH A 2 602 31 HOH HOH . Q 9 HOH A 3 603 10 HOH HOH . Q 9 HOH A 4 604 42 HOH HOH . Q 9 HOH A 5 605 63 HOH HOH . Q 9 HOH A 6 606 25 HOH HOH . Q 9 HOH A 7 607 24 HOH HOH . Q 9 HOH A 8 608 129 HOH HOH . Q 9 HOH A 9 609 65 HOH HOH . Q 9 HOH A 10 610 6 HOH HOH . Q 9 HOH A 11 611 68 HOH HOH . Q 9 HOH A 12 612 47 HOH HOH . Q 9 HOH A 13 613 37 HOH HOH . Q 9 HOH A 14 614 57 HOH HOH . Q 9 HOH A 15 615 121 HOH HOH . Q 9 HOH A 16 616 34 HOH HOH . Q 9 HOH A 17 617 43 HOH HOH . Q 9 HOH A 18 618 32 HOH HOH . Q 9 HOH A 19 619 130 HOH HOH . Q 9 HOH A 20 620 30 HOH HOH . Q 9 HOH A 21 621 39 HOH HOH . Q 9 HOH A 22 622 62 HOH HOH . Q 9 HOH A 23 623 56 HOH HOH . Q 9 HOH A 24 624 16 HOH HOH . Q 9 HOH A 25 625 29 HOH HOH . Q 9 HOH A 26 626 53 HOH HOH . Q 9 HOH A 27 627 45 HOH HOH . Q 9 HOH A 28 628 11 HOH HOH . Q 9 HOH A 29 629 59 HOH HOH . Q 9 HOH A 30 630 64 HOH HOH . Q 9 HOH A 31 631 60 HOH HOH . Q 9 HOH A 32 632 26 HOH HOH . Q 9 HOH A 33 633 41 HOH HOH . Q 9 HOH A 34 634 58 HOH HOH . Q 9 HOH A 35 635 124 HOH HOH . Q 9 HOH A 36 636 38 HOH HOH . Q 9 HOH A 37 637 44 HOH HOH . Q 9 HOH A 38 638 54 HOH HOH . Q 9 HOH A 39 639 48 HOH HOH . Q 9 HOH A 40 640 46 HOH HOH . R 9 HOH B 1 601 74 HOH HOH . R 9 HOH B 2 602 134 HOH HOH . R 9 HOH B 3 603 70 HOH HOH . R 9 HOH B 4 604 20 HOH HOH . R 9 HOH B 5 605 78 HOH HOH . R 9 HOH B 6 606 73 HOH HOH . R 9 HOH B 7 607 72 HOH HOH . R 9 HOH B 8 608 69 HOH HOH . R 9 HOH B 9 609 132 HOH HOH . R 9 HOH B 10 610 14 HOH HOH . R 9 HOH B 11 611 133 HOH HOH . R 9 HOH B 12 612 7 HOH HOH . R 9 HOH B 13 613 138 HOH HOH . R 9 HOH B 14 614 15 HOH HOH . R 9 HOH B 15 615 4 HOH HOH . R 9 HOH B 16 616 2 HOH HOH . R 9 HOH B 17 617 76 HOH HOH . R 9 HOH B 18 618 75 HOH HOH . R 9 HOH B 19 619 13 HOH HOH . R 9 HOH B 20 620 137 HOH HOH . R 9 HOH B 21 621 139 HOH HOH . R 9 HOH B 22 622 136 HOH HOH . R 9 HOH B 23 623 71 HOH HOH . R 9 HOH B 24 624 77 HOH HOH . R 9 HOH B 25 625 135 HOH HOH . R 9 HOH B 26 626 125 HOH HOH . S 9 HOH C 1 601 92 HOH HOH . S 9 HOH C 2 602 90 HOH HOH . S 9 HOH C 3 603 79 HOH HOH . S 9 HOH C 4 604 23 HOH HOH . S 9 HOH C 5 605 83 HOH HOH . S 9 HOH C 6 606 18 HOH HOH . S 9 HOH C 7 607 22 HOH HOH . S 9 HOH C 8 608 84 HOH HOH . S 9 HOH C 9 609 148 HOH HOH . S 9 HOH C 10 610 145 HOH HOH . S 9 HOH C 11 611 5 HOH HOH . S 9 HOH C 12 612 88 HOH HOH . S 9 HOH C 13 613 94 HOH HOH . S 9 HOH C 14 614 141 HOH HOH . S 9 HOH C 15 615 89 HOH HOH . S 9 HOH C 16 616 144 HOH HOH . S 9 HOH C 17 617 21 HOH HOH . S 9 HOH C 18 618 147 HOH HOH . S 9 HOH C 19 619 146 HOH HOH . S 9 HOH C 20 620 85 HOH HOH . S 9 HOH C 21 621 87 HOH HOH . S 9 HOH C 22 622 82 HOH HOH . S 9 HOH C 23 623 143 HOH HOH . S 9 HOH C 24 624 86 HOH HOH . S 9 HOH C 25 625 93 HOH HOH . S 9 HOH C 26 626 142 HOH HOH . S 9 HOH C 27 627 140 HOH HOH . S 9 HOH C 28 628 126 HOH HOH . T 9 HOH D 1 601 106 HOH HOH . T 9 HOH D 2 602 96 HOH HOH . T 9 HOH D 3 603 95 HOH HOH . T 9 HOH D 4 604 52 HOH HOH . T 9 HOH D 5 605 91 HOH HOH . T 9 HOH D 6 606 105 HOH HOH . T 9 HOH D 7 607 50 HOH HOH . T 9 HOH D 8 608 128 HOH HOH . T 9 HOH D 9 609 108 HOH HOH . T 9 HOH D 10 610 51 HOH HOH . T 9 HOH D 11 611 107 HOH HOH . T 9 HOH D 12 612 17 HOH HOH . T 9 HOH D 13 613 12 HOH HOH . T 9 HOH D 14 614 116 HOH HOH . T 9 HOH D 15 615 111 HOH HOH . T 9 HOH D 16 616 9 HOH HOH . T 9 HOH D 17 617 8 HOH HOH . T 9 HOH D 18 618 104 HOH HOH . T 9 HOH D 19 619 19 HOH HOH . T 9 HOH D 20 620 109 HOH HOH . T 9 HOH D 21 621 1 HOH HOH . T 9 HOH D 22 622 118 HOH HOH . T 9 HOH D 23 623 100 HOH HOH . T 9 HOH D 24 624 127 HOH HOH . T 9 HOH D 25 625 112 HOH HOH . T 9 HOH D 26 626 117 HOH HOH . T 9 HOH D 27 627 149 HOH HOH . T 9 HOH D 28 628 99 HOH HOH . T 9 HOH D 29 629 150 HOH HOH . T 9 HOH D 30 630 97 HOH HOH . T 9 HOH D 31 631 102 HOH HOH . T 9 HOH D 32 632 103 HOH HOH . T 9 HOH D 33 633 98 HOH HOH . T 9 HOH D 34 634 119 HOH HOH . T 9 HOH D 35 635 113 HOH HOH . T 9 HOH D 36 636 101 HOH HOH . U 9 HOH E 1 201 55 HOH HOH . U 9 HOH E 2 202 120 HOH HOH . U 9 HOH E 3 203 131 HOH HOH . U 9 HOH E 4 204 110 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 . . . H 6 4.099 21.405 33.563 1 39.02 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . H 6 5.573 22.014 33.55 1 37.9 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . H 6 3.02 22.263 34.39 1 35.18 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . H 6 4.115 20.027 34.171 1 44.52 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . H 6 3.641 21.315 32.043 1 42.55 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . H 6 2.291 20.747 31.413 1 45.5 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . H 6 1.363 21.926 30.833 1 66.36 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . H 6 1.555 20.019 32.472 1 52.9 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . H 6 2.89 19.789 30.259 1 42.28 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . H 6 2.699 20.027 28.863 1 38.65 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . H 6 2.124 18.727 28.315 1 44.12 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . H 6 0.904 18.443 29.033 1 33.92 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . H 6 1.768 18.852 26.826 1 41.75 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . H 6 1.94 17.564 26.249 1 43.15 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . H 6 0.278 19.254 26.905 1 43.9 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . H 6 -0.46 18.861 25.758 1 48.18 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . H 6 -0.182 18.374 28.087 1 38.91 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . H 6 -1.327 18.892 28.825 1 41.98 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . H 6 -1.376 20.056 29.56 1 44.16 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . H 6 -2.554 20.155 30.105 1 40.64 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . H 6 -3.305 19.073 29.765 1 42.63 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . H 6 -4.612 18.65 30.057 1 44.91 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . H 6 -5.334 19.32 30.775 1 43.6 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . H 6 -5.045 17.478 29.523 1 46.19 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . H 6 -4.221 16.734 28.733 1 41.16 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . H 6 -4.661 15.552 28.215 1 40.57 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . H 6 -3.004 17.107 28.449 1 39.11 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . H 6 -2.523 18.256 28.943 1 37.4 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 47 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 338 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #