data_1OIV
#
_model_server_result.job_id            Sd2krnoQFK7s5DLji6geAQ 
_model_server_result.datetime_utc      '2024-11-24 11:56:26' 
_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          1oiv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":1174}' 
#
_entry.id    1OIV 
#
_exptl.entry_id    1OIV 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            1OIV 
_cell.length_a            47.349 
_cell.length_b            69.701 
_cell.length_c            108.277 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1OIV 
_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        PQS 
_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 
#
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 F 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 79 n n 
PB O2B GDP sing 80 n n 
PB O3B GDP sing 81 n n 
PB O3A GDP sing 82 n n 
O2B HOB2 GDP sing 83 n n 
O3B HOB3 GDP sing 84 n n 
O3A PA GDP sing 85 n n 
PA O1A GDP doub 86 n n 
PA O2A GDP sing 87 n n 
PA O5' GDP sing 88 n n 
O2A HOA2 GDP sing 89 n n 
O5' C5' GDP sing 90 n n 
C5' C4' GDP sing 91 n n 
C5' H5' GDP sing 92 n n 
C5' "H5''" GDP sing 93 n n 
C4' O4' GDP sing 94 n n 
C4' C3' GDP sing 95 n n 
C4' H4' GDP sing 96 n n 
O4' C1' GDP sing 97 n n 
C3' O3' GDP sing 98 n n 
C3' C2' GDP sing 99 n n 
C3' H3' GDP sing 100 n n 
O3' HO3' GDP sing 101 n n 
C2' O2' GDP sing 102 n n 
C2' C1' GDP sing 103 n n 
C2' H2' GDP sing 104 n n 
O2' HO2' GDP sing 105 n n 
C1' N9 GDP sing 106 n n 
C1' H1' GDP sing 107 n n 
N9 C8 GDP sing 108 n y 
N9 C4 GDP sing 109 n y 
C8 N7 GDP doub 110 n y 
C8 H8 GDP sing 111 n n 
N7 C5 GDP sing 112 n y 
C5 C6 GDP sing 113 n n 
C5 C4 GDP doub 114 n y 
C6 O6 GDP doub 115 n n 
C6 N1 GDP sing 116 n n 
N1 C2 GDP sing 117 n n 
N1 HN1 GDP sing 118 n n 
C2 N2 GDP sing 119 n n 
C2 N3 GDP doub 120 n n 
N2 HN21 GDP sing 121 n n 
N2 HN22 GDP sing 122 n n 
N3 C4 GDP sing 123 n n 
#
_atom_sites.entry_id                     1OIV 
_atom_sites.fract_transf_matrix[1][1]    0.02112 
_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]    0.014347 
_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]    0.009235 
_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 1174 1174 GDP GDP . 
D 3 SO4 A 1 1175 1175 SO4 SO4 . 
E 4 EDO B 1 1174 1174 EDO EDO . 
F 2 GDP B 1 1175 1175 GDP GDP . 
G 5 HOH A 1 2001 2001 HOH HOH . 
G 5 HOH A 2 2002 2002 HOH HOH . 
G 5 HOH A 3 2003 2003 HOH HOH . 
G 5 HOH A 4 2004 2004 HOH HOH . 
G 5 HOH A 5 2005 2005 HOH HOH . 
G 5 HOH A 6 2006 2006 HOH HOH . 
G 5 HOH A 7 2007 2007 HOH HOH . 
G 5 HOH A 8 2008 2008 HOH HOH . 
G 5 HOH A 9 2009 2009 HOH HOH . 
G 5 HOH A 10 2010 2010 HOH HOH . 
G 5 HOH A 11 2011 2011 HOH HOH . 
G 5 HOH A 12 2012 2012 HOH HOH . 
G 5 HOH A 13 2013 2013 HOH HOH . 
G 5 HOH A 14 2014 2014 HOH HOH . 
G 5 HOH A 15 2015 2015 HOH HOH . 
G 5 HOH A 16 2016 2016 HOH HOH . 
G 5 HOH A 17 2017 2017 HOH HOH . 
G 5 HOH A 18 2018 2018 HOH HOH . 
G 5 HOH A 19 2019 2019 HOH HOH . 
G 5 HOH A 20 2020 2020 HOH HOH . 
G 5 HOH A 21 2021 2021 HOH HOH . 
G 5 HOH A 22 2022 2022 HOH HOH . 
G 5 HOH A 23 2023 2023 HOH HOH . 
G 5 HOH A 24 2024 2024 HOH HOH . 
G 5 HOH A 25 2025 2025 HOH HOH . 
G 5 HOH A 26 2026 2026 HOH HOH . 
G 5 HOH A 27 2027 2027 HOH HOH . 
G 5 HOH A 28 2028 2028 HOH HOH . 
G 5 HOH A 29 2029 2029 HOH HOH . 
G 5 HOH A 30 2030 2030 HOH HOH . 
G 5 HOH A 31 2031 2031 HOH HOH . 
G 5 HOH A 32 2032 2032 HOH HOH . 
G 5 HOH A 33 2033 2033 HOH HOH . 
G 5 HOH A 34 2034 2034 HOH HOH . 
G 5 HOH A 35 2035 2035 HOH HOH . 
G 5 HOH A 36 2036 2036 HOH HOH . 
G 5 HOH A 37 2037 2037 HOH HOH . 
G 5 HOH A 38 2038 2038 HOH HOH . 
G 5 HOH A 39 2039 2039 HOH HOH . 
G 5 HOH A 40 2040 2040 HOH HOH . 
G 5 HOH A 41 2041 2041 HOH HOH . 
G 5 HOH A 42 2042 2042 HOH HOH . 
G 5 HOH A 43 2043 2043 HOH HOH . 
G 5 HOH A 44 2044 2044 HOH HOH . 
G 5 HOH A 45 2045 2045 HOH HOH . 
G 5 HOH A 46 2046 2046 HOH HOH . 
G 5 HOH A 47 2047 2047 HOH HOH . 
G 5 HOH A 48 2048 2048 HOH HOH . 
G 5 HOH A 49 2049 2049 HOH HOH . 
G 5 HOH A 50 2050 2050 HOH HOH . 
G 5 HOH A 51 2051 2051 HOH HOH . 
G 5 HOH A 52 2052 2052 HOH HOH . 
G 5 HOH A 53 2053 2053 HOH HOH . 
G 5 HOH A 54 2054 2054 HOH HOH . 
G 5 HOH A 55 2055 2055 HOH HOH . 
G 5 HOH A 56 2056 2056 HOH HOH . 
G 5 HOH A 57 2057 2057 HOH HOH . 
G 5 HOH A 58 2058 2058 HOH HOH . 
G 5 HOH A 59 2059 2059 HOH HOH . 
G 5 HOH A 60 2060 2060 HOH HOH . 
G 5 HOH A 61 2061 2061 HOH HOH . 
G 5 HOH A 62 2062 2062 HOH HOH . 
G 5 HOH A 63 2063 2063 HOH HOH . 
G 5 HOH A 64 2064 2064 HOH HOH . 
G 5 HOH A 65 2065 2065 HOH HOH . 
G 5 HOH A 66 2066 2066 HOH HOH . 
G 5 HOH A 67 2067 2067 HOH HOH . 
G 5 HOH A 68 2068 2068 HOH HOH . 
G 5 HOH A 69 2069 2069 HOH HOH . 
G 5 HOH A 70 2070 2070 HOH HOH . 
G 5 HOH A 71 2071 2071 HOH HOH . 
G 5 HOH A 72 2072 2072 HOH HOH . 
G 5 HOH A 73 2073 2073 HOH HOH . 
G 5 HOH A 74 2074 2074 HOH HOH . 
G 5 HOH A 75 2075 2075 HOH HOH . 
G 5 HOH A 76 2076 2076 HOH HOH . 
G 5 HOH A 77 2077 2077 HOH HOH . 
G 5 HOH A 78 2078 2078 HOH HOH . 
G 5 HOH A 79 2079 2079 HOH HOH . 
G 5 HOH A 80 2080 2080 HOH HOH . 
G 5 HOH A 81 2081 2081 HOH HOH . 
G 5 HOH A 82 2082 2082 HOH HOH . 
G 5 HOH A 83 2083 2083 HOH HOH . 
G 5 HOH A 84 2084 2084 HOH HOH . 
H 5 HOH B 1 2001 2001 HOH HOH . 
H 5 HOH B 2 2002 2002 HOH HOH . 
H 5 HOH B 3 2003 2003 HOH HOH . 
H 5 HOH B 4 2004 2004 HOH HOH . 
H 5 HOH B 5 2005 2005 HOH HOH . 
H 5 HOH B 6 2006 2006 HOH HOH . 
H 5 HOH B 7 2007 2007 HOH HOH . 
H 5 HOH B 8 2008 2008 HOH HOH . 
H 5 HOH B 9 2009 2009 HOH HOH . 
H 5 HOH B 10 2010 2010 HOH HOH . 
H 5 HOH B 11 2011 2011 HOH HOH . 
H 5 HOH B 12 2012 2012 HOH HOH . 
H 5 HOH B 13 2013 2013 HOH HOH . 
H 5 HOH B 14 2014 2014 HOH HOH . 
H 5 HOH B 15 2015 2015 HOH HOH . 
H 5 HOH B 16 2016 2016 HOH HOH . 
H 5 HOH B 17 2017 2017 HOH HOH . 
H 5 HOH B 18 2018 2018 HOH HOH . 
H 5 HOH B 19 2019 2019 HOH HOH . 
H 5 HOH B 20 2020 2020 HOH HOH . 
H 5 HOH B 21 2021 2021 HOH HOH . 
H 5 HOH B 22 2022 2022 HOH HOH . 
H 5 HOH B 23 2023 2023 HOH HOH . 
H 5 HOH B 24 2024 2024 HOH HOH . 
H 5 HOH B 25 2025 2025 HOH HOH . 
H 5 HOH B 26 2026 2026 HOH HOH . 
H 5 HOH B 27 2027 2027 HOH HOH . 
H 5 HOH B 28 2028 2028 HOH HOH . 
H 5 HOH B 29 2029 2029 HOH HOH . 
H 5 HOH B 30 2030 2030 HOH HOH . 
H 5 HOH B 31 2031 2031 HOH HOH . 
H 5 HOH B 32 2032 2032 HOH HOH . 
H 5 HOH B 33 2033 2033 HOH HOH . 
H 5 HOH B 34 2034 2034 HOH HOH . 
H 5 HOH B 35 2035 2035 HOH HOH . 
H 5 HOH B 36 2036 2036 HOH HOH . 
H 5 HOH B 37 2037 2037 HOH HOH . 
H 5 HOH B 38 2038 2038 HOH HOH . 
H 5 HOH B 39 2039 2039 HOH HOH . 
H 5 HOH B 40 2040 2040 HOH HOH . 
H 5 HOH B 41 2041 2041 HOH HOH . 
H 5 HOH B 42 2042 2042 HOH HOH . 
H 5 HOH B 43 2043 2043 HOH HOH . 
H 5 HOH B 44 2044 2044 HOH HOH . 
H 5 HOH B 45 2045 2045 HOH HOH . 
H 5 HOH B 46 2046 2046 HOH HOH . 
H 5 HOH B 47 2047 2047 HOH HOH . 
H 5 HOH B 48 2048 2048 HOH HOH . 
H 5 HOH B 49 2049 2049 HOH HOH . 
H 5 HOH B 50 2050 2050 HOH HOH . 
H 5 HOH B 51 2051 2051 HOH HOH . 
H 5 HOH B 52 2052 2052 HOH HOH . 
H 5 HOH B 53 2053 2053 HOH HOH . 
H 5 HOH B 54 2054 2054 HOH HOH . 
H 5 HOH B 55 2055 2055 HOH HOH . 
H 5 HOH B 56 2056 2056 HOH HOH . 
H 5 HOH B 57 2057 2057 HOH HOH . 
H 5 HOH B 58 2058 2058 HOH HOH . 
H 5 HOH B 59 2059 2059 HOH HOH . 
H 5 HOH B 60 2060 2060 HOH HOH . 
H 5 HOH B 61 2061 2061 HOH HOH . 
H 5 HOH B 62 2062 2062 HOH HOH . 
H 5 HOH B 63 2063 2063 HOH HOH . 
H 5 HOH B 64 2064 2064 HOH HOH . 
H 5 HOH B 65 2065 2065 HOH HOH . 
H 5 HOH B 66 2066 2066 HOH HOH . 
H 5 HOH B 67 2067 2067 HOH HOH . 
H 5 HOH B 68 2068 2068 HOH HOH . 
H 5 HOH B 69 2069 2069 HOH HOH . 
H 5 HOH B 70 2070 2070 HOH HOH . 
H 5 HOH B 71 2071 2071 HOH HOH . 
H 5 HOH B 72 2072 2072 HOH HOH . 
H 5 HOH B 73 2073 2073 HOH HOH . 
H 5 HOH B 74 2074 2074 HOH HOH . 
H 5 HOH B 75 2075 2075 HOH HOH . 
H 5 HOH B 76 2076 2076 HOH HOH . 
H 5 HOH B 77 2077 2077 HOH HOH . 
H 5 HOH B 78 2078 2078 HOH HOH . 
H 5 HOH B 79 2079 2079 HOH HOH . 
H 5 HOH B 80 2080 2080 HOH HOH . 
H 5 HOH B 81 2081 2081 HOH HOH . 
H 5 HOH B 82 2082 2082 HOH HOH . 
H 5 HOH B 83 2083 2083 HOH HOH . 
H 5 HOH B 84 2084 2084 HOH HOH . 
H 5 HOH B 85 2085 2085 HOH HOH . 
H 5 HOH B 86 2086 2086 HOH HOH . 
H 5 HOH B 87 2087 2087 HOH HOH . 
H 5 HOH B 88 2088 2088 HOH HOH . 
H 5 HOH B 89 2089 2089 HOH HOH . 
H 5 HOH B 90 2090 2090 HOH HOH . 
H 5 HOH B 91 2091 2091 HOH HOH . 
H 5 HOH B 92 2092 2092 HOH HOH . 
H 5 HOH B 93 2093 2093 HOH HOH . 
H 5 HOH B 94 2094 2094 HOH HOH . 
H 5 HOH B 95 2095 2095 HOH HOH . 
H 5 HOH B 96 2096 2096 HOH HOH . 
H 5 HOH B 97 2097 2097 HOH HOH . 
H 5 HOH B 98 2098 2098 HOH HOH . 
H 5 HOH B 99 2099 2099 HOH HOH . 
H 5 HOH B 100 2100 2100 HOH HOH . 
H 5 HOH B 101 2101 2101 HOH HOH . 
H 5 HOH B 102 2102 2102 HOH HOH . 
H 5 HOH B 103 2103 2103 HOH HOH . 
H 5 HOH B 104 2104 2104 HOH HOH . 
H 5 HOH B 105 2105 2105 HOH HOH . 
H 5 HOH B 106 2106 2106 HOH HOH . 
H 5 HOH B 107 2107 2107 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 -6.617 11.781 13.377 1 21.4 ? PB GDP 1174 A 1 
HETATM 2 O O1B GDP . . . C 2 -7.988 11.299 13.106 1 25.85 ? O1B GDP 1174 A 1 
HETATM 3 O O2B GDP . . . C 2 -6.087 11.64 14.769 1 20.25 ? O2B GDP 1174 A 1 
HETATM 4 O O3B GDP . . . C 2 -5.474 11.08 12.634 1 22.64 ? O3B GDP 1174 A 1 
HETATM 5 O O3A GDP . . . C 2 -6.523 13.473 13.193 1 22.09 ? O3A GDP 1174 A 1 
HETATM 6 P PA GDP . . . C 2 -6.95 14.278 11.84 1 21.15 ? PA GDP 1174 A 1 
HETATM 7 O O1A GDP . . . C 2 -5.557 14.73 11.578 1 18.21 ? O1A GDP 1174 A 1 
HETATM 8 O O2A GDP . . . C 2 -7.587 13.66 10.647 1 22.87 ? O2A GDP 1174 A 1 
HETATM 9 O O5' GDP . . . C 2 -7.649 15.555 12.487 1 20.16 ? O5' GDP 1174 A 1 
HETATM 10 C C5' GDP . . . C 2 -8.993 15.646 12.91 1 20.68 ? C5' GDP 1174 A 1 
HETATM 11 C C4' GDP . . . C 2 -9.525 17.031 12.522 1 19.77 ? C4' GDP 1174 A 1 
HETATM 12 O O4' GDP . . . C 2 -9.061 18.149 13.375 1 21.7 ? O4' GDP 1174 A 1 
HETATM 13 C C3' GDP . . . C 2 -9.125 17.545 11.091 1 20.61 ? C3' GDP 1174 A 1 
HETATM 14 O O3' GDP . . . C 2 -10.27 18.298 10.626 1 21.05 ? O3' GDP 1174 A 1 
HETATM 15 C C2' GDP . . . C 2 -7.941 18.489 11.319 1 19.21 ? C2' GDP 1174 A 1 
HETATM 16 O O2' GDP . . . C 2 -7.812 19.531 10.363 1 21.88 ? O2' GDP 1174 A 1 
HETATM 17 C C1' GDP . . . C 2 -8.204 19.03 12.694 1 19.69 ? C1' GDP 1174 A 1 
HETATM 18 N N9 GDP . . . C 2 -6.926 19.266 13.471 1 22.19 ? N9 GDP 1174 A 1 
HETATM 19 C C8 GDP . . . C 2 -5.751 18.554 13.588 1 22.01 ? C8 GDP 1174 A 1 
HETATM 20 N N7 GDP . . . C 2 -4.877 19.135 14.358 1 20.7 ? N7 GDP 1174 A 1 
HETATM 21 C C5 GDP . . . C 2 -5.49 20.305 14.785 1 20.59 ? C5 GDP 1174 A 1 
HETATM 22 C C6 GDP . . . C 2 -5.047 21.373 15.636 1 21.2 ? C6 GDP 1174 A 1 
HETATM 23 O O6 GDP . . . C 2 -3.944 21.481 16.201 1 20.9 ? O6 GDP 1174 A 1 
HETATM 24 N N1 GDP . . . C 2 -6.039 22.388 15.801 1 20.99 ? N1 GDP 1174 A 1 
HETATM 25 C C2 GDP . . . C 2 -7.296 22.373 15.216 1 22.88 ? C2 GDP 1174 A 1 
HETATM 26 N N2 GDP . . . C 2 -8.089 23.409 15.485 1 24.14 ? N2 GDP 1174 A 1 
HETATM 27 N N3 GDP . . . C 2 -7.722 21.377 14.406 1 22.57 ? N3 GDP 1174 A 1 
HETATM 28 C C4 GDP . . . C 2 -6.774 20.407 14.252 1 21.44 ? C4 GDP 1174 A 1 
#
_model_server_stats.io_time_ms              68 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           284 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           28 
#