data_2DCU # _model_server_result.job_id JWlxP8u_7IsGaN73CpQbPQ _model_server_result.datetime_utc '2024-10-13 09:13:23' _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 2dcu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":2001}' # _entry.id 2DCU # _exptl.entry_id 2DCU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 5 _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 2DCU _cell.length_a 69.198 _cell.length_b 76.561 _cell.length_c 97.857 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2DCU _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 5 _struct_asym.id E _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 disulf ? disulf1 B SG CYS 110 B CYS 110 1_555 B SG CYS 131 B CYS 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.9 ? metalc ? metalc1 A OG1 THR 25 A THR 25 1_555 C MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.571 ? metalc ? metalc2 A SG CYS 61 A CYS 61 1_555 D ZN ZN . A ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc3 A SG CYS 64 A CYS 64 1_555 D ZN ZN . A ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc4 A SG CYS 73 A CYS 73 1_555 D ZN ZN . A ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc5 A SG CYS 76 A CYS 76 1_555 D ZN ZN . A ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? metalc ? metalc6 C MG MG . A MG 1001 1_555 E O3B GDP . A GDP 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.703 ? metalc ? metalc7 C MG MG . A MG 1001 1_555 G O HOH . A HOH 3057 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? metalc ? metalc8 B SG CYS 107 B CYS 107 1_555 F ZN ZN . B ZN 3002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc9 B SG CYS 110 B CYS 110 1_555 F ZN ZN . B ZN 3002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? metalc ? metalc10 B SG CYS 128 B CYS 128 1_555 F ZN ZN . B ZN 3002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc11 B SG CYS 131 B CYS 131 1_555 F ZN ZN . B ZN 3002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? # _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 2DCU _atom_sites.fract_transf_matrix[1][1] 0.014451 _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] 0.013061 _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] 0.010219 _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 1001 1 MG MG . D 4 ZN A 1 3001 1 ZN ZN . E 5 GDP A 1 2001 1 GDP MG . F 4 ZN B 1 3002 1 ZN ZN . G 6 HOH A 1 3002 1 HOH HOH . G 6 HOH A 2 3003 2 HOH HOH . G 6 HOH A 3 3004 3 HOH HOH . G 6 HOH A 4 3005 5 HOH HOH . G 6 HOH A 5 3006 7 HOH HOH . G 6 HOH A 6 3007 8 HOH HOH . G 6 HOH A 7 3008 9 HOH HOH . G 6 HOH A 8 3009 10 HOH HOH . G 6 HOH A 9 3010 11 HOH HOH . G 6 HOH A 10 3011 12 HOH HOH . G 6 HOH A 11 3012 13 HOH HOH . G 6 HOH A 12 3013 14 HOH HOH . G 6 HOH A 13 3014 15 HOH HOH . G 6 HOH A 14 3015 16 HOH HOH . G 6 HOH A 15 3016 17 HOH HOH . G 6 HOH A 16 3017 18 HOH HOH . G 6 HOH A 17 3018 19 HOH HOH . G 6 HOH A 18 3019 21 HOH HOH . G 6 HOH A 19 3020 23 HOH HOH . G 6 HOH A 20 3021 26 HOH HOH . G 6 HOH A 21 3022 28 HOH HOH . G 6 HOH A 22 3023 30 HOH HOH . G 6 HOH A 23 3024 31 HOH HOH . G 6 HOH A 24 3025 32 HOH HOH . G 6 HOH A 25 3026 33 HOH HOH . G 6 HOH A 26 3027 35 HOH HOH . G 6 HOH A 27 3028 36 HOH HOH . G 6 HOH A 28 3029 37 HOH HOH . G 6 HOH A 29 3030 40 HOH HOH . G 6 HOH A 30 3031 41 HOH HOH . G 6 HOH A 31 3032 42 HOH HOH . G 6 HOH A 32 3033 43 HOH HOH . G 6 HOH A 33 3034 44 HOH HOH . G 6 HOH A 34 3035 45 HOH HOH . G 6 HOH A 35 3036 46 HOH HOH . G 6 HOH A 36 3037 47 HOH HOH . G 6 HOH A 37 3038 50 HOH HOH . G 6 HOH A 38 3039 51 HOH HOH . G 6 HOH A 39 3040 52 HOH HOH . G 6 HOH A 40 3041 53 HOH HOH . G 6 HOH A 41 3042 54 HOH HOH . G 6 HOH A 42 3043 55 HOH HOH . G 6 HOH A 43 3044 56 HOH HOH . G 6 HOH A 44 3045 57 HOH HOH . G 6 HOH A 45 3046 58 HOH HOH . G 6 HOH A 46 3047 59 HOH HOH . G 6 HOH A 47 3048 60 HOH HOH . G 6 HOH A 48 3049 62 HOH HOH . G 6 HOH A 49 3050 63 HOH HOH . G 6 HOH A 50 3051 64 HOH HOH . G 6 HOH A 51 3052 65 HOH HOH . G 6 HOH A 52 3053 68 HOH HOH . G 6 HOH A 53 3054 69 HOH HOH . G 6 HOH A 54 3055 71 HOH HOH . G 6 HOH A 55 3056 72 HOH HOH . G 6 HOH A 56 3057 73 HOH HOH . G 6 HOH A 57 3058 75 HOH HOH . G 6 HOH A 58 3059 76 HOH HOH . G 6 HOH A 59 3060 78 HOH HOH . G 6 HOH A 60 3061 79 HOH HOH . G 6 HOH A 61 3062 80 HOH HOH . G 6 HOH A 62 3063 81 HOH HOH . G 6 HOH A 63 3064 82 HOH HOH . G 6 HOH A 64 3065 83 HOH HOH . G 6 HOH A 65 3066 85 HOH HOH . G 6 HOH A 66 3067 86 HOH HOH . G 6 HOH A 67 3068 88 HOH HOH . G 6 HOH A 68 3069 89 HOH HOH . G 6 HOH A 69 3070 91 HOH HOH . G 6 HOH A 70 3071 92 HOH HOH . G 6 HOH A 71 3072 93 HOH HOH . G 6 HOH A 72 3073 94 HOH HOH . G 6 HOH A 73 3074 95 HOH HOH . G 6 HOH A 74 3075 97 HOH HOH . G 6 HOH A 75 3076 98 HOH HOH . G 6 HOH A 76 3077 99 HOH HOH . G 6 HOH A 77 3078 100 HOH HOH . G 6 HOH A 78 3079 101 HOH HOH . G 6 HOH A 79 3080 102 HOH HOH . G 6 HOH A 80 3081 103 HOH HOH . G 6 HOH A 81 3082 104 HOH HOH . G 6 HOH A 82 3083 105 HOH HOH . G 6 HOH A 83 3084 106 HOH HOH . G 6 HOH A 84 3085 107 HOH HOH . G 6 HOH A 85 3086 108 HOH HOH . H 6 HOH B 1 3003 4 HOH HOH . H 6 HOH B 2 3004 6 HOH HOH . H 6 HOH B 3 3005 20 HOH HOH . H 6 HOH B 4 3006 22 HOH HOH . H 6 HOH B 5 3007 24 HOH HOH . H 6 HOH B 6 3008 25 HOH HOH . H 6 HOH B 7 3009 27 HOH HOH . H 6 HOH B 8 3010 29 HOH HOH . H 6 HOH B 9 3011 34 HOH HOH . H 6 HOH B 10 3012 38 HOH HOH . H 6 HOH B 11 3013 39 HOH HOH . H 6 HOH B 12 3014 48 HOH HOH . H 6 HOH B 13 3015 49 HOH HOH . H 6 HOH B 14 3016 61 HOH HOH . H 6 HOH B 15 3017 66 HOH HOH . H 6 HOH B 16 3018 67 HOH HOH . H 6 HOH B 17 3019 70 HOH HOH . H 6 HOH B 18 3020 74 HOH HOH . H 6 HOH B 19 3021 77 HOH HOH . H 6 HOH B 20 3022 84 HOH HOH . H 6 HOH B 21 3023 87 HOH HOH . H 6 HOH B 22 3024 90 HOH HOH . H 6 HOH B 23 3025 96 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 . . . E 5 38.435 47.901 -7.756 1 26.16 ? PB GDP 2001 A 1 HETATM 2 O O1B GDP . . . E 5 39.69 47.699 -8.404 1 28.52 ? O1B GDP 2001 A 1 HETATM 3 O O2B GDP . . . E 5 37.399 46.677 -8.19 1 23.41 ? O2B GDP 2001 A 1 HETATM 4 O O3B GDP . . . E 5 38.83 47.975 -6.259 1 21.74 ? O3B GDP 2001 A 1 HETATM 5 O O3A GDP . . . E 5 38.017 49.162 -8.379 1 26.95 ? O3A GDP 2001 A 1 HETATM 6 P PA GDP . . . E 5 38.182 50.598 -7.873 1 27.22 ? PA GDP 2001 A 1 HETATM 7 O O1A GDP . . . E 5 37.557 51.274 -6.708 1 26.46 ? O1A GDP 2001 A 1 HETATM 8 O O2A GDP . . . E 5 39.754 50.857 -7.805 1 30.7 ? O2A GDP 2001 A 1 HETATM 9 O O5' GDP . . . E 5 37.68 51.113 -9.339 1 28.89 ? O5' GDP 2001 A 1 HETATM 10 C C5' GDP . . . E 5 38.385 52.28 -9.288 1 29.56 ? C5' GDP 2001 A 1 HETATM 11 C C4' GDP . . . E 5 38.472 53.028 -10.515 1 29.24 ? C4' GDP 2001 A 1 HETATM 12 O O4' GDP . . . E 5 37.191 53.078 -11.216 1 30.21 ? O4' GDP 2001 A 1 HETATM 13 C C3' GDP . . . E 5 38.78 54.283 -9.88 1 30.24 ? C3' GDP 2001 A 1 HETATM 14 O O3' GDP . . . E 5 39.608 55.18 -10.623 1 29.08 ? O3' GDP 2001 A 1 HETATM 15 C C2' GDP . . . E 5 37.359 54.768 -9.564 1 30.27 ? C2' GDP 2001 A 1 HETATM 16 O O2' GDP . . . E 5 37.249 56.075 -9.073 1 30.12 ? O2' GDP 2001 A 1 HETATM 17 C C1' GDP . . . E 5 36.677 54.412 -10.923 1 30.93 ? C1' GDP 2001 A 1 HETATM 18 N N9 GDP . . . E 5 35.231 54.351 -10.779 1 33.4 ? N9 GDP 2001 A 1 HETATM 19 C C8 GDP . . . E 5 34.482 53.601 -9.882 1 33.95 ? C8 GDP 2001 A 1 HETATM 20 N N7 GDP . . . E 5 33.194 53.815 -10.053 1 34.42 ? N7 GDP 2001 A 1 HETATM 21 C C5 GDP . . . E 5 33.088 54.71 -11.082 1 33.48 ? C5 GDP 2001 A 1 HETATM 22 C C6 GDP . . . E 5 31.954 55.329 -11.692 1 33.75 ? C6 GDP 2001 A 1 HETATM 23 O O6 GDP . . . E 5 30.799 55.131 -11.395 1 35.54 ? O6 GDP 2001 A 1 HETATM 24 N N1 GDP . . . E 5 32.239 56.22 -12.734 1 33.61 ? N1 GDP 2001 A 1 HETATM 25 C C2 GDP . . . E 5 33.525 56.489 -13.117 1 34.06 ? C2 GDP 2001 A 1 HETATM 26 N N2 GDP . . . E 5 33.767 57.373 -14.137 1 35.33 ? N2 GDP 2001 A 1 HETATM 27 N N3 GDP . . . E 5 34.555 55.917 -12.533 1 33.77 ? N3 GDP 2001 A 1 HETATM 28 C C4 GDP . . . E 5 34.369 55.044 -11.515 1 34.01 ? C4 GDP 2001 A 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #