data_2FA9 # _model_server_result.job_id aDPCL0_eNqkFbr6hwHCThg _model_server_result.datetime_utc '2024-11-29 16:07:39' _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 2fa9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":1001}' # _entry.id 2FA9 # _exptl.entry_id 2FA9 _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 72.75 _cell.angle_gamma 90 _cell.entry_id 2FA9 _cell.length_a 53.215 _cell.length_b 61.62 _cell.length_c 71.165 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2FA9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,I 1 1 B,F,G,H,J 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 ? 4 E N N ? 4 H 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 OG1 THR 30 A THR 39 1_555 C MG MG . A MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? metalc ? metalc2 E O1B GDP . A GDP 1002 1_555 C MG MG . A MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.442 ? metalc ? metalc3 C MG MG . A MG 1004 1_555 I O HOH . A HOH 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc4 C MG MG . A MG 1004 1_555 I O HOH . A HOH 2044 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.393 ? metalc ? metalc5 C MG MG . A MG 1004 1_555 I O HOH . A HOH 2063 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc6 C MG MG . A MG 1004 1_555 I O HOH . A HOH 2064 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc7 B OG1 THR 30 B THR 39 1_555 F MG MG . B MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.85 ? metalc ? metalc8 H O3B GDP . B GDP 1001 1_555 F MG MG . B MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.979 ? metalc ? metalc9 F MG MG . B MG 1003 1_555 J O HOH . B HOH 2058 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.511 ? metalc ? metalc10 F MG MG . B MG 1003 1_555 J O HOH . B HOH 2059 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc11 F MG MG . B MG 1003 1_555 J O HOH . B HOH 2060 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? # _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 2FA9 _atom_sites.fract_transf_matrix[1][1] 0.018792 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] -0.005835 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016228 _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] 0.014714 _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 MG A 1 1004 1004 MG MG . D 3 SO4 A 1 2002 2002 SO4 SO4 . E 4 GDP A 1 1002 1002 GDP GDP . F 2 MG B 1 1003 1003 MG MG . G 3 SO4 B 1 2001 2001 SO4 SO4 . H 4 GDP B 1 1001 1001 GDP GDP . I 5 HOH A 1 2003 1 HOH HOH . I 5 HOH A 2 2004 4 HOH HOH . I 5 HOH A 3 2005 5 HOH HOH . I 5 HOH A 4 2006 6 HOH HOH . I 5 HOH A 5 2007 7 HOH HOH . I 5 HOH A 6 2008 8 HOH HOH . I 5 HOH A 7 2009 9 HOH HOH . I 5 HOH A 8 2010 10 HOH HOH . I 5 HOH A 9 2011 13 HOH HOH . I 5 HOH A 10 2012 14 HOH HOH . I 5 HOH A 11 2013 16 HOH HOH . I 5 HOH A 12 2014 18 HOH HOH . I 5 HOH A 13 2015 19 HOH HOH . I 5 HOH A 14 2016 21 HOH HOH . I 5 HOH A 15 2017 22 HOH HOH . I 5 HOH A 16 2018 27 HOH HOH . I 5 HOH A 17 2019 29 HOH HOH . I 5 HOH A 18 2020 30 HOH HOH . I 5 HOH A 19 2021 33 HOH HOH . I 5 HOH A 20 2022 35 HOH HOH . I 5 HOH A 21 2023 36 HOH HOH . I 5 HOH A 22 2024 37 HOH HOH . I 5 HOH A 23 2025 38 HOH HOH . I 5 HOH A 24 2026 40 HOH HOH . I 5 HOH A 25 2027 43 HOH HOH . I 5 HOH A 26 2028 44 HOH HOH . I 5 HOH A 27 2029 45 HOH HOH . I 5 HOH A 28 2030 47 HOH HOH . I 5 HOH A 29 2031 49 HOH HOH . I 5 HOH A 30 2032 51 HOH HOH . I 5 HOH A 31 2033 55 HOH HOH . I 5 HOH A 32 2034 58 HOH HOH . I 5 HOH A 33 2035 59 HOH HOH . I 5 HOH A 34 2036 65 HOH HOH . I 5 HOH A 35 2037 68 HOH HOH . I 5 HOH A 36 2038 69 HOH HOH . I 5 HOH A 37 2039 70 HOH HOH . I 5 HOH A 38 2040 73 HOH HOH . I 5 HOH A 39 2041 74 HOH HOH . I 5 HOH A 40 2042 75 HOH HOH . I 5 HOH A 41 2043 76 HOH HOH . I 5 HOH A 42 2044 77 HOH HOH . I 5 HOH A 43 2045 80 HOH HOH . I 5 HOH A 44 2046 81 HOH HOH . I 5 HOH A 45 2047 85 HOH HOH . I 5 HOH A 46 2048 87 HOH HOH . I 5 HOH A 47 2049 88 HOH HOH . I 5 HOH A 48 2050 91 HOH HOH . I 5 HOH A 49 2051 92 HOH HOH . I 5 HOH A 50 2052 93 HOH HOH . I 5 HOH A 51 2053 95 HOH HOH . I 5 HOH A 52 2054 96 HOH HOH . I 5 HOH A 53 2055 98 HOH HOH . I 5 HOH A 54 2056 100 HOH HOH . I 5 HOH A 55 2057 101 HOH HOH . I 5 HOH A 56 2058 102 HOH HOH . I 5 HOH A 57 2059 106 HOH HOH . I 5 HOH A 58 2060 110 HOH HOH . I 5 HOH A 59 2061 113 HOH HOH . I 5 HOH A 60 2062 114 HOH HOH . I 5 HOH A 61 2063 118 HOH HOH . I 5 HOH A 62 2064 119 HOH HOH . J 5 HOH B 1 2002 2 HOH HOH . J 5 HOH B 2 2003 3 HOH HOH . J 5 HOH B 3 2004 11 HOH HOH . J 5 HOH B 4 2005 12 HOH HOH . J 5 HOH B 5 2006 15 HOH HOH . J 5 HOH B 6 2007 17 HOH HOH . J 5 HOH B 7 2008 20 HOH HOH . J 5 HOH B 8 2009 23 HOH HOH . J 5 HOH B 9 2010 24 HOH HOH . J 5 HOH B 10 2011 25 HOH HOH . J 5 HOH B 11 2012 26 HOH HOH . J 5 HOH B 12 2013 28 HOH HOH . J 5 HOH B 13 2014 31 HOH HOH . J 5 HOH B 14 2015 32 HOH HOH . J 5 HOH B 15 2016 34 HOH HOH . J 5 HOH B 16 2017 39 HOH HOH . J 5 HOH B 17 2018 41 HOH HOH . J 5 HOH B 18 2019 42 HOH HOH . J 5 HOH B 19 2020 46 HOH HOH . J 5 HOH B 20 2021 48 HOH HOH . J 5 HOH B 21 2022 50 HOH HOH . J 5 HOH B 22 2023 52 HOH HOH . J 5 HOH B 23 2024 53 HOH HOH . J 5 HOH B 24 2025 54 HOH HOH . J 5 HOH B 25 2026 56 HOH HOH . J 5 HOH B 26 2027 57 HOH HOH . J 5 HOH B 27 2028 60 HOH HOH . J 5 HOH B 28 2029 61 HOH HOH . J 5 HOH B 29 2030 62 HOH HOH . J 5 HOH B 30 2031 63 HOH HOH . J 5 HOH B 31 2032 64 HOH HOH . J 5 HOH B 32 2033 66 HOH HOH . J 5 HOH B 33 2034 67 HOH HOH . J 5 HOH B 34 2035 71 HOH HOH . J 5 HOH B 35 2036 72 HOH HOH . J 5 HOH B 36 2037 78 HOH HOH . J 5 HOH B 37 2038 79 HOH HOH . J 5 HOH B 38 2039 82 HOH HOH . J 5 HOH B 39 2040 83 HOH HOH . J 5 HOH B 40 2041 84 HOH HOH . J 5 HOH B 41 2042 86 HOH HOH . J 5 HOH B 42 2043 89 HOH HOH . J 5 HOH B 43 2044 90 HOH HOH . J 5 HOH B 44 2045 94 HOH HOH . J 5 HOH B 45 2046 97 HOH HOH . J 5 HOH B 46 2047 99 HOH HOH . J 5 HOH B 47 2048 103 HOH HOH . J 5 HOH B 48 2049 104 HOH HOH . J 5 HOH B 49 2050 105 HOH HOH . J 5 HOH B 50 2051 107 HOH HOH . J 5 HOH B 51 2052 108 HOH HOH . J 5 HOH B 52 2053 109 HOH HOH . J 5 HOH B 53 2054 111 HOH HOH . J 5 HOH B 54 2055 112 HOH HOH . J 5 HOH B 55 2056 115 HOH HOH . J 5 HOH B 56 2057 116 HOH HOH . J 5 HOH B 57 2058 117 HOH HOH . J 5 HOH B 58 2059 120 HOH HOH . J 5 HOH B 59 2060 121 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 4 20.948 11.995 19.331 1 20.53 ? PB GDP 1001 B 1 HETATM 2 O O1B GDP . . . H 4 21.366 12.225 20.711 1 37.01 ? O1B GDP 1001 B 1 HETATM 3 O O2B GDP . . . H 4 19.378 11.749 19.323 1 34.08 ? O2B GDP 1001 B 1 HETATM 4 O O3B GDP . . . H 4 21.749 10.779 18.742 1 30.62 ? O3B GDP 1001 B 1 HETATM 5 O O3A GDP . . . H 4 21.235 13.294 18.499 1 31.58 ? O3A GDP 1001 B 1 HETATM 6 P PA GDP . . . H 4 22.694 13.313 17.84 1 28.53 ? PA GDP 1001 B 1 HETATM 7 O O1A GDP . . . H 4 23.819 13.161 18.676 1 24.2 ? O1A GDP 1001 B 1 HETATM 8 O O2A GDP . . . H 4 22.755 12.132 16.762 1 30.19 ? O2A GDP 1001 B 1 HETATM 9 O O5' GDP . . . H 4 22.661 14.649 16.997 1 32.92 ? O5' GDP 1001 B 1 HETATM 10 C C5' GDP . . . H 4 23.877 14.803 16.331 1 38.61 ? C5' GDP 1001 B 1 HETATM 11 C C4' GDP . . . H 4 23.749 16.1 15.59 1 34.32 ? C4' GDP 1001 B 1 HETATM 12 O O4' GDP . . . H 4 23.516 17.14 16.56 1 31.15 ? O4' GDP 1001 B 1 HETATM 13 C C3' GDP . . . H 4 25.031 16.355 14.83 1 34.94 ? C3' GDP 1001 B 1 HETATM 14 O O3' GDP . . . H 4 24.778 16.41 13.423 1 34.84 ? O3' GDP 1001 B 1 HETATM 15 C C2' GDP . . . H 4 25.575 17.672 15.395 1 38.22 ? C2' GDP 1001 B 1 HETATM 16 O O2' GDP . . . H 4 25.717 18.662 14.359 1 47.73 ? O2' GDP 1001 B 1 HETATM 17 C C1' GDP . . . H 4 24.552 18.121 16.461 1 33 ? C1' GDP 1001 B 1 HETATM 18 N N9 GDP . . . H 4 25.186 18.344 17.768 1 26.13 ? N9 GDP 1001 B 1 HETATM 19 C C8 GDP . . . H 4 25.371 17.446 18.802 1 23.84 ? C8 GDP 1001 B 1 HETATM 20 N N7 GDP . . . H 4 25.972 18.034 19.796 1 16.14 ? N7 GDP 1001 B 1 HETATM 21 C C5 GDP . . . H 4 26.202 19.327 19.461 1 22.17 ? C5 GDP 1001 B 1 HETATM 22 C C6 GDP . . . H 4 26.807 20.447 20.108 1 20.45 ? C6 GDP 1001 B 1 HETATM 23 O O6 GDP . . . H 4 27.26 20.339 21.221 1 20.95 ? O6 GDP 1001 B 1 HETATM 24 N N1 GDP . . . H 4 26.865 21.646 19.439 1 22.56 ? N1 GDP 1001 B 1 HETATM 25 C C2 GDP . . . H 4 26.346 21.769 18.16 1 26.17 ? C2 GDP 1001 B 1 HETATM 26 N N2 GDP . . . H 4 26.41 22.975 17.507 1 25.09 ? N2 GDP 1001 B 1 HETATM 27 N N3 GDP . . . H 4 25.786 20.738 17.554 1 23.52 ? N3 GDP 1001 B 1 HETATM 28 C C4 GDP . . . H 4 25.696 19.527 18.158 1 23.47 ? C4 GDP 1001 B 1 # _model_server_stats.io_time_ms 50 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #