data_2Y4K # _model_server_result.job_id NJ-bR3Mk8oikroMjnMT7YA _model_server_result.datetime_utc '2024-11-08 08:57:05' _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 2y4k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 2Y4K # _exptl.entry_id 2Y4K _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _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 90 _cell.angle_gamma 120 _cell.entry_id 2Y4K _cell.length_a 149.646 _cell.length_b 149.646 _cell.length_c 154.112 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2Y4K _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 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 PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_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,F,G,H,P 1 1 B,I,J,K,L,M,N,O,Q 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 ? 3 D N N ? 3 J 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 OD2 ASP 102 A ASP 102 1_555 C MG MG . A MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc2 C MG MG . A MG 400 1_555 D O2B GDP . A GDP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? metalc ? metalc3 C MG MG . A MG 400 1_555 D O2A GDP . A GDP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.736 ? metalc ? metalc4 B OD1 ASP 102 B ASP 102 1_555 I MG MG . B MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.789 ? metalc ? metalc5 B OD2 ASP 102 B ASP 102 1_555 I MG MG . B MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.828 ? metalc ? metalc6 I MG MG . B MG 400 1_555 J O2A GDP . B GDP 401 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.089 ? metalc ? metalc7 I MG MG . B MG 400 1_555 J O2A GDP . B GDP 401 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.73 ? metalc ? metalc8 I MG MG . B MG 400 1_555 J O2B GDP . B GDP 401 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.348 ? # _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 87 n n PB O2B GDP sing 88 n n PB O3B GDP sing 89 n n PB O3A GDP sing 90 n n O2B HOB2 GDP sing 91 n n O3B HOB3 GDP sing 92 n n O3A PA GDP sing 93 n n PA O1A GDP doub 94 n n PA O2A GDP sing 95 n n PA O5' GDP sing 96 n n O2A HOA2 GDP sing 97 n n O5' C5' GDP sing 98 n n C5' C4' GDP sing 99 n n C5' H5' GDP sing 100 n n C5' "H5''" GDP sing 101 n n C4' O4' GDP sing 102 n n C4' C3' GDP sing 103 n n C4' H4' GDP sing 104 n n O4' C1' GDP sing 105 n n C3' O3' GDP sing 106 n n C3' C2' GDP sing 107 n n C3' H3' GDP sing 108 n n O3' HO3' GDP sing 109 n n C2' O2' GDP sing 110 n n C2' C1' GDP sing 111 n n C2' H2' GDP sing 112 n n O2' HO2' GDP sing 113 n n C1' N9 GDP sing 114 n n C1' H1' GDP sing 115 n n N9 C8 GDP sing 116 n y N9 C4 GDP sing 117 n y C8 N7 GDP doub 118 n y C8 H8 GDP sing 119 n n N7 C5 GDP sing 120 n y C5 C6 GDP sing 121 n n C5 C4 GDP doub 122 n y C6 O6 GDP doub 123 n n C6 N1 GDP sing 124 n n N1 C2 GDP sing 125 n n N1 HN1 GDP sing 126 n n C2 N2 GDP sing 127 n n C2 N3 GDP doub 128 n n N2 HN21 GDP sing 129 n n N2 HN22 GDP sing 130 n n N3 C4 GDP sing 131 n n # _atom_sites.entry_id 2Y4K _atom_sites.fract_transf_matrix[1][1] 0.006682 _atom_sites.fract_transf_matrix[1][2] 0.003858 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007716 _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] 0.006489 _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 1 400 400 MG MG . D 3 GDP A 1 401 401 GDP GDP . E 4 CL A 1 402 402 CL CL . F 5 FMT A 1 501 501 FMT FMT . G 5 FMT A 1 502 502 FMT FMT . H 5 FMT A 1 503 503 FMT FMT . I 2 MG B 1 400 400 MG MG . J 3 GDP B 1 401 401 GDP GDP . K 4 CL B 1 402 402 CL CL . L 6 TRS B 1 501 501 TRS TRS . M 5 FMT B 1 502 502 FMT FMT . N 5 FMT B 1 503 503 FMT FMT . O 5 FMT B 1 504 504 FMT FMT . P 7 HOH A 1 2001 2001 HOH HOH . P 7 HOH A 2 2002 2002 HOH HOH . P 7 HOH A 3 2003 2003 HOH HOH . P 7 HOH A 4 2004 2004 HOH HOH . P 7 HOH A 5 2005 2005 HOH HOH . P 7 HOH A 6 2006 2006 HOH HOH . P 7 HOH A 7 2007 2007 HOH HOH . P 7 HOH A 8 2008 2008 HOH HOH . P 7 HOH A 9 2009 2009 HOH HOH . P 7 HOH A 10 2010 2010 HOH HOH . P 7 HOH A 11 2011 2011 HOH HOH . P 7 HOH A 12 2012 2012 HOH HOH . P 7 HOH A 13 2013 2013 HOH HOH . P 7 HOH A 14 2014 2014 HOH HOH . P 7 HOH A 15 2015 2015 HOH HOH . P 7 HOH A 16 2016 2016 HOH HOH . P 7 HOH A 17 2017 2017 HOH HOH . P 7 HOH A 18 2018 2018 HOH HOH . P 7 HOH A 19 2019 2019 HOH HOH . P 7 HOH A 20 2020 2020 HOH HOH . P 7 HOH A 21 2021 2021 HOH HOH . P 7 HOH A 22 2022 2022 HOH HOH . P 7 HOH A 23 2023 2023 HOH HOH . P 7 HOH A 24 2024 2024 HOH HOH . P 7 HOH A 25 2025 2025 HOH HOH . P 7 HOH A 26 2026 2026 HOH HOH . P 7 HOH A 27 2027 2027 HOH HOH . P 7 HOH A 28 2028 2028 HOH HOH . P 7 HOH A 29 2029 2029 HOH HOH . P 7 HOH A 30 2030 2030 HOH HOH . P 7 HOH A 31 2031 2031 HOH HOH . P 7 HOH A 32 2032 2032 HOH HOH . P 7 HOH A 33 2033 2033 HOH HOH . P 7 HOH A 34 2034 2034 HOH HOH . P 7 HOH A 35 2035 2035 HOH HOH . P 7 HOH A 36 2036 2036 HOH HOH . P 7 HOH A 37 2037 2037 HOH HOH . P 7 HOH A 38 2038 2038 HOH HOH . P 7 HOH A 39 2039 2039 HOH HOH . P 7 HOH A 40 2040 2040 HOH HOH . P 7 HOH A 41 2041 2041 HOH HOH . P 7 HOH A 42 2042 2042 HOH HOH . P 7 HOH A 43 2043 2043 HOH HOH . P 7 HOH A 44 2044 2044 HOH HOH . P 7 HOH A 45 2045 2045 HOH HOH . P 7 HOH A 46 2046 2046 HOH HOH . P 7 HOH A 47 2047 2047 HOH HOH . P 7 HOH A 48 2048 2048 HOH HOH . P 7 HOH A 49 2049 2049 HOH HOH . P 7 HOH A 50 2050 2050 HOH HOH . P 7 HOH A 51 2051 2051 HOH HOH . P 7 HOH A 52 2052 2052 HOH HOH . P 7 HOH A 53 2053 2053 HOH HOH . P 7 HOH A 54 2054 2054 HOH HOH . P 7 HOH A 55 2055 2055 HOH HOH . P 7 HOH A 56 2056 2056 HOH HOH . P 7 HOH A 57 2057 2057 HOH HOH . P 7 HOH A 58 2058 2058 HOH HOH . P 7 HOH A 59 2059 2059 HOH HOH . P 7 HOH A 60 2060 2060 HOH HOH . P 7 HOH A 61 2061 2061 HOH HOH . P 7 HOH A 62 2062 2062 HOH HOH . P 7 HOH A 63 2063 2063 HOH HOH . P 7 HOH A 64 2064 2064 HOH HOH . P 7 HOH A 65 2065 2065 HOH HOH . P 7 HOH A 66 2066 2066 HOH HOH . P 7 HOH A 67 2067 2067 HOH HOH . P 7 HOH A 68 2068 2068 HOH HOH . P 7 HOH A 69 2069 2069 HOH HOH . P 7 HOH A 70 2070 2070 HOH HOH . Q 7 HOH B 1 2001 2001 HOH HOH . Q 7 HOH B 2 2002 2002 HOH HOH . Q 7 HOH B 3 2003 2003 HOH HOH . Q 7 HOH B 4 2004 2004 HOH HOH . Q 7 HOH B 5 2005 2005 HOH HOH . Q 7 HOH B 6 2006 2006 HOH HOH . Q 7 HOH B 7 2007 2007 HOH HOH . Q 7 HOH B 8 2008 2008 HOH HOH . Q 7 HOH B 9 2009 2009 HOH HOH . Q 7 HOH B 10 2010 2010 HOH HOH . Q 7 HOH B 11 2011 2011 HOH HOH . Q 7 HOH B 12 2012 2012 HOH HOH . Q 7 HOH B 13 2013 2013 HOH HOH . Q 7 HOH B 14 2014 2014 HOH HOH . Q 7 HOH B 15 2015 2015 HOH HOH . Q 7 HOH B 16 2016 2016 HOH HOH . Q 7 HOH B 17 2017 2017 HOH HOH . Q 7 HOH B 18 2018 2018 HOH HOH . Q 7 HOH B 19 2019 2019 HOH HOH . Q 7 HOH B 20 2020 2020 HOH HOH . Q 7 HOH B 21 2021 2021 HOH HOH . Q 7 HOH B 22 2022 2022 HOH HOH . Q 7 HOH B 23 2023 2023 HOH HOH . Q 7 HOH B 24 2024 2024 HOH HOH . Q 7 HOH B 25 2025 2025 HOH HOH . Q 7 HOH B 26 2026 2026 HOH HOH . Q 7 HOH B 27 2027 2027 HOH HOH . Q 7 HOH B 28 2028 2028 HOH HOH . Q 7 HOH B 29 2029 2029 HOH HOH . Q 7 HOH B 30 2030 2030 HOH HOH . Q 7 HOH B 31 2031 2031 HOH HOH . Q 7 HOH B 32 2032 2032 HOH HOH . Q 7 HOH B 33 2033 2033 HOH HOH . Q 7 HOH B 34 2034 2034 HOH HOH . Q 7 HOH B 35 2035 2035 HOH HOH . Q 7 HOH B 36 2036 2036 HOH HOH . Q 7 HOH B 37 2037 2037 HOH HOH . Q 7 HOH B 38 2038 2038 HOH HOH . Q 7 HOH B 39 2039 2039 HOH HOH . Q 7 HOH B 40 2040 2040 HOH HOH . Q 7 HOH B 41 2041 2041 HOH HOH . Q 7 HOH B 42 2042 2042 HOH HOH . Q 7 HOH B 43 2043 2043 HOH HOH . Q 7 HOH B 44 2044 2044 HOH HOH . Q 7 HOH B 45 2045 2045 HOH HOH . Q 7 HOH B 46 2046 2046 HOH HOH . Q 7 HOH B 47 2047 2047 HOH HOH . Q 7 HOH B 48 2048 2048 HOH HOH . Q 7 HOH B 49 2049 2049 HOH HOH . Q 7 HOH B 50 2050 2050 HOH HOH . Q 7 HOH B 51 2051 2051 HOH HOH . Q 7 HOH B 52 2052 2052 HOH HOH . Q 7 HOH B 53 2053 2053 HOH HOH . Q 7 HOH B 54 2054 2054 HOH HOH . Q 7 HOH B 55 2055 2055 HOH HOH . Q 7 HOH B 56 2056 2056 HOH HOH . Q 7 HOH B 57 2057 2057 HOH HOH . Q 7 HOH B 58 2058 2058 HOH HOH . Q 7 HOH B 59 2059 2059 HOH HOH . Q 7 HOH B 60 2060 2060 HOH HOH . Q 7 HOH B 61 2061 2061 HOH HOH . Q 7 HOH B 62 2062 2062 HOH HOH . Q 7 HOH B 63 2063 2063 HOH HOH . Q 7 HOH B 64 2064 2064 HOH HOH . Q 7 HOH B 65 2065 2065 HOH HOH . Q 7 HOH B 66 2066 2066 HOH HOH . Q 7 HOH B 67 2067 2067 HOH HOH . Q 7 HOH B 68 2068 2068 HOH HOH . Q 7 HOH B 69 2069 2069 HOH HOH . Q 7 HOH B 70 2070 2070 HOH HOH . Q 7 HOH B 71 2071 2071 HOH HOH . Q 7 HOH B 72 2072 2072 HOH HOH . Q 7 HOH B 73 2073 2073 HOH HOH . Q 7 HOH B 74 2074 2074 HOH HOH . Q 7 HOH B 75 2075 2075 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 3 38.783 -45.14 -5.061 1 85.61 ? PB GDP 401 A 1 HETATM 2 O O1B GDP . . . D 3 40.005 -45.026 -5.96 1 85.37 ? O1B GDP 401 A 1 HETATM 3 O O2B GDP . . . D 3 37.503 -45.144 -5.911 1 85.26 ? O2B GDP 401 A 1 HETATM 4 O O3B GDP . . . D 3 38.891 -46.403 -4.206 1 83.14 ? O3B GDP 401 A 1 HETATM 5 O O3A GDP . . . D 3 38.838 -43.854 -4.061 1 79.75 ? O3A GDP 401 A 1 HETATM 6 P PA GDP . . . D 3 38.247 -42.398 -4.381 1 73.41 ? PA GDP 401 A 1 HETATM 7 O O1A GDP . . . D 3 39.373 -41.387 -4.395 1 73.54 ? O1A GDP 401 A 1 HETATM 8 O O2A GDP . . . D 3 37.424 -42.357 -5.659 1 73.92 ? O2A GDP 401 A 1 HETATM 9 O O5' GDP . . . D 3 37.306 -42.308 -3.096 1 70.55 ? O5' GDP 401 A 1 HETATM 10 C C5' GDP . . . D 3 36.343 -43.315 -2.78 1 64.2 ? C5' GDP 401 A 1 HETATM 11 C C4' GDP . . . D 3 35.069 -42.622 -2.282 1 62.78 ? C4' GDP 401 A 1 HETATM 12 O O4' GDP . . . D 3 35.174 -42.11 -0.936 1 61.82 ? O4' GDP 401 A 1 HETATM 13 C C3' GDP . . . D 3 34.702 -41.418 -3.123 1 61.64 ? C3' GDP 401 A 1 HETATM 14 O O3' GDP . . . D 3 33.276 -41.342 -3.114 1 59.94 ? O3' GDP 401 A 1 HETATM 15 C C2' GDP . . . D 3 35.325 -40.259 -2.348 1 61.64 ? C2' GDP 401 A 1 HETATM 16 O O2' GDP . . . D 3 34.668 -39.031 -2.585 1 62.47 ? O2' GDP 401 A 1 HETATM 17 C C1' GDP . . . D 3 35.138 -40.678 -0.91 1 60.52 ? C1' GDP 401 A 1 HETATM 18 N N9 GDP . . . D 3 36.202 -40.226 0.005 1 59.2 ? N9 GDP 401 A 1 HETATM 19 C C8 GDP . . . D 3 37.543 -40.42 -0.119 1 58.99 ? C8 GDP 401 A 1 HETATM 20 N N7 GDP . . . D 3 38.213 -39.906 0.953 1 56.75 ? N7 GDP 401 A 1 HETATM 21 C C5 GDP . . . D 3 37.286 -39.386 1.783 1 56.7 ? C5 GDP 401 A 1 HETATM 22 C C6 GDP . . . D 3 37.295 -38.669 3.083 1 56.01 ? C6 GDP 401 A 1 HETATM 23 O O6 GDP . . . D 3 38.364 -38.445 3.677 1 55.46 ? O6 GDP 401 A 1 HETATM 24 N N1 GDP . . . D 3 36.119 -38.305 3.607 1 55.98 ? N1 GDP 401 A 1 HETATM 25 C C2 GDP . . . D 3 34.935 -38.537 2.984 1 56.02 ? C2 GDP 401 A 1 HETATM 26 N N2 GDP . . . D 3 33.782 -38.12 3.581 1 54.74 ? N2 GDP 401 A 1 HETATM 27 N N3 GDP . . . D 3 34.853 -39.177 1.787 1 54.44 ? N3 GDP 401 A 1 HETATM 28 C C4 GDP . . . D 3 35.966 -39.601 1.155 1 56.86 ? C4 GDP 401 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 223 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 28 #