data_3E70
#
_model_server_result.job_id            uvIB3QQdZoCX3Vsre7T-Lw 
_model_server_result.datetime_utc      '2024-12-01 18:58:52' 
_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          3e70 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":1001}' 
#
_entry.id    3E70 
#
_exptl.entry_id    3E70 
_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          107.42 
_cell.angle_gamma         90 
_cell.entry_id            3E70 
_cell.length_a            113.122 
_cell.length_b            53.034 
_cell.length_c            61.26 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3E70 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_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,E 
_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 B N N 
? 2 D 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 B O1B GDP . C GDP 1001 1_555 C MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? 
metalc ? metalc2 C MG MG . C MG 1002 1_555 E O HOH . C HOH 2046 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? 
metalc ? metalc3 C MG MG . C MG 1002 1_555 E O HOH . C HOH 2056 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? 
#
_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 70 n n 
PB O2B GDP sing 71 n n 
PB O3B GDP sing 72 n n 
PB O3A GDP sing 73 n n 
O2B HOB2 GDP sing 74 n n 
O3B HOB3 GDP sing 75 n n 
O3A PA GDP sing 76 n n 
PA O1A GDP doub 77 n n 
PA O2A GDP sing 78 n n 
PA O5' GDP sing 79 n n 
O2A HOA2 GDP sing 80 n n 
O5' C5' GDP sing 81 n n 
C5' C4' GDP sing 82 n n 
C5' H5' GDP sing 83 n n 
C5' "H5''" GDP sing 84 n n 
C4' O4' GDP sing 85 n n 
C4' C3' GDP sing 86 n n 
C4' H4' GDP sing 87 n n 
O4' C1' GDP sing 88 n n 
C3' O3' GDP sing 89 n n 
C3' C2' GDP sing 90 n n 
C3' H3' GDP sing 91 n n 
O3' HO3' GDP sing 92 n n 
C2' O2' GDP sing 93 n n 
C2' C1' GDP sing 94 n n 
C2' H2' GDP sing 95 n n 
O2' HO2' GDP sing 96 n n 
C1' N9 GDP sing 97 n n 
C1' H1' GDP sing 98 n n 
N9 C8 GDP sing 99 n y 
N9 C4 GDP sing 100 n y 
C8 N7 GDP doub 101 n y 
C8 H8 GDP sing 102 n n 
N7 C5 GDP sing 103 n y 
C5 C6 GDP sing 104 n n 
C5 C4 GDP doub 105 n y 
C6 O6 GDP doub 106 n n 
C6 N1 GDP sing 107 n n 
N1 C2 GDP sing 108 n n 
N1 HN1 GDP sing 109 n n 
C2 N2 GDP sing 110 n n 
C2 N3 GDP doub 111 n n 
N2 HN21 GDP sing 112 n n 
N2 HN22 GDP sing 113 n n 
N3 C4 GDP sing 114 n n 
#
_atom_sites.entry_id                     3E70 
_atom_sites.fract_transf_matrix[1][1]    0.00884 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002774 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.018856 
_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]    0.017109 
_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 GDP C 1 1001 1001 GDP GDP . 
C 3 MG C 1 1002 1002 MG MG . 
D 2 GDP C 1 2001 2001 GDP GDP . 
E 4 HOH C 1 2002 2002 HOH HOH . 
E 4 HOH C 2 2003 2003 HOH HOH . 
E 4 HOH C 3 2004 2004 HOH HOH . 
E 4 HOH C 4 2005 2005 HOH HOH . 
E 4 HOH C 5 2006 2006 HOH HOH . 
E 4 HOH C 6 2007 2007 HOH HOH . 
E 4 HOH C 7 2008 2008 HOH HOH . 
E 4 HOH C 8 2009 2009 HOH HOH . 
E 4 HOH C 9 2010 2010 HOH HOH . 
E 4 HOH C 10 2011 2011 HOH HOH . 
E 4 HOH C 11 2012 2012 HOH HOH . 
E 4 HOH C 12 2013 2013 HOH HOH . 
E 4 HOH C 13 2014 2014 HOH HOH . 
E 4 HOH C 14 2015 2015 HOH HOH . 
E 4 HOH C 15 2016 2016 HOH HOH . 
E 4 HOH C 16 2017 2017 HOH HOH . 
E 4 HOH C 17 2018 2018 HOH HOH . 
E 4 HOH C 18 2019 2019 HOH HOH . 
E 4 HOH C 19 2020 2020 HOH HOH . 
E 4 HOH C 20 2021 2021 HOH HOH . 
E 4 HOH C 21 2022 2022 HOH HOH . 
E 4 HOH C 22 2023 2023 HOH HOH . 
E 4 HOH C 23 2024 2024 HOH HOH . 
E 4 HOH C 24 2025 2025 HOH HOH . 
E 4 HOH C 25 2026 2026 HOH HOH . 
E 4 HOH C 26 2027 2027 HOH HOH . 
E 4 HOH C 27 2028 2028 HOH HOH . 
E 4 HOH C 28 2029 2029 HOH HOH . 
E 4 HOH C 29 2030 2030 HOH HOH . 
E 4 HOH C 30 2031 2031 HOH HOH . 
E 4 HOH C 31 2032 2032 HOH HOH . 
E 4 HOH C 32 2033 2033 HOH HOH . 
E 4 HOH C 33 2034 2034 HOH HOH . 
E 4 HOH C 34 2035 2035 HOH HOH . 
E 4 HOH C 35 2036 2036 HOH HOH . 
E 4 HOH C 36 2037 2037 HOH HOH . 
E 4 HOH C 37 2038 2038 HOH HOH . 
E 4 HOH C 38 2039 2039 HOH HOH . 
E 4 HOH C 39 2040 2040 HOH HOH . 
E 4 HOH C 40 2041 2041 HOH HOH . 
E 4 HOH C 41 2042 2042 HOH HOH . 
E 4 HOH C 42 2043 2043 HOH HOH . 
E 4 HOH C 43 2044 2044 HOH HOH . 
E 4 HOH C 44 2046 2046 HOH HOH . 
E 4 HOH C 45 2047 2047 HOH HOH . 
E 4 HOH C 46 2048 2048 HOH HOH . 
E 4 HOH C 47 2049 2049 HOH HOH . 
E 4 HOH C 48 2050 2050 HOH HOH . 
E 4 HOH C 49 2051 2051 HOH HOH . 
E 4 HOH C 50 2052 2052 HOH HOH . 
E 4 HOH C 51 2053 2053 HOH HOH . 
E 4 HOH C 52 2054 2054 HOH HOH . 
E 4 HOH C 53 2055 2055 HOH HOH . 
E 4 HOH C 54 2056 2056 HOH HOH . 
E 4 HOH C 55 2058 2058 HOH HOH . 
E 4 HOH C 56 2059 2059 HOH HOH . 
E 4 HOH C 57 2060 2060 HOH HOH . 
E 4 HOH C 58 2062 2062 HOH HOH . 
E 4 HOH C 59 2063 2063 HOH HOH . 
E 4 HOH C 60 2064 2064 HOH HOH . 
E 4 HOH C 61 2065 2065 HOH HOH . 
E 4 HOH C 62 2066 2066 HOH HOH . 
E 4 HOH C 63 2067 2067 HOH HOH . 
E 4 HOH C 64 2068 2068 HOH HOH . 
E 4 HOH C 65 2069 2069 HOH HOH . 
E 4 HOH C 66 2070 2070 HOH HOH . 
E 4 HOH C 67 2071 2071 HOH HOH . 
E 4 HOH C 68 2072 2072 HOH HOH . 
E 4 HOH C 69 2073 2073 HOH HOH . 
E 4 HOH C 70 2075 2075 HOH HOH . 
E 4 HOH C 71 2077 2077 HOH HOH . 
E 4 HOH C 72 2078 2078 HOH HOH . 
E 4 HOH C 73 2079 2079 HOH HOH . 
E 4 HOH C 74 2080 2080 HOH HOH . 
E 4 HOH C 75 2081 2081 HOH HOH . 
E 4 HOH C 76 2082 2082 HOH HOH . 
E 4 HOH C 77 2083 2083 HOH HOH . 
E 4 HOH C 78 2084 2084 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 . . . B 2 -20.074 25.789 11.744 1 41.28 ? PB GDP 1001 C 1 
HETATM 2 O O1B GDP . . . B 2 -19.618 24.635 12.592 1 39.1 ? O1B GDP 1001 C 1 
HETATM 3 O O2B GDP . . . B 2 -20.151 27.122 12.42 1 38.46 ? O2B GDP 1001 C 1 
HETATM 4 O O3B GDP . . . B 2 -19.129 25.994 10.573 1 40.16 ? O3B GDP 1001 C 1 
HETATM 5 O O3A GDP . . . B 2 -21.5 25.429 11.111 1 44.56 ? O3A GDP 1001 C 1 
HETATM 6 P PA GDP . . . B 2 -22.584 24.409 11.719 1 42.52 ? PA GDP 1001 C 1 
HETATM 7 O O1A GDP . . . B 2 -22.931 24.777 13.138 1 40.58 ? O1A GDP 1001 C 1 
HETATM 8 O O2A GDP . . . B 2 -22.205 22.947 11.582 1 33.33 ? O2A GDP 1001 C 1 
HETATM 9 O O5' GDP . . . B 2 -23.758 24.746 10.669 1 45.56 ? O5' GDP 1001 C 1 
HETATM 10 C C5' GDP . . . B 2 -24.41 26.014 10.672 1 47.61 ? C5' GDP 1001 C 1 
HETATM 11 C C4' GDP . . . B 2 -25.778 25.838 10.026 1 47.25 ? C4' GDP 1001 C 1 
HETATM 12 O O4' GDP . . . B 2 -25.629 25.343 8.695 1 46.89 ? O4' GDP 1001 C 1 
HETATM 13 C C3' GDP . . . B 2 -26.595 24.808 10.781 1 50.67 ? C3' GDP 1001 C 1 
HETATM 14 O O3' GDP . . . B 2 -27.942 25.271 10.885 1 48.9 ? O3' GDP 1001 C 1 
HETATM 15 C C2' GDP . . . B 2 -26.583 23.585 9.902 1 53.45 ? C2' GDP 1001 C 1 
HETATM 16 O O2' GDP . . . B 2 -27.794 22.828 10.028 1 49.17 ? O2' GDP 1001 C 1 
HETATM 17 C C1' GDP . . . B 2 -26.475 24.208 8.53 1 52.19 ? C1' GDP 1001 C 1 
HETATM 18 N N9 GDP . . . B 2 -25.968 23.245 7.531 1 49.22 ? N9 GDP 1001 C 1 
HETATM 19 C C8 GDP . . . B 2 -24.815 22.552 7.544 1 40.8 ? C8 GDP 1001 C 1 
HETATM 20 N N7 GDP . . . B 2 -24.718 21.77 6.434 1 43.89 ? N7 GDP 1001 C 1 
HETATM 21 C C5 GDP . . . B 2 -25.827 21.97 5.691 1 44.6 ? C5 GDP 1001 C 1 
HETATM 22 C C6 GDP . . . B 2 -26.371 21.471 4.408 1 49.9 ? C6 GDP 1001 C 1 
HETATM 23 O O6 GDP . . . B 2 -25.715 20.644 3.747 1 47.42 ? O6 GDP 1001 C 1 
HETATM 24 N N1 GDP . . . B 2 -27.567 21.934 3.99 1 46.23 ? N1 GDP 1001 C 1 
HETATM 25 C C2 GDP . . . B 2 -28.261 22.833 4.724 1 45.85 ? C2 GDP 1001 C 1 
HETATM 26 N N2 GDP . . . B 2 -29.454 23.275 4.284 1 41.5 ? N2 GDP 1001 C 1 
HETATM 27 N N3 GDP . . . B 2 -27.827 23.331 5.912 1 46.49 ? N3 GDP 1001 C 1 
HETATM 28 C C4 GDP . . . B 2 -26.644 22.938 6.428 1 47.98 ? C4 GDP 1001 C 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           284 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           28 
#