data_3ZID
#
_model_server_result.job_id            vO6-CQkVeUw9dIpnM2jPiQ 
_model_server_result.datetime_utc      '2024-12-22 02:12:59' 
_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          3zid 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":999}' 
#
_entry.id    3ZID 
#
_exptl.entry_id    3ZID 
_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    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          91.42 
_cell.angle_gamma         90 
_cell.entry_id            3ZID 
_cell.length_a            44.547 
_cell.length_b            107.011 
_cell.length_c            76.966 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3ZID 
_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
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,E 1 1 
B,D,F 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
? 2 C N N 
? 2 D N N 
#
_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                     3ZID 
_atom_sites.fract_transf_matrix[1][1]    0.022448 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000556 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009345 
_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]    0.012997 
_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 GDP A 1 999 999 GDP GDP . 
D 2 GDP B 1 999 999 GDP GDP . 
E 3 HOH A 1 2001 2001 HOH HOH . 
E 3 HOH A 2 2002 2002 HOH HOH . 
E 3 HOH A 3 2003 2003 HOH HOH . 
E 3 HOH A 4 2004 2004 HOH HOH . 
E 3 HOH A 5 2005 2005 HOH HOH . 
E 3 HOH A 6 2006 2006 HOH HOH . 
E 3 HOH A 7 2007 2007 HOH HOH . 
E 3 HOH A 8 2008 2008 HOH HOH . 
E 3 HOH A 9 2009 2009 HOH HOH . 
E 3 HOH A 10 2010 2010 HOH HOH . 
E 3 HOH A 11 2011 2011 HOH HOH . 
E 3 HOH A 12 2012 2012 HOH HOH . 
E 3 HOH A 13 2013 2013 HOH HOH . 
E 3 HOH A 14 2014 2014 HOH HOH . 
E 3 HOH A 15 2015 2015 HOH HOH . 
E 3 HOH A 16 2016 2016 HOH HOH . 
E 3 HOH A 17 2017 2017 HOH HOH . 
E 3 HOH A 18 2018 2018 HOH HOH . 
E 3 HOH A 19 2019 2019 HOH HOH . 
E 3 HOH A 20 2020 2020 HOH HOH . 
E 3 HOH A 21 2021 2021 HOH HOH . 
E 3 HOH A 22 2022 2022 HOH HOH . 
E 3 HOH A 23 2023 2023 HOH HOH . 
E 3 HOH A 24 2024 2024 HOH HOH . 
E 3 HOH A 25 2025 2025 HOH HOH . 
E 3 HOH A 26 2026 2026 HOH HOH . 
E 3 HOH A 27 2027 2027 HOH HOH . 
E 3 HOH A 28 2028 2028 HOH HOH . 
E 3 HOH A 29 2029 2029 HOH HOH . 
E 3 HOH A 30 2030 2030 HOH HOH . 
E 3 HOH A 31 2031 2031 HOH HOH . 
E 3 HOH A 32 2032 2032 HOH HOH . 
E 3 HOH A 33 2033 2033 HOH HOH . 
E 3 HOH A 34 2034 2034 HOH HOH . 
E 3 HOH A 35 2035 2035 HOH HOH . 
E 3 HOH A 36 2036 2036 HOH HOH . 
E 3 HOH A 37 2037 2037 HOH HOH . 
E 3 HOH A 38 2038 2038 HOH HOH . 
E 3 HOH A 39 2039 2039 HOH HOH . 
E 3 HOH A 40 2040 2040 HOH HOH . 
E 3 HOH A 41 2041 2041 HOH HOH . 
E 3 HOH A 42 2042 2042 HOH HOH . 
E 3 HOH A 43 2043 2043 HOH HOH . 
E 3 HOH A 44 2044 2044 HOH HOH . 
E 3 HOH A 45 2045 2045 HOH HOH . 
E 3 HOH A 46 2046 2046 HOH HOH . 
E 3 HOH A 47 2047 2047 HOH HOH . 
E 3 HOH A 48 2048 2048 HOH HOH . 
E 3 HOH A 49 2049 2049 HOH HOH . 
E 3 HOH A 50 2050 2050 HOH HOH . 
E 3 HOH A 51 2051 2051 HOH HOH . 
E 3 HOH A 52 2052 2052 HOH HOH . 
E 3 HOH A 53 2053 2053 HOH HOH . 
E 3 HOH A 54 2054 2054 HOH HOH . 
E 3 HOH A 55 2055 2055 HOH HOH . 
E 3 HOH A 56 2056 2056 HOH HOH . 
E 3 HOH A 57 2057 2057 HOH HOH . 
E 3 HOH A 58 2058 2058 HOH HOH . 
E 3 HOH A 59 2059 2059 HOH HOH . 
E 3 HOH A 60 2060 2060 HOH HOH . 
E 3 HOH A 61 2061 2061 HOH HOH . 
E 3 HOH A 62 2062 2062 HOH HOH . 
E 3 HOH A 63 2063 2063 HOH HOH . 
E 3 HOH A 64 2064 2064 HOH HOH . 
E 3 HOH A 65 2065 2065 HOH HOH . 
E 3 HOH A 66 2066 2066 HOH HOH . 
E 3 HOH A 67 2067 2067 HOH HOH . 
E 3 HOH A 68 2068 2068 HOH HOH . 
E 3 HOH A 69 2069 2069 HOH HOH . 
E 3 HOH A 70 2070 2070 HOH HOH . 
E 3 HOH A 71 2071 2071 HOH HOH . 
E 3 HOH A 72 2072 2072 HOH HOH . 
E 3 HOH A 73 2073 2073 HOH HOH . 
E 3 HOH A 74 2074 2074 HOH HOH . 
E 3 HOH A 75 2075 2075 HOH HOH . 
E 3 HOH A 76 2076 2076 HOH HOH . 
E 3 HOH A 77 2077 2077 HOH HOH . 
E 3 HOH A 78 2078 2078 HOH HOH . 
E 3 HOH A 79 2079 2079 HOH HOH . 
E 3 HOH A 80 2080 2080 HOH HOH . 
E 3 HOH A 81 2081 2081 HOH HOH . 
E 3 HOH A 82 2082 2082 HOH HOH . 
E 3 HOH A 83 2083 2083 HOH HOH . 
E 3 HOH A 84 2084 2084 HOH HOH . 
E 3 HOH A 85 2085 2085 HOH HOH . 
E 3 HOH A 86 2086 2086 HOH HOH . 
E 3 HOH A 87 2087 2087 HOH HOH . 
E 3 HOH A 88 2088 2088 HOH HOH . 
E 3 HOH A 89 2089 2089 HOH HOH . 
E 3 HOH A 90 2090 2090 HOH HOH . 
E 3 HOH A 91 2091 2091 HOH HOH . 
E 3 HOH A 92 2092 2092 HOH HOH . 
E 3 HOH A 93 2093 2093 HOH HOH . 
E 3 HOH A 94 2094 2094 HOH HOH . 
E 3 HOH A 95 2095 2095 HOH HOH . 
E 3 HOH A 96 2096 2096 HOH HOH . 
E 3 HOH A 97 2097 2097 HOH HOH . 
E 3 HOH A 98 2098 2098 HOH HOH . 
E 3 HOH A 99 2099 2099 HOH HOH . 
E 3 HOH A 100 2100 2100 HOH HOH . 
F 3 HOH B 1 2001 2001 HOH HOH . 
F 3 HOH B 2 2002 2002 HOH HOH . 
F 3 HOH B 3 2003 2003 HOH HOH . 
F 3 HOH B 4 2004 2004 HOH HOH . 
F 3 HOH B 5 2005 2005 HOH HOH . 
F 3 HOH B 6 2006 2006 HOH HOH . 
F 3 HOH B 7 2007 2007 HOH HOH . 
F 3 HOH B 8 2008 2008 HOH HOH . 
F 3 HOH B 9 2009 2009 HOH HOH . 
F 3 HOH B 10 2010 2010 HOH HOH . 
F 3 HOH B 11 2011 2011 HOH HOH . 
F 3 HOH B 12 2012 2012 HOH HOH . 
F 3 HOH B 13 2013 2013 HOH HOH . 
F 3 HOH B 14 2014 2014 HOH HOH . 
F 3 HOH B 15 2015 2015 HOH HOH . 
F 3 HOH B 16 2016 2016 HOH HOH . 
F 3 HOH B 17 2017 2017 HOH HOH . 
F 3 HOH B 18 2018 2018 HOH HOH . 
F 3 HOH B 19 2019 2019 HOH HOH . 
F 3 HOH B 20 2020 2020 HOH HOH . 
F 3 HOH B 21 2021 2021 HOH HOH . 
F 3 HOH B 22 2022 2022 HOH HOH . 
F 3 HOH B 23 2023 2023 HOH HOH . 
F 3 HOH B 24 2024 2024 HOH HOH . 
F 3 HOH B 25 2025 2025 HOH HOH . 
F 3 HOH B 26 2026 2026 HOH HOH . 
F 3 HOH B 27 2027 2027 HOH HOH . 
F 3 HOH B 28 2028 2028 HOH HOH . 
F 3 HOH B 29 2029 2029 HOH HOH . 
F 3 HOH B 30 2030 2030 HOH HOH . 
F 3 HOH B 31 2031 2031 HOH HOH . 
F 3 HOH B 32 2032 2032 HOH HOH . 
F 3 HOH B 33 2033 2033 HOH HOH . 
F 3 HOH B 34 2034 2034 HOH HOH . 
F 3 HOH B 35 2035 2035 HOH HOH . 
F 3 HOH B 36 2036 2036 HOH HOH . 
F 3 HOH B 37 2037 2037 HOH HOH . 
F 3 HOH B 38 2038 2038 HOH HOH . 
F 3 HOH B 39 2039 2039 HOH HOH . 
F 3 HOH B 40 2040 2040 HOH HOH . 
F 3 HOH B 41 2041 2041 HOH HOH . 
F 3 HOH B 42 2042 2042 HOH HOH . 
F 3 HOH B 43 2043 2043 HOH HOH . 
F 3 HOH B 44 2044 2044 HOH HOH . 
F 3 HOH B 45 2045 2045 HOH HOH . 
F 3 HOH B 46 2046 2046 HOH HOH . 
F 3 HOH B 47 2047 2047 HOH HOH . 
F 3 HOH B 48 2048 2048 HOH HOH . 
F 3 HOH B 49 2049 2049 HOH HOH . 
F 3 HOH B 50 2050 2050 HOH HOH . 
F 3 HOH B 51 2051 2051 HOH HOH . 
F 3 HOH B 52 2052 2052 HOH HOH . 
F 3 HOH B 53 2053 2053 HOH HOH . 
F 3 HOH B 54 2054 2054 HOH HOH . 
F 3 HOH B 55 2055 2055 HOH HOH . 
F 3 HOH B 56 2056 2056 HOH HOH . 
F 3 HOH B 57 2057 2057 HOH HOH . 
F 3 HOH B 58 2058 2058 HOH HOH . 
F 3 HOH B 59 2059 2059 HOH HOH . 
F 3 HOH B 60 2060 2060 HOH HOH . 
F 3 HOH B 61 2061 2061 HOH HOH . 
F 3 HOH B 62 2062 2062 HOH HOH . 
F 3 HOH B 63 2063 2063 HOH HOH . 
F 3 HOH B 64 2064 2064 HOH HOH . 
F 3 HOH B 65 2065 2065 HOH HOH . 
F 3 HOH B 66 2066 2066 HOH HOH . 
F 3 HOH B 67 2067 2067 HOH HOH . 
F 3 HOH B 68 2068 2068 HOH HOH . 
F 3 HOH B 69 2069 2069 HOH HOH . 
F 3 HOH B 70 2070 2070 HOH HOH . 
F 3 HOH B 71 2071 2071 HOH HOH . 
F 3 HOH B 72 2072 2072 HOH HOH . 
F 3 HOH B 73 2073 2073 HOH HOH . 
F 3 HOH B 74 2074 2074 HOH HOH . 
F 3 HOH B 75 2075 2075 HOH HOH . 
F 3 HOH B 76 2076 2076 HOH HOH . 
F 3 HOH B 77 2077 2077 HOH HOH . 
F 3 HOH B 78 2078 2078 HOH HOH . 
F 3 HOH B 79 2079 2079 HOH HOH . 
F 3 HOH B 80 2080 2080 HOH HOH . 
F 3 HOH B 81 2081 2081 HOH HOH . 
F 3 HOH B 82 2082 2082 HOH HOH . 
F 3 HOH B 83 2083 2083 HOH HOH . 
F 3 HOH B 84 2084 2084 HOH HOH . 
F 3 HOH B 85 2085 2085 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 2 15.032 -15.937 -16.415 1 21.5 ? PB GDP 999 A 1 
HETATM 2 O O1B GDP . . . C 2 14.522 -14.61 -15.88 1 19.75 ? O1B GDP 999 A 1 
HETATM 3 O O2B GDP . . . C 2 14.723 -17.045 -15.427 1 20.81 ? O2B GDP 999 A 1 
HETATM 4 O O3B GDP . . . C 2 14.352 -16.207 -17.746 1 21.17 ? O3B GDP 999 A 1 
HETATM 5 O O3A GDP . . . C 2 16.606 -15.831 -16.705 1 30.29 ? O3A GDP 999 A 1 
HETATM 6 P PA GDP . . . C 2 17.695 -15.582 -15.552 1 21.73 ? PA GDP 999 A 1 
HETATM 7 O O1A GDP . . . C 2 18.498 -16.812 -15.308 1 19 ? O1A GDP 999 A 1 
HETATM 8 O O2A GDP . . . C 2 17.11 -15.013 -14.278 1 22.06 ? O2A GDP 999 A 1 
HETATM 9 O O5' GDP . . . C 2 18.547 -14.438 -16.256 1 25.02 ? O5' GDP 999 A 1 
HETATM 10 C C5' GDP . . . C 2 19.866 -14.731 -16.69 1 26.63 ? C5' GDP 999 A 1 
HETATM 11 C C4' GDP . . . C 2 20.772 -13.611 -16.199 1 22.92 ? C4' GDP 999 A 1 
HETATM 12 O O4' GDP . . . C 2 20.786 -13.65 -14.771 1 18.04 ? O4' GDP 999 A 1 
HETATM 13 C C3' GDP . . . C 2 22.177 -13.876 -16.666 1 15.33 ? C3' GDP 999 A 1 
HETATM 14 O O3' GDP . . . C 2 22.825 -12.608 -16.741 1 22.01 ? O3' GDP 999 A 1 
HETATM 15 C C2' GDP . . . C 2 22.743 -14.694 -15.538 1 21.96 ? C2' GDP 999 A 1 
HETATM 16 O O2' GDP . . . C 2 24.154 -14.518 -15.479 1 20.99 ? O2' GDP 999 A 1 
HETATM 17 C C1' GDP . . . C 2 22.082 -14.065 -14.328 1 19.8 ? C1' GDP 999 A 1 
HETATM 18 N N9 GDP . . . C 2 21.832 -14.974 -13.209 1 18.52 ? N9 GDP 999 A 1 
HETATM 19 C C8 GDP . . . C 2 21.186 -16.156 -13.242 1 17.14 ? C8 GDP 999 A 1 
HETATM 20 N N7 GDP . . . C 2 21.093 -16.678 -11.995 1 24.03 ? N7 GDP 999 A 1 
HETATM 21 C C5 GDP . . . C 2 21.692 -15.807 -11.157 1 17.03 ? C5 GDP 999 A 1 
HETATM 22 C C6 GDP . . . C 2 21.933 -15.724 -9.714 1 14.57 ? C6 GDP 999 A 1 
HETATM 23 O O6 GDP . . . C 2 21.574 -16.643 -8.967 1 21.86 ? O6 GDP 999 A 1 
HETATM 24 N N1 GDP . . . C 2 22.566 -14.65 -9.245 1 14.27 ? N1 GDP 999 A 1 
HETATM 25 C C2 GDP . . . C 2 22.982 -13.653 -10.037 1 17.84 ? C2 GDP 999 A 1 
HETATM 26 N N2 GDP . . . C 2 23.624 -12.611 -9.468 1 17.35 ? N2 GDP 999 A 1 
HETATM 27 N N3 GDP . . . C 2 22.8 -13.641 -11.38 1 18.13 ? N3 GDP 999 A 1 
HETATM 28 C C4 GDP . . . C 2 22.161 -14.678 -11.965 1 20.2 ? C4 GDP 999 A 1 
#
_model_server_stats.io_time_ms              116 
_model_server_stats.parse_time_ms           99 
_model_server_stats.create_model_time_ms    54 
_model_server_stats.query_time_ms           424 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           28 
#