data_6STF # _model_server_result.job_id '_fr7AVztj0efT2YJFHefvw' _model_server_result.datetime_utc '2024-11-04 20:22:32' _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 6stf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":901}' # _entry.id 6STF # _exptl.entry_id 6STF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 5 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 100.48 _cell.angle_gamma 90 _cell.entry_id 6STF _cell.length_a 117.55 _cell.length_b 75.18 _cell.length_c 107.7 _cell.Z_PDB 20 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6STF _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 ? monomeric 1 author_defined_assembly 4 ? monomeric 1 author_defined_assembly 5 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,F,G,P 1 1 B,H,I,Q 2 1 C,J,K,R 3 1 D,L,M,S 4 1 E,N,O,T 5 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 ? 2 F N N ? 2 H N N ? 2 J N N ? 2 L N N ? 2 N 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 covale ? covale1 A C ALA 106 A ALA 110 1_555 A N SEP 107 A SEP 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale2 A C SEP 107 A SEP 111 1_555 A N ALA 108 A ALA 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale3 B C ALA 106 B ALA 110 1_555 B N SEP 107 B SEP 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? covale ? covale4 B C SEP 107 B SEP 111 1_555 B N ALA 108 B ALA 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale5 C C ALA 106 C ALA 110 1_555 C N SEP 107 C SEP 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? covale ? covale6 C C SEP 107 C SEP 111 1_555 C N ALA 108 C ALA 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale7 D C ALA 106 D ALA 110 1_555 D N SEP 107 D SEP 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale8 D C SEP 107 D SEP 111 1_555 D N ALA 108 D ALA 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale9 E C ALA 106 E ALA 110 1_555 E N SEP 107 E SEP 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? covale ? covale10 E C SEP 107 E SEP 111 1_555 E N ALA 108 E ALA 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? metalc ? metalc1 A OG1 THR 18 A THR 22 1_555 G MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? metalc ? metalc2 F O3B GDP . A GDP 901 1_555 G MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? metalc ? metalc3 G MG MG . A MG 902 1_555 P O HOH . A HOH 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.927 ? metalc ? metalc4 G MG MG . A MG 902 1_555 P O HOH . A HOH 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.965 ? metalc ? metalc5 G MG MG . A MG 902 1_555 P O HOH . A HOH 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc6 G MG MG . A MG 902 1_555 P O HOH . A HOH 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? metalc ? metalc7 B OG1 THR 18 B THR 22 1_555 I MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? metalc ? metalc8 H O3B GDP . B GDP 901 1_555 I MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? metalc ? metalc9 I MG MG . B MG 902 1_555 Q O HOH . B HOH 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.891 ? metalc ? metalc10 I MG MG . B MG 902 1_555 Q O HOH . B HOH 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? metalc ? metalc11 I MG MG . B MG 902 1_555 Q O HOH . B HOH 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.887 ? metalc ? metalc12 I MG MG . B MG 902 1_555 Q O HOH . B HOH 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc13 C OG1 THR 18 C THR 22 1_555 K MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc14 J O3B GDP . C GDP 901 1_555 K MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? metalc ? metalc15 K MG MG . C MG 902 1_555 R O HOH . C HOH 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc16 K MG MG . C MG 902 1_555 R O HOH . C HOH 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc17 K MG MG . C MG 902 1_555 R O HOH . C HOH 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc18 K MG MG . C MG 902 1_555 R O HOH . C HOH 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.912 ? metalc ? metalc19 D OG1 THR 18 D THR 22 1_555 M MG MG . D MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc20 L O3B GDP . D GDP 901 1_555 M MG MG . D MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc21 M MG MG . D MG 902 1_555 S O HOH . D HOH 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.895 ? metalc ? metalc22 M MG MG . D MG 902 1_555 S O HOH . D HOH 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.921 ? metalc ? metalc23 M MG MG . D MG 902 1_555 S O HOH . D HOH 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.946 ? metalc ? metalc24 M MG MG . D MG 902 1_555 S O HOH . D HOH 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.932 ? metalc ? metalc25 E OG1 THR 18 E THR 22 1_555 O MG MG . E MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc26 N O2B GDP . E GDP 901 1_555 O MG MG . E MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc27 O MG MG . E MG 902 1_555 T O HOH . E HOH 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? metalc ? metalc28 O MG MG . E MG 902 1_555 T O HOH . E HOH 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? metalc ? metalc29 O MG MG . E MG 902 1_555 T O HOH . E HOH 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc30 O MG MG . E MG 902 1_555 T O HOH . E HOH 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? # _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 6STF _atom_sites.fract_transf_matrix[1][1] 0.008507 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001573 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013301 _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] 0.009442 _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 2 GDP A 1 901 901 GDP GDP . G 3 MG A 1 902 902 MG MG . H 2 GDP B 1 901 901 GDP GDP . I 3 MG B 1 902 902 MG MG . J 2 GDP C 1 901 901 GDP GDP . K 3 MG C 1 902 902 MG MG . L 2 GDP D 1 901 901 GDP GDP . M 3 MG D 1 902 902 MG MG . N 2 GDP E 1 901 901 GDP GDP . O 3 MG E 1 902 902 MG MG . P 4 HOH A 1 1001 19 HOH HOH . P 4 HOH A 2 1002 8 HOH HOH . P 4 HOH A 3 1003 26 HOH HOH . P 4 HOH A 4 1004 1 HOH HOH . P 4 HOH A 5 1005 42 HOH HOH . P 4 HOH A 6 1006 41 HOH HOH . P 4 HOH A 7 1007 28 HOH HOH . P 4 HOH A 8 1008 43 HOH HOH . Q 4 HOH B 1 1001 16 HOH HOH . Q 4 HOH B 2 1002 46 HOH HOH . Q 4 HOH B 3 1003 24 HOH HOH . Q 4 HOH B 4 1004 5 HOH HOH . Q 4 HOH B 5 1005 22 HOH HOH . Q 4 HOH B 6 1006 45 HOH HOH . Q 4 HOH B 7 1007 4 HOH HOH . Q 4 HOH B 8 1008 44 HOH HOH . Q 4 HOH B 9 1009 6 HOH HOH . R 4 HOH C 1 1001 40 HOH HOH . R 4 HOH C 2 1002 48 HOH HOH . R 4 HOH C 3 1003 25 HOH HOH . R 4 HOH C 4 1004 49 HOH HOH . R 4 HOH C 5 1005 13 HOH HOH . R 4 HOH C 6 1006 33 HOH HOH . R 4 HOH C 7 1007 47 HOH HOH . R 4 HOH C 8 1008 27 HOH HOH . R 4 HOH C 9 1009 21 HOH HOH . R 4 HOH C 10 1010 15 HOH HOH . R 4 HOH C 11 1011 12 HOH HOH . S 4 HOH D 1 1001 53 HOH HOH . S 4 HOH D 2 1002 9 HOH HOH . S 4 HOH D 3 1003 50 HOH HOH . S 4 HOH D 4 1004 52 HOH HOH . S 4 HOH D 5 1005 2 HOH HOH . S 4 HOH D 6 1006 51 HOH HOH . S 4 HOH D 7 1007 36 HOH HOH . S 4 HOH D 8 1008 39 HOH HOH . T 4 HOH E 1 1001 35 HOH HOH . T 4 HOH E 2 1002 55 HOH HOH . T 4 HOH E 3 1003 31 HOH HOH . T 4 HOH E 4 1004 34 HOH HOH . T 4 HOH E 5 1005 7 HOH HOH . T 4 HOH E 6 1006 54 HOH HOH . T 4 HOH E 7 1007 38 HOH HOH . T 4 HOH E 8 1008 56 HOH HOH . T 4 HOH E 9 1009 29 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 2 -9.021 36.014 30.171 1 39.29 ? PB GDP 901 B 1 HETATM 2 O O1B GDP . . . H 2 -8.091 35.039 29.491 1 39.92 ? O1B GDP 901 B 1 HETATM 3 O O2B GDP . . . H 2 -10.439 35.511 30.31 1 38.79 ? O2B GDP 901 B 1 HETATM 4 O O3B GDP . . . H 2 -8.46 36.641 31.427 1 39.18 ? O3B GDP 901 B 1 HETATM 5 O O3A GDP . . . H 2 -9.159 37.221 29.11 1 38.76 ? O3A GDP 901 B 1 HETATM 6 P PA GDP . . . H 2 -8.249 38.548 29.188 1 38.93 ? PA GDP 901 B 1 HETATM 7 O O1A GDP . . . H 2 -6.798 38.16 29.031 1 39.98 ? O1A GDP 901 B 1 HETATM 8 O O2A GDP . . . H 2 -8.69 39.363 30.38 1 38.77 ? O2A GDP 901 B 1 HETATM 9 O O5' GDP . . . H 2 -8.696 39.34 27.862 1 38.3 ? O5' GDP 901 B 1 HETATM 10 C C5' GDP . . . H 2 -8.648 38.697 26.59 1 38.09 ? C5' GDP 901 B 1 HETATM 11 C C4' GDP . . . H 2 -8.488 39.723 25.476 1 37.88 ? C4' GDP 901 B 1 HETATM 12 O O4' GDP . . . H 2 -9.748 40.364 25.245 1 36.74 ? O4' GDP 901 B 1 HETATM 13 C C3' GDP . . . H 2 -7.482 40.814 25.824 1 37.81 ? C3' GDP 901 B 1 HETATM 14 O O3' GDP . . . H 2 -6.658 41.13 24.705 1 38.73 ? O3' GDP 901 B 1 HETATM 15 C C2' GDP . . . H 2 -8.327 42.013 26.18 1 37.12 ? C2' GDP 901 B 1 HETATM 16 O O2' GDP . . . H 2 -7.706 43.243 25.796 1 37.38 ? O2' GDP 901 B 1 HETATM 17 C C1' GDP . . . H 2 -9.631 41.778 25.433 1 36.84 ? C1' GDP 901 B 1 HETATM 18 N N9 GDP . . . H 2 -10.776 42.324 26.204 1 36.28 ? N9 GDP 901 B 1 HETATM 19 C C8 GDP . . . H 2 -11.117 41.996 27.465 1 35.87 ? C8 GDP 901 B 1 HETATM 20 N N7 GDP . . . H 2 -12.212 42.691 27.866 1 35.46 ? N7 GDP 901 B 1 HETATM 21 C C5 GDP . . . H 2 -12.585 43.48 26.845 1 35.74 ? C5 GDP 901 B 1 HETATM 22 C C6 GDP . . . H 2 -13.661 44.466 26.59 1 35.96 ? C6 GDP 901 B 1 HETATM 23 O O6 GDP . . . H 2 -14.51 44.731 27.466 1 36.22 ? O6 GDP 901 B 1 HETATM 24 N N1 GDP . . . H 2 -13.699 45.069 25.393 1 36.04 ? N1 GDP 901 B 1 HETATM 25 C C2 GDP . . . H 2 -12.799 44.806 24.425 1 36.28 ? C2 GDP 901 B 1 HETATM 26 N N2 GDP . . . H 2 -12.902 45.455 23.24 1 36.8 ? N2 GDP 901 B 1 HETATM 27 N N3 GDP . . . H 2 -11.788 43.912 24.588 1 36.23 ? N3 GDP 901 B 1 HETATM 28 C C4 GDP . . . H 2 -11.634 43.235 25.751 1 36.07 ? C4 GDP 901 B 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 46 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #