data_3LO5
#
_model_server_result.job_id            -vtQO1Lmyzt0XoZxWirSOA 
_model_server_result.datetime_utc      '2025-01-25 08:42:42' 
_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          3lo5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":180}' 
#
_entry.id    3LO5 
#
_exptl.entry_id    3LO5 
_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    3 
_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            3LO5 
_cell.length_a            92.475 
_cell.length_b            102.184 
_cell.length_c            117.82 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3LO5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        23 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 2 2 2' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
? monomeric 1 author_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,D,E,L 1 1 
B,F,G,H,M 2 1 
C,I,J,K,N 3 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 D N N 
? 2 F N N 
? 2 I 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 E CA CA . A CA 167 1_555 D O1A GDP . A GDP 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.713 ? 
metalc ? metalc2 H CA CA . C CA 168 1_555 F O1A GDP . C GDP 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.823 ? 
metalc ? metalc3 H CA CA . C CA 168 1_555 F O2B GDP . C GDP 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.98 ? 
metalc ? metalc4 C OD2 ASP 30 E ASP 30 1_555 K CA CA . E CA 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.994 ? 
metalc ? metalc5 C OD2 ASP 33 E ASP 33 1_555 J CA CA . E CA 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.678 ? 
metalc ? metalc6 J CA CA . E CA 167 1_555 N O HOH . E HOH 176 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.846 ? 
metalc ? metalc7 J CA CA . E CA 167 1_555 I O1A GDP . E GDP 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.606 ? 
#
_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                     3LO5 
_atom_sites.fract_transf_matrix[1][1]    0.010814 
_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]    0.009786 
_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]    0.008488 
_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
D 2 GDP A 1 180 180 GDP GDP . 
E 3 CA A 1 167 167 CA CA . 
F 2 GDP C 1 180 180 GDP GDP . 
G 4 SO4 C 1 167 167 SO4 SO4 . 
H 3 CA C 1 168 168 CA CA . 
I 2 GDP E 1 180 180 GDP GDP . 
J 3 CA E 1 167 167 CA CA . 
K 3 CA E 1 168 168 CA CA . 
L 5 HOH A 1 168 168 HOH HOH . 
L 5 HOH A 2 169 169 HOH HOH . 
L 5 HOH A 3 170 170 HOH HOH . 
L 5 HOH A 4 171 171 HOH HOH . 
L 5 HOH A 5 172 172 HOH HOH . 
L 5 HOH A 6 173 173 HOH HOH . 
L 5 HOH A 7 174 174 HOH HOH . 
L 5 HOH A 8 175 175 HOH HOH . 
L 5 HOH A 9 176 176 HOH HOH . 
L 5 HOH A 10 177 177 HOH HOH . 
L 5 HOH A 11 178 178 HOH HOH . 
L 5 HOH A 12 179 179 HOH HOH . 
L 5 HOH A 13 181 181 HOH HOH . 
L 5 HOH A 14 182 182 HOH HOH . 
L 5 HOH A 15 183 183 HOH HOH . 
L 5 HOH A 16 184 184 HOH HOH . 
L 5 HOH A 17 185 185 HOH HOH . 
L 5 HOH A 18 187 187 HOH HOH . 
M 5 HOH C 1 169 169 HOH HOH . 
M 5 HOH C 2 170 170 HOH HOH . 
M 5 HOH C 3 171 171 HOH HOH . 
M 5 HOH C 4 172 172 HOH HOH . 
M 5 HOH C 5 173 173 HOH HOH . 
M 5 HOH C 6 174 174 HOH HOH . 
M 5 HOH C 7 175 175 HOH HOH . 
M 5 HOH C 8 176 176 HOH HOH . 
M 5 HOH C 9 177 177 HOH HOH . 
M 5 HOH C 10 178 178 HOH HOH . 
M 5 HOH C 11 179 179 HOH HOH . 
M 5 HOH C 12 181 181 HOH HOH . 
M 5 HOH C 13 182 182 HOH HOH . 
M 5 HOH C 14 183 183 HOH HOH . 
M 5 HOH C 15 184 184 HOH HOH . 
M 5 HOH C 16 185 185 HOH HOH . 
M 5 HOH C 17 186 186 HOH HOH . 
M 5 HOH C 18 187 187 HOH HOH . 
M 5 HOH C 19 188 188 HOH HOH . 
M 5 HOH C 20 189 189 HOH HOH . 
M 5 HOH C 21 190 190 HOH HOH . 
M 5 HOH C 22 191 191 HOH HOH . 
M 5 HOH C 23 192 192 HOH HOH . 
M 5 HOH C 24 193 193 HOH HOH . 
M 5 HOH C 25 194 194 HOH HOH . 
M 5 HOH C 26 195 195 HOH HOH . 
M 5 HOH C 27 196 196 HOH HOH . 
M 5 HOH C 28 197 197 HOH HOH . 
N 5 HOH E 1 169 169 HOH HOH . 
N 5 HOH E 2 170 170 HOH HOH . 
N 5 HOH E 3 171 171 HOH HOH . 
N 5 HOH E 4 172 172 HOH HOH . 
N 5 HOH E 5 173 173 HOH HOH . 
N 5 HOH E 6 174 174 HOH HOH . 
N 5 HOH E 7 175 175 HOH HOH . 
N 5 HOH E 8 176 176 HOH HOH . 
N 5 HOH E 9 177 177 HOH HOH . 
N 5 HOH E 10 178 178 HOH HOH . 
N 5 HOH E 11 179 179 HOH HOH . 
N 5 HOH E 12 181 181 HOH HOH . 
N 5 HOH E 13 182 182 HOH HOH . 
N 5 HOH E 14 183 183 HOH HOH . 
N 5 HOH E 15 185 185 HOH HOH . 
N 5 HOH E 16 186 186 HOH HOH . 
N 5 HOH E 17 187 187 HOH HOH . 
N 5 HOH E 18 188 188 HOH HOH . 
N 5 HOH E 19 189 189 HOH HOH . 
N 5 HOH E 20 190 190 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 . . . I 2 -15.709 -28.959 -62.986 1 42.76 ? PB GDP 180 E 1 
HETATM 2 O O1B GDP . . . I 2 -16.889 -29.84 -62.662 1 55.57 ? O1B GDP 180 E 1 
HETATM 3 O O2B GDP . . . I 2 -16.159 -27.52 -62.953 1 50.05 ? O2B GDP 180 E 1 
HETATM 4 O O3B GDP . . . I 2 -15.142 -29.316 -64.342 1 45.2 ? O3B GDP 180 E 1 
HETATM 5 O O3A GDP . . . I 2 -14.592 -29.158 -61.855 1 38.25 ? O3A GDP 180 E 1 
HETATM 6 P PA GDP . . . I 2 -13.041 -29.376 -62.215 1 43.02 ? PA GDP 180 E 1 
HETATM 7 O O1A GDP . . . I 2 -12.531 -28.318 -63.151 1 43.47 ? O1A GDP 180 E 1 
HETATM 8 O O2A GDP . . . I 2 -12.79 -30.757 -62.776 1 53.37 ? O2A GDP 180 E 1 
HETATM 9 O O5' GDP . . . I 2 -12.392 -29.191 -60.76 1 46.65 ? O5' GDP 180 E 1 
HETATM 10 C C5' GDP . . . I 2 -12.407 -27.892 -60.175 1 50.62 ? C5' GDP 180 E 1 
HETATM 11 C C4' GDP . . . I 2 -11.211 -27.769 -59.252 1 42.48 ? C4' GDP 180 E 1 
HETATM 12 O O4' GDP . . . I 2 -11.286 -28.809 -58.281 1 32.98 ? O4' GDP 180 E 1 
HETATM 13 C C3' GDP . . . I 2 -9.944 -27.98 -60.056 1 39.94 ? C3' GDP 180 E 1 
HETATM 14 O O3' GDP . . . I 2 -8.988 -26.982 -59.693 1 47.99 ? O3' GDP 180 E 1 
HETATM 15 C C2' GDP . . . I 2 -9.424 -29.339 -59.652 1 32.39 ? C2' GDP 180 E 1 
HETATM 16 O O2' GDP . . . I 2 -8.001 -29.284 -59.504 1 36.3 ? O2' GDP 180 E 1 
HETATM 17 C C1' GDP . . . I 2 -10.109 -29.617 -58.324 1 32.41 ? C1' GDP 180 E 1 
HETATM 18 N N9 GDP . . . I 2 -10.482 -31.045 -58.195 1 26.26 ? N9 GDP 180 E 1 
HETATM 19 C C8 GDP . . . I 2 -11.306 -31.744 -58.994 1 33.09 ? C8 GDP 180 E 1 
HETATM 20 N N7 GDP . . . I 2 -11.422 -33.026 -58.566 1 38.04 ? N7 GDP 180 E 1 
HETATM 21 C C5 GDP . . . I 2 -10.662 -33.16 -57.466 1 32.71 ? C5 GDP 180 E 1 
HETATM 22 C C6 GDP . . . I 2 -10.33 -34.241 -56.51 1 30.48 ? C6 GDP 180 E 1 
HETATM 23 O O6 GDP . . . I 2 -10.811 -35.386 -56.647 1 40.74 ? O6 GDP 180 E 1 
HETATM 24 N N1 GDP . . . I 2 -9.498 -33.954 -55.498 1 28.41 ? N1 GDP 180 E 1 
HETATM 25 C C2 GDP . . . I 2 -8.963 -32.728 -55.329 1 29.76 ? C2 GDP 180 E 1 
HETATM 26 N N2 GDP . . . I 2 -8.129 -32.506 -54.287 1 37.18 ? N2 GDP 180 E 1 
HETATM 27 N N3 GDP . . . I 2 -9.224 -31.694 -56.164 1 29.83 ? N3 GDP 180 E 1 
HETATM 28 C C4 GDP . . . I 2 -10.05 -31.848 -57.225 1 35.09 ? C4 GDP 180 E 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           257 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           28 
#