data_2W2T
#
_model_server_result.job_id            w-y-kD2BZxd6cZShzlCjFg 
_model_server_result.datetime_utc      '2024-11-02 05:22:35' 
_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          2w2t 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":1181}' 
#
_entry.id    2W2T 
#
_exptl.entry_id    2W2T 
_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    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            2W2T 
_cell.length_a            42.205 
_cell.length_b            98.106 
_cell.length_c            108.064 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2W2T 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
_pdbx_struct_assembly.method_details        PQS 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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                      3 
_struct_asym.id                             C 
_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 A OG1 THR 23 A THR 17 1_555 B MG MG . A MG 1180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? 
metalc ? metalc2 B MG MG . A MG 1180 1_555 C O1B GDP . A GDP 1181 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? 
metalc ? metalc3 B MG MG . A MG 1180 1_555 D O HOH . A HOH 2013 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? 
metalc ? metalc4 B MG MG . A MG 1180 1_555 D O HOH . A HOH 2058 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? 
metalc ? metalc5 B MG MG . A MG 1180 1_555 D O HOH . A HOH 2135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? 
metalc ? metalc6 B MG MG . A MG 1180 1_555 D O HOH . A HOH 2138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? 
#
_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                     2W2T 
_atom_sites.fract_transf_matrix[1][1]    0.023694 
_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]    0.010193 
_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]    0.009254 
_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
B 2 MG A 1 1180 1180 MG MG . 
C 3 GDP A 1 1181 1181 GDP GDP . 
D 4 HOH A 1 2001 2001 HOH HOH . 
D 4 HOH A 2 2002 2002 HOH HOH . 
D 4 HOH A 3 2003 2003 HOH HOH . 
D 4 HOH A 4 2004 2004 HOH HOH . 
D 4 HOH A 5 2005 2005 HOH HOH . 
D 4 HOH A 6 2006 2006 HOH HOH . 
D 4 HOH A 7 2007 2007 HOH HOH . 
D 4 HOH A 8 2008 2008 HOH HOH . 
D 4 HOH A 9 2009 2009 HOH HOH . 
D 4 HOH A 10 2010 2010 HOH HOH . 
D 4 HOH A 11 2011 2011 HOH HOH . 
D 4 HOH A 12 2012 2012 HOH HOH . 
D 4 HOH A 13 2013 2013 HOH HOH . 
D 4 HOH A 14 2014 2014 HOH HOH . 
D 4 HOH A 15 2015 2015 HOH HOH . 
D 4 HOH A 16 2016 2016 HOH HOH . 
D 4 HOH A 17 2017 2017 HOH HOH . 
D 4 HOH A 18 2018 2018 HOH HOH . 
D 4 HOH A 19 2019 2019 HOH HOH . 
D 4 HOH A 20 2020 2020 HOH HOH . 
D 4 HOH A 21 2021 2021 HOH HOH . 
D 4 HOH A 22 2022 2022 HOH HOH . 
D 4 HOH A 23 2023 2023 HOH HOH . 
D 4 HOH A 24 2024 2024 HOH HOH . 
D 4 HOH A 25 2025 2025 HOH HOH . 
D 4 HOH A 26 2026 2026 HOH HOH . 
D 4 HOH A 27 2027 2027 HOH HOH . 
D 4 HOH A 28 2028 2028 HOH HOH . 
D 4 HOH A 29 2029 2029 HOH HOH . 
D 4 HOH A 30 2030 2030 HOH HOH . 
D 4 HOH A 31 2031 2031 HOH HOH . 
D 4 HOH A 32 2032 2032 HOH HOH . 
D 4 HOH A 33 2033 2033 HOH HOH . 
D 4 HOH A 34 2034 2034 HOH HOH . 
D 4 HOH A 35 2035 2035 HOH HOH . 
D 4 HOH A 36 2036 2036 HOH HOH . 
D 4 HOH A 37 2037 2037 HOH HOH . 
D 4 HOH A 38 2038 2038 HOH HOH . 
D 4 HOH A 39 2039 2039 HOH HOH . 
D 4 HOH A 40 2040 2040 HOH HOH . 
D 4 HOH A 41 2041 2041 HOH HOH . 
D 4 HOH A 42 2042 2042 HOH HOH . 
D 4 HOH A 43 2043 2043 HOH HOH . 
D 4 HOH A 44 2044 2044 HOH HOH . 
D 4 HOH A 45 2045 2045 HOH HOH . 
D 4 HOH A 46 2046 2046 HOH HOH . 
D 4 HOH A 47 2047 2047 HOH HOH . 
D 4 HOH A 48 2048 2048 HOH HOH . 
D 4 HOH A 49 2049 2049 HOH HOH . 
D 4 HOH A 50 2050 2050 HOH HOH . 
D 4 HOH A 51 2051 2051 HOH HOH . 
D 4 HOH A 52 2052 2052 HOH HOH . 
D 4 HOH A 53 2053 2053 HOH HOH . 
D 4 HOH A 54 2054 2054 HOH HOH . 
D 4 HOH A 55 2056 2056 HOH HOH . 
D 4 HOH A 56 2057 2057 HOH HOH . 
D 4 HOH A 57 2058 2058 HOH HOH . 
D 4 HOH A 58 2059 2059 HOH HOH . 
D 4 HOH A 59 2060 2060 HOH HOH . 
D 4 HOH A 60 2061 2061 HOH HOH . 
D 4 HOH A 61 2062 2062 HOH HOH . 
D 4 HOH A 62 2063 2063 HOH HOH . 
D 4 HOH A 63 2064 2064 HOH HOH . 
D 4 HOH A 64 2065 2065 HOH HOH . 
D 4 HOH A 65 2066 2066 HOH HOH . 
D 4 HOH A 66 2067 2067 HOH HOH . 
D 4 HOH A 67 2068 2068 HOH HOH . 
D 4 HOH A 68 2069 2069 HOH HOH . 
D 4 HOH A 69 2070 2070 HOH HOH . 
D 4 HOH A 70 2071 2071 HOH HOH . 
D 4 HOH A 71 2072 2072 HOH HOH . 
D 4 HOH A 72 2073 2073 HOH HOH . 
D 4 HOH A 73 2074 2074 HOH HOH . 
D 4 HOH A 74 2075 2075 HOH HOH . 
D 4 HOH A 75 2076 2076 HOH HOH . 
D 4 HOH A 76 2077 2077 HOH HOH . 
D 4 HOH A 77 2078 2078 HOH HOH . 
D 4 HOH A 78 2079 2079 HOH HOH . 
D 4 HOH A 79 2080 2080 HOH HOH . 
D 4 HOH A 80 2081 2081 HOH HOH . 
D 4 HOH A 81 2082 2082 HOH HOH . 
D 4 HOH A 82 2083 2083 HOH HOH . 
D 4 HOH A 83 2084 2084 HOH HOH . 
D 4 HOH A 84 2085 2085 HOH HOH . 
D 4 HOH A 85 2086 2086 HOH HOH . 
D 4 HOH A 86 2087 2087 HOH HOH . 
D 4 HOH A 87 2088 2088 HOH HOH . 
D 4 HOH A 88 2089 2089 HOH HOH . 
D 4 HOH A 89 2090 2090 HOH HOH . 
D 4 HOH A 90 2091 2091 HOH HOH . 
D 4 HOH A 91 2092 2092 HOH HOH . 
D 4 HOH A 92 2093 2093 HOH HOH . 
D 4 HOH A 93 2094 2094 HOH HOH . 
D 4 HOH A 94 2095 2095 HOH HOH . 
D 4 HOH A 95 2096 2096 HOH HOH . 
D 4 HOH A 96 2097 2097 HOH HOH . 
D 4 HOH A 97 2098 2098 HOH HOH . 
D 4 HOH A 98 2099 2099 HOH HOH . 
D 4 HOH A 99 2100 2100 HOH HOH . 
D 4 HOH A 100 2101 2101 HOH HOH . 
D 4 HOH A 101 2102 2102 HOH HOH . 
D 4 HOH A 102 2103 2103 HOH HOH . 
D 4 HOH A 103 2104 2104 HOH HOH . 
D 4 HOH A 104 2105 2105 HOH HOH . 
D 4 HOH A 105 2106 2106 HOH HOH . 
D 4 HOH A 106 2107 2107 HOH HOH . 
D 4 HOH A 107 2108 2108 HOH HOH . 
D 4 HOH A 108 2109 2109 HOH HOH . 
D 4 HOH A 109 2110 2110 HOH HOH . 
D 4 HOH A 110 2111 2111 HOH HOH . 
D 4 HOH A 111 2112 2112 HOH HOH . 
D 4 HOH A 112 2113 2113 HOH HOH . 
D 4 HOH A 113 2114 2114 HOH HOH . 
D 4 HOH A 114 2115 2115 HOH HOH . 
D 4 HOH A 115 2116 2116 HOH HOH . 
D 4 HOH A 116 2117 2117 HOH HOH . 
D 4 HOH A 117 2118 2118 HOH HOH . 
D 4 HOH A 118 2119 2119 HOH HOH . 
D 4 HOH A 119 2120 2120 HOH HOH . 
D 4 HOH A 120 2121 2121 HOH HOH . 
D 4 HOH A 121 2122 2122 HOH HOH . 
D 4 HOH A 122 2123 2123 HOH HOH . 
D 4 HOH A 123 2124 2124 HOH HOH . 
D 4 HOH A 124 2125 2125 HOH HOH . 
D 4 HOH A 125 2126 2126 HOH HOH . 
D 4 HOH A 126 2127 2127 HOH HOH . 
D 4 HOH A 127 2128 2128 HOH HOH . 
D 4 HOH A 128 2129 2129 HOH HOH . 
D 4 HOH A 129 2130 2130 HOH HOH . 
D 4 HOH A 130 2131 2131 HOH HOH . 
D 4 HOH A 131 2132 2132 HOH HOH . 
D 4 HOH A 132 2133 2133 HOH HOH . 
D 4 HOH A 133 2134 2134 HOH HOH . 
D 4 HOH A 134 2135 2135 HOH HOH . 
D 4 HOH A 135 2136 2136 HOH HOH . 
D 4 HOH A 136 2137 2137 HOH HOH . 
D 4 HOH A 137 2138 2138 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 . . . C 3 -11.757 -30.03 19.045 1 28.77 ? PB GDP 1181 A 1 
HETATM 2 O O1B GDP . . . C 3 -11.227 -28.937 19.936 1 27.92 ? O1B GDP 1181 A 1 
HETATM 3 O O2B GDP . . . C 3 -12.97 -30.74 19.666 1 30.46 ? O2B GDP 1181 A 1 
HETATM 4 O O3B GDP . . . C 3 -12.01 -29.106 17.82 1 28.61 ? O3B GDP 1181 A 1 
HETATM 5 O O3A GDP . . . C 3 -10.579 -31.121 18.755 1 32.89 ? O3A GDP 1181 A 1 
HETATM 6 P PA GDP . . . C 3 -9.274 -31.531 19.74 1 30.54 ? PA GDP 1181 A 1 
HETATM 7 O O1A GDP . . . C 3 -8.312 -30.393 19.76 1 29.02 ? O1A GDP 1181 A 1 
HETATM 8 O O2A GDP . . . C 3 -9.885 -32.077 21.008 1 29.66 ? O2A GDP 1181 A 1 
HETATM 9 O O5' GDP . . . C 3 -8.777 -32.716 18.766 1 32.69 ? O5' GDP 1181 A 1 
HETATM 10 C C5' GDP . . . C 3 -9.667 -33.786 18.481 1 32.71 ? C5' GDP 1181 A 1 
HETATM 11 C C4' GDP . . . C 3 -8.912 -35.068 18.151 1 35.1 ? C4' GDP 1181 A 1 
HETATM 12 O O4' GDP . . . C 3 -8.087 -34.798 17.046 1 36.76 ? O4' GDP 1181 A 1 
HETATM 13 C C3' GDP . . . C 3 -7.955 -35.475 19.276 1 35.73 ? C3' GDP 1181 A 1 
HETATM 14 O O3' GDP . . . C 3 -7.993 -36.898 19.294 1 34.82 ? O3' GDP 1181 A 1 
HETATM 15 C C2' GDP . . . C 3 -6.569 -34.973 18.86 1 35.01 ? C2' GDP 1181 A 1 
HETATM 16 O O2' GDP . . . C 3 -5.466 -35.779 19.362 1 41.69 ? O2' GDP 1181 A 1 
HETATM 17 C C1' GDP . . . C 3 -6.692 -34.975 17.354 1 35.59 ? C1' GDP 1181 A 1 
HETATM 18 N N9 GDP . . . C 3 -5.888 -33.9 16.669 1 34.35 ? N9 GDP 1181 A 1 
HETATM 19 C C8 GDP . . . C 3 -5.927 -32.557 16.839 1 34.38 ? C8 GDP 1181 A 1 
HETATM 20 N N7 GDP . . . C 3 -5.083 -31.861 16.039 1 30.76 ? N7 GDP 1181 A 1 
HETATM 21 C C5 GDP . . . C 3 -4.438 -32.816 15.355 1 34.44 ? C5 GDP 1181 A 1 
HETATM 22 C C6 GDP . . . C 3 -3.365 -32.828 14.342 1 35.02 ? C6 GDP 1181 A 1 
HETATM 23 O O6 GDP . . . C 3 -2.894 -31.727 14.003 1 34.01 ? O6 GDP 1181 A 1 
HETATM 24 N N1 GDP . . . C 3 -2.974 -34.035 13.884 1 37.15 ? N1 GDP 1181 A 1 
HETATM 25 C C2 GDP . . . C 3 -3.514 -35.225 14.271 1 37.07 ? C2 GDP 1181 A 1 
HETATM 26 N N2 GDP . . . C 3 -3.108 -36.43 13.776 1 38.38 ? N2 GDP 1181 A 1 
HETATM 27 N N3 GDP . . . C 3 -4.476 -35.287 15.205 1 38.04 ? N3 GDP 1181 A 1 
HETATM 28 C C4 GDP . . . C 3 -4.945 -34.144 15.78 1 36.78 ? C4 GDP 1181 A 1 
#
_model_server_stats.io_time_ms              67 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           360 
_model_server_stats.encode_time_ms          15 
_model_server_stats.element_count           28 
#